Australian Biosecurity Genomic Database

The Australian Biosecurity Genomic Database is a curated collection of viral reference genomes based on the National Notifiable Disease List of Terrestrial Animals and the National List of Reportable Diseases of Aquatic Animals. The database is provided as a FASTA file that can be used to screen high-throughput sequencing (HTS) data generated from animals, animal products, or environmental samples.

The latest version of the database contains 92 viruses, representing 33 viral families. Sequences were acquired from the National Center for Biotechnology Information (NCBI) Nucleotide database, using high-quality whole genome reference sequences from RefSeq where possible. Each virus species was represented by a single isolate and segmented genomes were merged so that each virus was represented by a single sequence to assist data analysis.

Licensing information

This work is licensed under Creative Commons Attribution-ShareAlike 4.0 International.

Access the database

To download, right-click on the button below, select “Save link as” and save the file so that its name ends with .fasta.

Access the Terrestrial Animal Disease Database
(2.0MB) Access the Aquatic Animal Disease Database
(2.4MB) Browse the GitHub Repository

Usage guidelines

1. Initial screening

Initial screening of HTS data for notifiable animal viruses can be performed by mapping reads to the Australian Biosecurity Genomic Database. Coverage of virus genomes in the database can then be measured by calculating the percentage of each genome sequence that is covered by reads. Further analysis can be performed to measure other coverage metrics such as the average number of reads that align to each genome sequence (fold coverage) and the similarity of the reads to the reference genome sequence (nucleotide identity).

Programs that can be used to perform read mapping include:

Short reads: BWA, BowTie2

Long reads: MiniMap

The alignment file (.bam) that is produced by these programs can then be analysed using programs such as SAMtools and BBMap to generate coverage metrics. It can also be used by sequence analysis programs such as Geneious or Tablet to visualise the alignment of reads to the virus genome.

2. Interpreting results

A triage system to rapidly assess confidence level (low, medium, and high) in the initial screening results has been developed utilising genome coverage metrics generated by read mapping to the Australian Biosecurity Genomic Database. The following are proposed coverage thresholds for the different confidence levels:

High confidence

Criteria: Virus genome sequence in the Australian Biosecurity Genomic Database has >10% coverage by reads with >95% pairwise nucleotide identity.

This level of virus genome coverage indicates that the notifiable virus or a closely related virus are likely to be present in the sample.

Further analyses of the HTS data should be performed to determine what virus is present in the sample, including an investigation into whether there is read coverage of a region used for species/strain demarcation (see below).

If further analysis indicates that the virus is notifiable, then the relevant State Veterinary Laboratory or the Office of the Chief Veterinary Officer should be contacted (see below).

Medium confidence

Criteria: Virus genome sequence in the Australian Biosecurity Genomic Database has >10% coverage by reads with <95% pairwise nucleotide identity or <10% coverage by reads with >95% pairwise nucleotide identity.

This level of virus genome coverage indicates that the notifiable virus or a closely related virus are possibly present in the sample, but could also be due to other factors, such as contamination.

Further analyses of the HTS data should be performed to determine what virus is present in the sample, including an investigation into whether there is read coverage of a region used for species/strain demarcation (see below).

If further analysis indicates that the virus is notifiable, then the relevant State Veterinary Laboratory or the Office of the Chief Veterinary Officer should be contacted (see below).

Low confidence

Criteria: Virus genome sequence in the Australian Biosecurity Genomic Database has <10% coverage by reads with <95% pairwise nucleotide identity.

This level of virus genome coverage indicates that positive detection of a notifiable virus is still possible but not well-supported by the initial screening data.

Despite low levels of non-specific genome coverage often being caused by conserved regions in closely related viruses or artefacts of host genomes, it is possible the low coverage is originating from a notifiable virus. Further analyses of the HTS data can help ascertain if a notifiable virus is present at a low titre or from a divergent strain (see below).

Regions used for virus species/strain demarcation can be found in the relevant taxonomy reports provided by the ICTV. Links to the reports are provided in the Notifiable Virus Compendium, along with other related information on the notifiable virus. The suggested thresholds above are based on initial testing with existing HTS datasets containing notifiable viruses. However, there may be cases that fall outside these thresholds and further testing of the Australian Biosecurity Genomic Database is required to develop robust detection criteria. Any suspected detections should be further investigated with additional analyses of the HTS data, with suggestions provided below.

3. Further analysis

Visualisation of read mapping results

The alignment files (.bam) generated by read mapping can be visualised to inspect the read coverage of the virus genome and assess its validity. Often non-specific coverage produced by artefacts from host genomes is recognisable by deep fold coverage of a small region and minimal coverage of the rest of the virus genome.

Large DNA viruses often have parts of the host genome incorporated in their own and may require higher thresholds for detection using genome read coverage to avoid false positives.

Programs that can be used to visualise read alignment files include:

Tablet (free)

Geneious (licensed)

Sequence identity of mapped reads

While genome coverage by reads is a good indicator of virus presence, it can be misleading when generated by closely related viruses, leading to false positives (Figure 1).

_{Figure 1: Coverage of the measles virus genome produced by a (A) false positive detection; (B) low-level true positive detection; and (C) high-level true positive detection. The false positive coverage plot was generated using reads from dolphin morbillivirus, which has partial sequence homology to measles virus. (Schlaberg et al. 2017)}

It can be helpful to determine how similar the reads are to the reference virus genome by measuring the pairwise identity, which can be generated by the same programs used to view alignment files. Pairwise identity is often included in species demarcation criteria and can be for a specific region or the whole genome.

Generating consensus sequences

The alignment files (.bam) produced by read mapping can also be used to generate consensus sequences, which can then be compared to a larger public database using online tools such as BLASTn (NCBI). A consensus sequence represents the most common nucleotide at each base of the virus genome that has read coverage and is usually longer than a single sequence read, allowing for greater sequence comparison to known sequences. Furthermore, tools such as BLASTx can translate the consensus sequence nucleotides into amino acids, which can be compared to protein databases to increase the breadth of the search results.

Comparison to larger databases can help detect notifiable viruses that may be divergent from the Australian Biosecurity Genomic Database reference, while also ruling out false positives that may be producing misleading genome coverage.

Consensus sequences can often be generated by the same programs used to view alignment files or by using alignment analysis programs such as SAMtools or BCFtools.

De novo assembly

Instead of mapping HTS reads to a database, a de novo assembly-based approach can be used, where the reads are assembled into larger contiguous sequences (contigs) and compared to larger databases, such as NCBI’s non-redundant (nr) database. The assembly approach enables unbiased detection of both known and new viruses but is a more time and resource-intensive process. It is useful to confirm any notifiable viruses detected via read mapping with contig assembly as it provides a separate method for detection and can characterize sequence diversity that may be masked by the alignment approach. However, as contig assembly requires overlapping reads, it may not be as sensitive as read mapping if there is low or scattered virus genome coverage.

Contacting the Chief Veterinary Office (CVO)

All notifiable virus detections must be reported to the relevant State Veterinary Laboratory or the Office of the Chief Veterinary Officer, as they can organise further investigation of the sample with the appropriate testing laboratory. Multiple different data analyses should be provided to support the suspected detection of a notifiable virus detection and physical samples may be requested if available for confirmatory testing using diagnostic methods such as serology, culturing, or PCR.

If there are any suspected detections, you can also call the Emergency Animal Disease Watch Hotline on 1800 675 888 (24 hours a day, every day of the year). If you are unsure of your results or would like to call a local veterinary officer, alternative numbers can be found for every state:

Australian Capital Territory

New South Wales

Northern Territory

Queensland

South Australia

Tasmania

Victoria

Western Australia

The emergency animal diseases field guide for veterinarians is also a valuable resource for the investigation and reporting of animal diseases in Australia.

Troubleshooting

Further testing of the database using a greater number of HTS datasets from a variety of sample types and host animals is recommended to further inform the metrics and thresholds chosen for the screening analysis criteria, which will help to address some of the limitations associated with this approach (Table 1). The addition of biological characteristics such as host and symptoms could improve the applicability of the criteria when dealing with low or medium confidence results.

_{Table 1: Recommendations to address the possible issues associated with the use of read mapping to a database to screen HTS data for viral sequences.}

References

Schlaberg, Robert et al. 2017. ‘Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection’. Archives of Pathology & Laboratory Medicine 141(6): 776–86.

Notifiable Virus Compendium

The Notifiable Virus Compendium (NVC) is a useful companion resource for the Australian Biosecurity Genomic Database.

Here you can find information specific to the viruses listed in the database to facilitate data analysis and help assess whether your high-throughout sequencing results indicate the presence of a notifiable disease in Australia.

Where available, the following information has been provided for each of the virus species:

The host species and associated notifiable animal disease
Virus genome classification and size
National Center for Biotechnology Information (NCBI) taxonomy ID and reference sequence accession numbers
Australian Reference Laboratory
Australian Veterinary Emergency Plan (AUSVETPLAN)
Diagnostic manuals provided by the World Organisation for Animal Health (WOAH; formerly, OIE)
Disease datasheet from the Centre for Agriculture and Biosciences International (CABI)
Taxonomy report by the International Committee on Taxonomy of Viruses (ICTV)
Genotype information and species demarcation criteria

DNA ASFARVIRIDAE

Asfivirus

African swine fever virus

Abbreviation: ASFV

Disease: African swine fever

Host: Swine (transmitted by soft ticks)

Genome: dsDNA, linear, non-segmented

Size: 170 - 194kb

NCBI Tax ID: 10497

NCBI RefSeq: NC_001659

Australian Reference Laboratory: CSIRO-ACDP (David Williams)

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1606/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.08.01_ASF.pdf

ICTV: https://ictv.global/report/chapter/asfarviridae/asfarviridae

Genotype info: 24 distinct genotypes

Demarcation criteria: The molecular epidemiology of the disease is investigated by sequencing of the 3’ terminal end of the B646L open reading frame encoding the p72 protein major capsid protein, which differentiates up to 24 distinct genotypes. To distinguish subgroups among closely related ASFV, sequence analysis of the tandem repeat sequences (TRS), located in the central variable region (CVR) within the B602L gene and in the intergenic region between the I73R and I329L genes, at the right end of the genome, is undertaken. Several other gene regions such as the E183L encoding p54 protein, the CP204L encoding p30 protein, and the protein encoded by the EP402R gene (CD2v), have been proved as useful tools to analyse ASFVs from different locations and hence track virus spread. (Source: WOAH)

DNA CIRCOVIRIDAE

Circovirus

Circovirus porcine2

Also known as: Porcine circovirus 2

Abbreviation: PCV-2

Disease: Porcine circovirus associated disease/post-weaning multi-systemic wasting syndrome (PMWS)

Despite being the causative agent of PMWS, PCV-2 infected pigs can be asymptomatic, so clinical diagnosis of PMWS is required for notification

Host: Swine

Genome: ssDNA virus, circular, non-segmented with 3 proteins

Size: ~1.7kb

NCBI Tax ID: 85708

NCBI RefSeq: NC_005148

WOAH: https://www.oie.int/app/uploads/2021/05/circoviruses-infection-with.pdf

ICTV: https://ictv.global/report/chapter/circoviridae/circoviridae/circovirus

Genotype info:

8 genotypes (PCV-2a to PCV-2h)

The clinical significance of the different genotypes varies and pigs infected with PCV-2 may not show any disease

Demarcation criteria:

Species: 80% genome-wide nucleotide sequence identity based on the distribution of pairwise identities. (Source: ICTV)

Genotype: maximum intra-genotype p-distance of 13% (calculated on the ORF2 (capsid) gene), bootstrap support at the corresponding internal node higher than 70% and at least 15 available sequences. (Source: https://doi.org/10.1371/journal.pone.0208585)

DNA ORTHOHERPESVIRIDAE

Alphaherpesvirinae

Mardivirus

Mardivirus anatidalpha1

Also known as:

Anatid alphaherpesvirus 1

Anatid herpesvirus 1

Duck enteritis virus

Duck plague virus

Abbreviation: AnAHV-1 or DEV

Disease: Duck herpes (duck viral enteritis/duck plague)

Host: Avian

Genome: dsDNA, linear, monopartite with 78 proteins

Size: 158kb

NCBI Tax ID: 104388

NCBI RefSeq: NC_013036

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.03.07_DVE.pdf

ICTV: https://ictv.global/report/chapter/orthoherpesviridae/orthoherpesviridae/mardivirus

Demarcation criteria: Phylogenetic comparison of complete gB and gC amino acid sequences with other available DVEV genome sequences (Source: https://doi.org/10.1016%2Fj.psj.2022.102392)

Varicellovirus

Varicellovirus equidalpha1

Also known as:

Equid alphaherpesvirus 1

Equine herpesvirus 1

Equine abortion virus

Abbreviation: EqAHV-1 or EAV

Disease: Equine rhinopneumonitis; equine herpesvirus myeloencephalopathy (EHM)

Host: Equine

Genome: dsDNA

Size: 150kb

NCBI Tax ID: 10326

NCBI RefSeq: NC_001491

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.05.09_EQUINE_RHINO.pdf

ICTV: https://ictv.global/report/chapter/orthoherpesviridae/orthoherpesviridae/varicellovirus

Genotype info:

A single nucleotide polymorphism (SNP) at position 2,254 of the DNA polymerase gene (ORF 30) is used as a marker of pathogenicity. This SNP is responsible for a single amino acid residue at position 752 of the viral DNA polymerase catalytic subunit.

Neuropathogenic genotype = D₇₅₂

Non-neuropathogenic genotype = N₇₅₂

New variant genotype = H₇₅₂

Demarcation criteria: Different genes have been used for phylogenetic comparison of EqAHV-1 including ORF30, ORF33, ORF34 and ORF68 (Source: https://doi.org/10.3390%2Fv11090851)

Varicellovirus suidalpha1

Also known as:

Suid alphaherpesvirus 1

Suid herpesvirus 1

Aujeszky’s disease virus

Pseudorabies virus

Abbreviation: SuAHV-1 or PRV

Disease: Aujeszky’s disease (pseudorabies)

Host: Swine

Genome: dsDNA, no RNA stage

Size: ~143kb

NCBI Tax ID: 10345

NCBI RefSeq: NC_006151

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1610/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.02_AUJESZKYS.pdf

ICTV: https://ictv.global/report/chapter/orthoherpesviridae/orthoherpesviridae/varicellovirus

Genotype info: Genotypes I and II

Demarcation criteria: Phylogenetic comparison of glycoprotein genes - the gC gene is commonly used due to its high variability (Source: https://doi.org/10.3390/v14051003)

Gammaherpesvirinae

Macavirus

Macavirus alcelaphinegamma1

Also known as:

Alcelaphine gammaherpesvirus 1

Alcelaphine herpesvirus 1

Bovid herpesvirus 3

Wildebeest-associated malignant catarrhal fever virus

Abbreviation: AlGHV-1 or MCFV

Disease: Wildebeest-associated malignant catarrhal fever (unapparent infection in wildebeest but usually fatal in cattle and other ungulates)

Host: Multiple

Genome: dsDNA virus, single linear (no RNA stage)

Size: 130kb

NCBI Tax ID: 35252

NCBI RefSeq: NC_002531

WOAH: https://www.oie.int/fileadmin/Home/eng/Health_standards/tahm/3.04.13_MCF.pdf

CABI: https://www.cabi.org/isc/datasheet/95229

ICTV: https://ictv.global/report/chapter/herpesviridae/herpesviridae/macavirus

Genotype info: Belongs to Type 1 ruminant rhadinovirus subgroup

Demarcation criteria: Phylogenetic comparison of amino acid sequences of DNA polymerase gene (Source: https://doi.org/10.1099/vir.0.81238-0)

DNA POXVIRIDAE

Orthopoxvirus

Camelpox virus

Also known as: Orthopoxvirus cameli virus

Abbreviation: CMPV

Disease: Camelpox

Host: Dromedary camels, Bactrian camels, Lama guanicoe

Genome: dsDNA, linear, non-segmented

Size: ~200kb

NCBI Tax ID: 28873

NCBI RefSeq: NC_003391

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.09.02_CAMELPOX.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.96010

ICTV: https://ictv.global/report/chapter/poxviridae/poxviridae/orthopoxvirus

Demarcation criteria: Within the conserved, core region of the genome, nucleotide sequence identity of >96% is observed between isolates of all non-North American species. Isolates within a species exhibit >98% nucleotide identity. Where nucleotide identity alone is insufficient to separate species, amino acid or nucleotide sequence identity between specific, commonly shared genes can also be used. Sequence polymorphisms within genes such as the hemagglutinin or A-type inclusion protein can frequently exhibit high levels of variation that provide the resolving power necessary to make demarcation decisions. (Source: ICTV)

Capripoxvirus

Goatpox virus

Abbreviation: GPV

Disease: Goat pox

Host: Sheep and goats

Genome: dsDNA, linear, non-segmented

Size: ~150kb

NCBI Tax ID: 186805

NCBI RefSeq: NC_004003

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1690/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.07.13_S_POX_G_POX.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.81538

ICTV: https://ictv.global/report/chapter/poxviridae/poxviridae/capripoxvirus

Demarcation criteria: The criteria of <98% nucleotide identity across the central core of the genome is used to delineate species, whereas >98% identity would indicate separate strains of the same species. (Source: ICTV)

Lumpy skin disease virus

Also known as: Neethling virus

Abbreviation: LSDV

Disease: Lumpy skin disease

Host: Bovine

Genome: dsDNA, linear, non-segmented

Size: ~150kb

NCBI Tax ID: 59509

NCBI RefSeq: NC_003027

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1653/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.04.12_LSD.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.76779

ICTV: https://ictv.global/report/chapter/poxviridae/poxviridae/capripoxvirus

Genotype info: Clades 1.1 and 1.2 (Source: https://doi.org/10.3390/v15071471)

Demarcation criteria: The criteria of <98% nucleotide identity across the central core of the genome is used to delineate species, whereas >98% identity would indicate separate strains of the same species. (Source: ICTV)

Sheeppox virus

Abbreviation: SPV

Disease: Sheep pox

Host: Sheep

Genome: dsDNA, linear, non-segmented

Size: ~150kb

NCBI Tax ID: 10266

NCBI RefSeq: NC_004002

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1690/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.07.13_S_POX_G_POX.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.64145

ICTV: https://ictv.global/report/chapter/poxviridae/poxviridae/capripoxvirus

Demarcation criteria: The criteria of <98% nucleotide identity across the central core of the genome is used to delineate species, whereas >98% identity would indicate separate strains of the same species. (Source: ICTV)

RNA ARTERIVIRIDAE

Alphaarterivirus

Alphaarterivirus equid

Also known as: Equine arteritis virus

Abbreviation: EAV

Disease: Equine viral arteritis

Host: Equids

Genome: +ssRNA, non-segmented

Size: 12-13kb

NCBI Tax ID: 2499620

NCBI RefSeq: NC_002532

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.05.10_EVA.pdf

ICTV: https://ictv.global/report/chapter/arteriviridae/arteriviridae/alphaarterivirus

Genotype info: Strains of EAV isolated from different regions of the world have been classified into different phylogenetic groups by sequence analysis of the GP3, GP5 and M envelope protein genes (ORFs 3, 5 and 6 respectively) and the nucleocapsid (N) protein gene (ORF 7). The GP5 gene has been found to be most useful and reliable for this purpose. The relationships between strains demonstrated by nucleotide sequencing are a useful molecular epidemiological tool for tracing the origin of outbreaks of EVA. (Source: WOAH)

Demarcation criteria: Phylogenetic analysis using genotype information above.

Betaarterivirus

Betaarterivirus suid 1

Also known as:

Porcine reproductive and respiratory syndrome virus

Swine infertility and respiratory syndrome virus

Lelystad virus

Abbreviation: PRRSV

Disease: Porcine reproductive and respiratory syndrome (blue ear disease)

Host: Swine

Genome: +ssRNA, non-segmented

Size: 14-16kb

NCBI Tax ID: 2499680

NCBI RefSeq: NC_043487

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1661/

WOAH: https://www.woah.org/app/uploads/2021/03/3-08-06-prrs.pdf

ICTV: https://ictv.global/report/chapter/arteriviridae/arteriviridae/betaarterivirus

Genotype info:

Type 1 = European (prototype = Lelystad virus)

Type 2 = North American (prototype = VR-2332)

~60% genome similarity between Type 1 and 2

Notes from WOAH manual:

Type 1 and 2 PRRSV differences are now becoming blurred as Type 2 PRRSV has been introduced into Europe and Type 1 virus has been discovered in North America.

Most PRRSV isolates from South America and much of Asia are of Type 2.

Most highly virulent Type 2 viruses in South-East Asia (highly pathogenic PRRSV) are characterised by amino acid deletions in the NSP2 region of the genome. However, there is good experimental evidence that these deletions do not determine virulence (Shi et al., 2010a; Zhou et al., 2010).

There is an increasing diversity among strains of the two genotypes, which has been attributed to the high error rate inherent in PRRSV replication and recombinations between strains (Murtaugh et al., 2010).

There have also been descriptions of east European strains of Type 1 PRRSV with a high degree of polymorphism, providing further insights into the emergence of the relatively new pathogen of pigs.

It has been proposed to distinguish subtypes 1, 2 and 3 within Type 1.

Moreover, mounting evidence indicates that an additional subtype (subtype 4) might exist (Stadejek et al., 2008; 2013).

Although nine different genetic lineages have been identified in Type 2 PRRSV, the overall level of diversity within type 2 does not exceed that observed for subtype 1 (Shi et al., 2010b; Stadejek et al., 2013).

Demarcation criteria: Phylogenetic analysis using the whole genome complete coding sequences (CDS) and the genotypes mentioned above is recommended as the high rate of recombination in PRRSV influences the reliability of any phylogenetic analysis using short genome fragments.

RNA ASTROVIRIDAE

Avastrovirus

Duck astrovirus

Also known as: Avastrovirus 3

Abbreviation: DAstV

Disease: Duck viral hepatitis (DVH) types II and III

Host: Avian

Genome: +ssRNA, linear, non-segmented

ORFs: 3 (ORF1a, ORF1b, and ORF2)

Size: 6.4 - 7.7kb

NCBI Tax ID: 1239441

NCBI RefSeq: NC_012437

WOAH: https://www.woah.org/fileadmin/Home/fr/Health_standards/tahm/3.03.08_DVH.pdf

ICTV: https://ictv.global/report_9th/RNApos/Astroviridae

Genotype info:

Duck astrovirus type 1 (DAstV-1) → causes DVH type II

Duck astrovirus type 2 (DAstV-2) → causes DVH type III

Demarcation criteria: Phylogenetic comparison of 434nt in ORF 1b with other astrovirus sequences can be used to differentiate DAstV-1 and DAstV-2. (Source: https://doi.org/10.1080/03079450802632056)

RNA BIRNAVIRIDAE

Avibirnavirus

Avibirnavirus gumboroense

Also known as:

Infectious bursal disease virus

Gumboro virus

Abbreviation: IBDV

Disease: Infectious bursal disease (very virulent and exotic antigenic variant forms)

Host: Avian

Genome: dsRNA, linear, 2 segments (A and B)

Size: 3.1kb and 2.7kb

NCBI Tax ID: 10995

NCBI RefSeq:

SegA: NC_004178

SegB: NC_004179

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1643/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.03.12_IBD.pdf

ICTV: https://ictv.global/report/chapter/birnaviridae/birnaviridae/avibirnavirus

Demarcation criteria: Phylogenetic comparison of either the middle third of the VP2 gene (Source: https://doi.org/10.1007/s007050050404) or the 5’ extremity of the VP1 gene (Source: https://doi.org/10.1099/vir.0.81184-0).

RNA BORNAVIRIDAE

Orthobornavirus

Orthobornavirus bornaense

Also known as:

Mammalian 1 orthobornavirus

Borna disease virus

Abbreviation: BoDV-1

Disease: Borna disease

Host: Multiple species including reptiles, fish, birds, and mammals

Genome: -ssRNA, non-segmented

Size: ~8.9kb

NCBI Tax ID: 1714619

NCBI RefSeq: NC_001607

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

FLI: https://www.fli.de/en/news/animal-disease-situation/bornaviruses/

ICTV: https://ictv.global/report/chapter/bornaviridae/bornaviridae/orthobornavirus

Genotype info: There are two members of the Orthobornavirus bornaense species: BoDV-1 and BoDV-2

Both cause disease in mammals

BoDV-1 strains occur globally, dominate the species, and display highly conserved genomes

Demarcation criteria: The species differentiation cut-off for pairwise sequence comparison of coding-complete genome sequences is defined as 72–75% (Source: ICTV).

RNA CALICIVIRIDAE

Vesivirus

Vesicular exanthema of swine virus

Also known as:

Swine vesicular exanthema virus

San Miguel sea lion virus

Abbreviation: VESV

Disease: Vesicular exanthema of swine

In pigs, the clinical disease is indistinguishable from vesicular stomatitis (Rhabdoviridae) and foot-and-mouth disease, Seneca Valley virus, and swine vesicular disease (all three are Picornaviridae)

Host: Swine; marine mammals incl. sea lions

Genome: +ssRNA, non-enveloped with 3 ORFs

Size: 8.2kb

NCBI Tax ID: 35612

NCBI RefSeq: NC_002551

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

MSD: https://www.msdvetmanual.com/generalized-conditions/vesicular-exanthema-of-swine

ICTV: https://ictv.global/report/chapter/caliciviridae/caliciviridae/vesivirus

Demarcation criteria: Membership of a Vesivirus species is based on phylogenetic differences, subtle variation in genome structure and host range. Phylogenetic comparison should be done with either WGS or the capsid protein amino acid sequence. (Source: https://doi.org/10.3201/eid2108.140900)

RNA CORONAVIRIDAE

Alphacoronavirus

Alphacoronavirus 1

Also known as:

Transmissible gastroenteritis virus

Porcine transmissible gastroenteritis coronavirus

Abbreviation: TGEV

Disease: Transmissible gastroenteritis

Host: Swine

Genome: ssRNA, linear with 8 proteins

Size: 28.5 - 30kb

NCBI Tax ID: 11149

NCBI RefSeq: NC_038861

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1703/

WOAH: https://www.woah.org/fileadmin/Home/fr/Health_standards/tahm/3.09.10_TRANSMISS_GASTRO.pdf

ICTV: https://ictv.global/report/chapter/coronaviridae/coronaviridae/alphacoronavirus

Genotype info:

Genotypes I (Ia and Ib) and II (Source: https://doi.org/10.3390/ijms21217898)

A distinct respiratory variant (porcine respiratory coronavirus or PRCV) has spread throughout many parts of the world and is now found in most countries where surveys for it have been conducted, one exception being Oceania. (Source: WOAH)

Demarcation criteria: Phylogenetic comparison using the whole genome complete coding sequences (CDS)

Porcine epidemic diarrhea virus

Abbreviation: PEDV

Disease: Porcine epidemic diarrhea

Host: Swine

Genome: ssRNA, linear with 6 proteins

Size: 28kb

NCBI Tax ID: 28295

NCBI RefSeq: NC_003436

AUSVETPLAN: https://animalhealthaustralia.com.au/download/8976/

WOAH: https://www.woah.org/fileadmin/Home/fr/Media_Center/docs/pdf/factsheet_PEDV.pdf

ICTV: https://ictv.global/report/chapter/coronaviridae/coronaviridae/alphacoronavirus

Genotype info: Three genotypes exist: G1-1 subgroup, G1-3 subgroup, and Group 3 (Source: https://doi.org/10.3389/fvets.2020.00435)

Demarcation criteria: Phylogenetic comparison using ORF3 amino acid sequence.

RNA FLAVIVIRIDAE

Orthoflavivirus

Orthoflavivirus encephalitidis

Also known as:

Tick-borne encephalitis virus

FSME virus

Abbreviation: TBEV

Disease: Tick-borne encephalitis

Clinically indistinguishable from louping ill (also antigenically and genomically similar to ILV)

Host: Multiple

Genome: +ssRNA, non-segmented

Size: ~10.5kb

NCBI Tax ID: 11084

NCBI RefSeq: NC_001672

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/app/uploads/2022/02/flavivirus-causing-tick-borne-encephalitis-infection-with.pdf

ICTV: https://ictv.global/report/chapter/flaviviridae/flaviviridae/orthoflavivirus

Genotype info: Five known subtypes: European (TBEV-Eu), Siberian (TBEVSib), Far Eastern (TBEV-Fe), Himalayan (TBEV-Him), and Baikalian (TBEV-Bkl)

Demarcation criteria: Phylogenetic comparison using the whole genome complete coding sequences (CDS) (Source: https://doi.org/10.3390/v12111240)

Orthoflavivirus japonicum

Also known as: Japanese encephalitis virus

Abbreviation: JEV

Disease: Japanese encephalitis

Host: Multiple

Genome: +ssRNA, non-segmented

Size: 11kb

NCBI Tax ID: 11072

NCBI RefSeq: NC_001437

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1647/

WOAH: https://www.oie.int/app/uploads/2021/03/japanese-encephalitis.pdf

CABI: https://www.cabi.org/isc/datasheet/78462

ICTV: https://ictv.global/report/chapter/flaviviridae/flaviviridae/orthoflavivirus

Genotype info: 5 genotypes (G1 - G5; Source: WOAH; https://doi.org/10.1089/vbz.2018.2291)

Demarcation criteria: Phylogenetic comparison of the viral envelope ‘E’ gene.

Orthoflavivirus loupingi

Also known as: Louping ill virus

Abbreviation: LIV

Disease: Louping ill

Clinically indistinguishable from tick-borne encephalitis (also antigenically and genomically similar to TBEV)

Host: Multiple

Genome: +ssRNA, non-segmented

Size: ~12kb

NCBI Tax ID: 11086

NCBI RefSeq: NC_001809

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/app/uploads/2022/02/flavivirus-infection-with-causing-louping-ill.pdf

ICTV: https://ictv.global/report/chapter/flaviviridae/flaviviridae/orthoflavivirus

Genotype info: British, Irish, Spanish and Turkish subtypes

Demarcation criteria: Phylogenetic comparison using the whole genome complete coding sequences (CDS) (Source: https://doi.org/10.1371/journal.pntd.0008133)

Orthoflavivirus nilense

Also known as:

West Nile virus (WNV)

Kunjin virus (Australian strain of WNV)

Abbreviation: WNV

Disease: West Nile fever

Host: Multiple

Genome: +ssRNA, non-segmented

Size: ~11.3kb

NCBI Tax ID: 11082

NCBI RefSeq: NC_001563

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.01.24_WEST_NILE.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.59558

ICTV: https://ictv.global/report/chapter/flaviviridae/flaviviridae/orthoflavivirus

Genotype info: Lineages 1 (1a and 1b) and 2 (Source: WOAH)

Kunjin virus is in lineage 1b and is endemic in parts of Australia

Lineages 1a and 2 have never been detected in Australia

Demarcation criteria: Phylogenetic comparison using the whole genome complete coding sequences (CDS) (Source: https://doi.org/10.3201%2Feid1805.111720)

Orthoflavivirus wesselsbronense

Also known as: Wesselsbron virus

Abbreviation: WESSV

Disease: Wesselbron disease

Clinically similar to Rift Valley fever (RVF)

Host: Sheep, goats and humans

Genome: +ssRNA, non-segmented

Size: ~10.8kb

NCBI Tax ID: 164416

NCBI RefSeq: NC_012735

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

MSD: https://www.msdvetmanual.com/generalized-conditions/wesselsbron-disease/wesselsbron-disease-in-animals

ICTV: https://ictv.global/report/chapter/flaviviridae/flaviviridae/orthoflavivirus

Demarcation criteria: Phylogenetic comparison using the whole genome complete coding sequences (CDS) (Source: https://doi.org/10.4269/ajtmh.22-0481)

Pestivirus

Pestivirus australiaense

Also known as:

Porcine pestivirus (PPeV) isolate Bungowannah

Bungowannah virus

Porcine myocarditis virus

Pestivirus F

Abbreviation: PPeV

Disease: Porcine myocarditis syndrome (PMC)

Host: Swine

Genome: +ssRNA, non-segmented

Size: 12.6kb

NCBI Tax ID: 412969

NCBI RefSeq: NC_023176

SHIC: https://www.swinehealth.org/wp-content/uploads/2021/08/shic-factsheet-atypical-porcine-pestivirus.pdf

ICTV: https://ictv.global/report/chapter/flaviviridaeport/flaviviridaeport/flaviviridae/pestivirus

Genotype info: Phylogenetic analysis of the E2 and NS5B coding sequencing and the full-length ORF can be used to perform genomic epidemiological investigation of outbreaks. (Source: https://doi.org/10.1007/s11262-019-01642-6)

Demarcation criteria: Pestiviruses can be assigned to species via phylogenetic comparison of conserved amino acid sequences in the regions 189–418, 1,547–2,321, 2,397–2,688 or 3,312–3,837 (numbered according to the first amino acid of the polyprotein if BVDV-1 Sd-1, M96751) (Source: ICTV)

Pestivirus suis

Also known as:

Classical swine fever virus (CSFV)

Hog cholera virus

Pestivirus C

Abbreviation: CSFV

Disease: Classical swine fever (hog cholera)

Host: Swine

Genome: +ssRNA, non-segmented

Size: 12.3kb

ORFs: 1 (3898aa)

NCBI Tax ID: 11096

NCBI RefSeq: NC_038912

Australian Reference Laboratory: CSIRO-ACDP (Trevor Drew)

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1633/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.08.03_CSF.pdf

CABI: https://www.cabi.org/isc/datasheet/79633

CSF Database: http://viro60.tiho-hannover.de/eg/csf/

ICTV: https://ictv.global/report/chapter/flaviviridaeport/flaviviridaeport/flaviviridae/pestivirus

Genotype info: 3 genotypes (CSFV-1, CSFV-2, and CSFV-3)

Demarcation criteria:

Species: Phylogenetic comparison of conserved amino acid sequences in the regions 189–418, 1,547–2,321, 2,397–2,688 or 3,312-3,837 (numbered according to the first amino acid of the polyprotein if BVDV-1 Sd-1, M96751) (Source: ICTV)

Genotype: Two regions have been extensively studied and provide large sets of sequence data with which new isolates can be compared. One lies within the 5’-nontranslated region (5’NTR) of the genome (150nt) and the other within the E2 major glycoprotein gene (190nt) (Source: WOAH)

Pestivirus tauri

Also known as:

Bovine viral diarrhea virus 2

Pestivirus B

Abbreviation: BVDV-2

Disease: Bovine viral diarrhea and mucosal disease

Host: Cattle

Genome: +ssRNA, non-segmented

Size: 12.5kb

NCBI Tax ID: 54315

NCBI RefSeq: NC_039237

Australian Reference Laboratory: EMAI (Peter Kirkland)

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.04.07_BVD.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.91725

ICTV: https://ictv.global/report/chapter/flaviviridaeport/flaviviridaeport/flaviviridae/pestivirus

Genotype info: 4 subgenotypes (BVDV2a-d)

Demarcation criteria:

Species: Phylogenetic comparison of conserved amino acid sequences in the regions 189–418, 1,547–2,321, 2,397–2,688 or 3,312-3,837 (numbered according to the first amino acid of the polyprotein if BVDV-1 Sd-1, M96751) (Source: ICTV)

Genotype: Phylogenetic comparison of N^pro, 5’ UTR or E2 regions. The complete ORF sequence can also be used. (Source: https://doi.org/10.1016/j.virol.2018.12.002)

RNA NAIROVIRIDAE

Orthonairovirus

Orthonairovirus haemorrhagiae

Also known as: Crimean-Congo hemorrhagic fever orthonairovirus

Abbreviation: CCHFV

Disease: Crimean–Congo haemorrhagic fever

Host: Multiple

Genome: -ssRNA, 3 segments (S, M, L)

Size: 12.2kb, 4.9kb, 1.7kb

NACBI Tax ID: 3052518

NCBI RefSeq:

S: NC_005302

M: NC_005300

L: NC_005301

WOAH: https://www.woah.org/fileadmin/Home/fr/Health_standards/tahm/3.01.05_CCHF.pdf

ICTV: https://ictv.global/report/chapter/nairoviridae/nairoviridae/orthonairovirus

Genotype info: There are nine genotypes: Africa 1-4, Asia 1-2, and Europe 1-3 (Source: WOAH)

Demarcation criteria: Phylogenetic comparison using S segment nucleotide sequence.

Orthonairovirus nairobiense

Also known as:

Nairobi sheep disease orthonairovirus

Ganjam virus

Abbreviation: NSDV

Disease: Nairobi sheep disease (NSD)

Host: Sheep and goats

Genome: -ssRNA, 3 segments (S, M, L)

Size: 12.2kb, 4.9kb, 1.7kb

NCBI Tax ID: 194540

NCBI RefSeq:

S: NC_034386

M: NC_034391

L: NC_034387

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/fr/Health_standards/tahm/3.10.01_BUNYAVIRAL_DISEASES.pdf

ICTV: https://talk.ictvonline.org/ictv-reports/ictv_online_report/negative-sense-rna-viruses/w/nairoviridae/1347/genus-orthonairovirus

Demarcation criteria: Phylogenetic comparison using S segment nucleotide sequence. (Source: WOAH)

RNA ORTHOMYXOVIRIDAE

Influenzavirus A

Influenza A virus

Also known as:

Influenza virus type A

Avian influenza virus

Equine influenza virus

Swine influenza virus

Abbreviation: FLUAV

Disease: Influenza (bird flu/horse flu/pig flu)

Host: Multiple; notifiable in birds, horses and pigs

Genome: -ssRNA, linear, 8 segments (1 - 8, or: PB2, PB1, PA, HA, NP, NA, M, NS)

Size: 2.3kb, 2.3kb, 2.2kb, 1.8kb, 1.6kb, 1.5kb, 1kb, 0.9kb

NCBI Tax ID: 11320

NCBI RefSeq:

PB2: NC_002023

PB1: NC_002022

PA: NC_002021

HA: NC_002020

NP: NC_002019

NA: NC_002018

M: NC_002017

NS: NC_002016

Australian Reference Laboratory: CSIRO-ACDP (Frank Wong)

AUSVETPLAN:

Avian: https://animalhealthaustralia.com.au/download/8952/

Equine: https://animalhealthaustralia.com.au/download/1635/

Swine: https://animalhealthaustralia.com.au/download/2052/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.03.04_AI.pdf

ICTV: https://ictv.global/report_9th/RNAneg/Orthomyxoviridae

Genotype info:

Isolates are designated by their serotype/host species/site of origin/strain designation/year of origin and (HA and NA subtype)

E.g. A/chicken/Novosibirsk/65/2005 (H5N1)

In order to determine the HA and NA subtype, the CDC’s Iterative Refinement Meta-Assembler (IRMA) program can be used with HTS reads: https://wonder.cdc.gov/amd/flu/irma/

Each AUSVETPLAN has more information about subtypes in the different host animals and their occurrence in Australia.

Demarcation criteria: Influenza A virus is the only species currently recognised in its genus, which is comprised of a cluster of strains that replicate as a continuous lineage and can genetically reassort with each other. Therefore, although 16 different HA subtypes and nine different NA subtypes are recognized among influenza viruses A replicating in birds, separate species designations have not been accorded to these subtypes. All isolates are capable of reassortment. (Source: ICTV)

RNA PARAMYXOVIRIDAE

Avulavirinae

Orthoavulavirus

Orthoavulavirus javaense

Also known as:

Newcastle disease virus

Avian orthoavulavirus 1

Avian paramyxovirus 1

Abbreviation: APMV1

Disease: Newcastle disease

Host: Avian

Genome: -ssRNA, non-segmented

Size: 15.1kb

NCBI Tax ID: 2560319

NCBI RefSeq: NC_039223

Australian Reference Laboratory: CSIRO-ACDP

AUSVETPLAN: https://animalhealthaustralia.com.au/download/9266/

WOAH: https://www.woah.org/fileadmin/Home/fr/Health_standards/tahm/3.03.14_NEWCASTLE_DIS.pdf

ICTV: https://ictv.global/report/chapter/paramyxoviridae/paramyxoviridae/orthoavulavirus

Genotype info:

Class I:

2 genotypes

Largely includes low virulence strains recovered from live bird markets and wild waterfowl worldwide.

Class II:

22 genotypes

Comprises the vast majority of viruses of high and low virulence isolated from poultry and wild birds.

Demarcation criteria:

Species: Phylogenetic comparison of the L gene amino acid sequences. Since the primary criterion is the tree topology, whether or not a virus belongs to the same species becomes a matter of branch length between the nearest node and the tip of the branch. This length is defined as 0.03 in the trees generated. (Source: ICTV)

Genotype: Phylogenetic comparison of the F gene nucleotide sequences. Whole genome sequences can also be used. (Source: WOAH)

Orthoparamyxovirinae

Henipavirus

Henipavirus hendraense

Also known as:

Hendra virus

Hendra henipavirus

Equine morbillivirus

Abbreviation: HeV

Disease: Hendra virus infection

Host: Multiple; notifiable in horses

Genome: -ssRNA, non-segmented

Size: 18.2kb

NCBI Tax ID: 3052223

NCBI RefSeq: NC_001906

Australian Reference Laboratory: CSIRO-ACDP (Kim Haplin)

AUSVETPLAN: https://animalhealthaustralia.com.au/download/5621/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.14_NIPAH_HENDRA.pdf

ICTV: https://ictv.global/report/chapter/paramyxoviridae/paramyxoviridae/henipavirus

Genotype info: There are two genotypes (HeV-g1 and HeV-g2)

Demarcation criteria:

Species: Phylogenetic comparison of the L gene amino acid sequences. Since the primary criterion is the tree topology, whether or not a virus belongs to the same species becomes a matter of branch length between the nearest node and the tip of the branch. This length is defined as 0.03 in the trees generated. (Source: ICTV)

Genotype: Phylogenetic comparison of the whole genome, N gene, or G gene nucleotide sequences. (Source: https://doi.org/10.1186/s12985-021-01652-7)

Henipavirus nipahense

Also known as:

Nipah virus

Nipah henipavirus

Abbreviation: NiV

Disease: Nipah virus infection; Nipah virus encephalitis

Host: Multiple; notifiable in swine

Genome: -ssRNA, non-segmented

Size: 18.2kb

NCBI Tax ID: 3052225

NCBI RefSeq: NC_002728

Australian Reference Laboratory: CSIRO-ACDP (Kim Haplin)

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.14_NIPAH_HENDRA.pdf

ICTV: https://ictv.global/report/chapter/paramyxoviridae/paramyxoviridae/henipavirus

Genotype info: There are two genotypes (B and M)

B genotypes are from Bangladesh and India

M genotypes are from Malaysia and Cambodia

Demarcation criteria:

Species: Phylogenetic comparison of the L gene amino acid sequences. Since the primary criterion is the tree topology, whether or not a virus belongs to the same species becomes a matter of branch length between the nearest node and the tip of the branch. This length is defined as 0.03 in the trees generated. (Source: ICTV)

Genotype: Phylogenetic comparison of the whole genome or the N gene nucleotide sequences. (Source: https://doi.org/10.3201/eid2505.181076)

Morbillivirus

Morbillivirus caprinae

Also known as:

Peste des petits ruminants virus

Small ruminant morbillivirus

Pseudorinderpest virus

Abbreviation: PPRV

Disease: Ovine rinderpest (peste des petits ruminants)

Host: Artiodactyls, especially ruminants and suids; notifiable in sheep

Genome: -ssRNA, non-segmented

Size: 15.9kb

NCBI Tax ID: 3052343

NCBI RefSeq: NC_006383

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1657/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.08.09_PPR.pdf

CABI: https://www.cabi.org/isc/datasheet/70165

ICTV: https://ictv.global/report/chapter/paramyxoviridae/paramyxoviridae/morbillivirus

Genotype info: Four genotypes (lineages) of PPRV are described:

Lineages I and II are found mainly in West Africa

Lineage III is generally found in East Africa

Lineage IV was known as the Asian lineage, but has now spread to the African continent and become the most prevalent lineage

Demarcation criteria:

Species: Phylogenetic comparison of the L gene amino acid sequences. Since the primary criterion is the tree topology, whether or not a virus belongs to the same species becomes a matter of branch length between the nearest node and the tip of the branch. This length is defined as 0.03 in the trees generated. (Source: ICTV)

Genotype: Phylogenetic comparison of the nucleoprotein (N) and/or fusion (F) protein gene nucleotide sequences. (Source: WOAH)

Morbillivirus pecoris

Also known as:

Rinderpest virus

Rinderpest morbillivirus

Abbreviation: RPV

Disease: Rinderpest; cattle plague

Host: Multiple (typically cattle, yaks and buffaloes)

Genome: -ssRNA, non-segmented

Size: 15.8kb

NCBI Tax ID: 11241

NCBI RefSeq: NC_006296

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1674/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.20_RINDERPEST.pdf

ICTV: https://ictv.global/report/chapter/paramyxoviridae/paramyxoviridae/morbillivirus

Genotype info: Three genotypes (lineages) of RPV are described:

Lineages I (Ethiopia and Sudan)

Lineage II (East and West Africa)

Lineage III (Asia)

Demarcation criteria:

Species: Phylogenetic comparison of the L gene amino acid sequences. Since the primary criterion is the tree topology, whether or not a virus belongs to the same species becomes a matter of branch length between the nearest node and the tip of the branch. This length is defined as 0.03 in the trees generated. (Source: ICTV)

Genotype: Phylogenetic comparison of the nucleoprotein (N) and/or fusion (F) protein gene nucleotide sequences. (Source: WOAH)

Rubulavirinae

Pararubulavirus

Pararubulavirus menangleense

Also known as:

Menangle virus

Menangle rubulavirus

Menangle pararubulavirus

Porcine paramyxovirus

Abbreviation: MenPV

Disease: Menangle virus infection

Host: Pigs, humans and bats

Genome: -ssRNA, non-segmented

Size: 15.5kb

NCBI Tax ID: 3052599

NCBI RefSeq: NC_039197

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

CFSPH: https://www.cfsph.iastate.edu/Factsheets/pdfs/menangle.pdf

ICTV: https://ictv.global/report/chapter/paramyxoviridae/paramyxoviridae/pararubulavirus

Demarcation criteria: For species, phylogenetic comparison of the L gene amino acid sequences. Since the primary criterion is the tree topology, whether or not a virus belongs to the same species becomes a matter of branch length between the nearest node and the tip of the branch. This length is defined as 0.03 in the trees generated. (Source: ICTV)

RNA PHENUIVIRIDAE

Phlebovirus

Phlebovirus riftense

Also known as:

Rift Valley fever virus

Rift Valley fever phlebovirus

Abbreviation: RVFV

Disease: Rift Valley fever

Host: Cattle, buffalo, sheep, goats, and camels (transmitted via mosquitoes and infected tissue)

Genome: -ssRNA, enveloped with 3 segments (L, M and S) coding for 6 proteins

Size: 11.5kb

NCBI Tax ID: 11588

NCBI RefSeq:

S: NC_014395

M: NC_014396

L: NC_014397

AUSVETPLAN: https://animalhealthaustralia.com.au/download/9095/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.18_RVF.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.66184

ICTV: https://ictv.global/report/chapter/phenuiviridae/phenuiviridae/phlebovirus

Genotype info: RVFV consists of a single serotype and low genetic diversity. (Source: WOAH)

Demarcation criteria: Less than 95% identity in the amino acid sequence of the RdRp. (Source: ICTV)

RNA PICORNAVIRIDAE

Aphthovirus

Foot-and-mouth disease virus

Also known as: Hoof and mouth disease virus

Abbreviation: FMDV

Disease: Foot and mouth disease (vesicular lesions)

Clinically indistinguishable from swine vesicular disease (genus Enterovirus) and vesicular disease in pigs caused by Seneca Valley virus (genus Senecavirus)

Host: Multiple - mainly cloven-hoofed animals

Genome: +ssRNA, linear, non-segmented

Size: 8.4kb

NCBI Tax ID: 12110

NCBI RefSeq: NC_039210

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1641/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.08_FMD.pdf

CABI: https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.82824

ICTV: https://ictv.global/report/chapter/picornaviridae/picornaviridae/aphthovirus

Genotype info:

Seven serotypes: A, O, C, SAT 1, SAT 2, SAT 3, Asia 1.

Each of the serotypes are divided into different topotypes.

Demarcation criteria:

According to the ICTV, members of a species of the genus Aphthovirus:

are less than 20% divergent in polyprotein aa sequence

are less than 30% divergent in P1 aa sequence

are less than 10% divergent in 2C+3CD aa sequence

share a common genome organization

share a natural host range

However, in order to differentiate the different FMDV serotypes, phylogenetic comparison of the VP1 nucleotide sequence with other FMDV VP1 sequences is required. (Source: WOAH)

Avihepatovirus

Avihepatovirus A

Also known as: Duck hepatitis A virus

Abbreviation: DHAV

Disease: Duck viral hepatitis (DVH) type I

Host: Avian

Genome: +ssRNA, linear, non-segmented

Size: ~7.9kb

NCBI Tax ID: 691956

NCBI RefSeq: NC_008250

WOAH: https://www.woah.org/fileadmin/Home/fr/Health_standards/tahm/3.03.08_DVH.pdf

ICTV: https://ictv.global/report/chapter/picornaviridae/picornaviridae/avihepatovirus

Genotype info:

3 genotypes (DHAV-1, DHAV-2 and DHAV-3)

DHAV-1 is the most prevalent

Demarcation criteria: Avihepatovirus A is the only species in the genus. Differentiation of the genotypes can be achieved via phylogenetic comparison of a 467bp region of the 3D gene (Source: WOAH), however, recent studies suggest the whole genome sequence provides the most accurate results. (Source: https://doi.org/10.1016/j.virusres.2023.199216)

Enterovirus

Enterovirus B

Also known as: Swine vesicular disease virus (variant of coxsackievirus B5)

Abbreviation: SVDV

Disease: Swine vesicular disease

Clinically indistinguishable from foot-and-mouth disease (genus Aphthovirus) and vesicular disease in pigs caused by Seneca Valley virus (genus Senecavirus)

Host: Swine

Genome: +ssRNA, linear, non-segmented

Size: 7.4kb

NCBI Tax ID: 12075

NCBI RefSeq: X54521

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1698/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.08.08_SVD.pdf

CABI: https://www.cabi.org/isc/datasheet/62454

ICTV: https://ictv.global/report/chapter/picornaviridae/picornaviridae/enterovirus

Genotype info: Notes from WOAH manual:

SVDV has been classified as a porcine variant of a human coxsackievirus B5 (Enterovirus B), in the family Picornaviridae.

All isolates are classified in a single serotype, with four distinguishable antigenic/genomic variants (Brocchi et al., 1997), which evolved sequentially in different time-periods, except for the third and fourth variants that were co-circulating in Italy during 1992–1993.

All SVDVs occurring since then diverge from a common origin and cluster in a unique antigenic/genomic lineage corresponding to the fourth and most recent group; however, two genomic sub-lineages are distinguishable within it (Knowles et al., 2007).

Antigenically and genetically, SVDV is closely related to the human virus coxsackievirus B5 and it has been suggested that it arose through recombination with another human enterovirus, coxsackievirus A9 (Bruhn et al., 2015).

A second adaptation of a human enterovirus to cause vesicular disease in pigs was reported in Russia in 1975 involving coxsackievirus B4, which is serologically distinct from SVDV/CV-B5 (Lomakina et al., 2016).

Demarcation criteria:

According to the ICTV, members of a species of the genus Enterovirus:

are less than 30% divergent in polyprotein aa sequence

are less than 40% divergent in P1 aa sequence

are less than 30% divergent in aa sequence of the non-structural proteins 2C + 3CD

share a common genome organization

However, to differentiate SVDV variants, phylogenetic comparison of the 1D or 3D genome regions is required. (Source: WOAH)

Senecavirus

Senecavirus A

Also known as:

Seneca Valley virus

Senecavirus A1

Abbreviation: SVV

Disease: Vesicular disease

Clinically indistinguishable from foot-and-mouth disease (genus Aphthovirus), swine vesicular disease (genus Enterovirus), vesicular exanthema of swine (family Caliciviridae, genus Vesivirus), and vesicular stomatitis (family Rhabdoviridae, genus Vesiculovirus)

Host: Swine

Genome: +ssRNA, linear, non-segmented

Size: 7.3kb

NCBI Tax ID: 390157

NCBI RefSeq: NC_011349

MSD: https://www.msdvetmanual.com/generalized-conditions/seneca-valley-virus-disease/seneca-valley-virus-disease-in-pigs

ICTV: https://ictv.global/report/chapter/picornaviridae/picornaviridae/senecavirus

Genotype info: 3 clades (I, II and III)

Demarcation criteria: Senecavirus A is the only species in the genus. Differentiation of the genotypes can be achieved via phylogenetic comparison of the VP1 nt or whole genome sequence. (Source: https://doi.org/10.1177/0300985816653990)

Teschovirus

Teschovirus A

Also known as:

Porcine teschovirus

Porcine enterovirus serotype 1

Abbreviation: PTV or TV A

Disease: Porcine enteroviral encephalomyelitis; swine paralysis; teschovirus encephalomyelitis (PTV 1 infection); Teschen/Talfan disease (other PTVs)

Host: Pigs and wild boars

Genome: +ssRNA, linear, non-segmented with P1, P2 and P3 regions

P1 is divergent (contains VP1, VP2, VP3 and VP4) while the rest of the genome is quite conserved

Size: 7.1kb (polyprotein = 2,199–2,236aa)

NCBI Tax ID: 118140

NCBI RefSeq: NC_003985

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/2.08.09_TESCHOVIRUS_ENCEPH.pdf

ICTV: https://ictv.global/report/chapter/picornaviridae/picornaviridae/teschovirus

Genotype info:

ICTV currently recognises 14 different Teschovirus A genotypes (PTV 1 - 14) (ICTV Virus Taxonomy: 2019 Release)

Yang et al. 2020 propose that Teschovirus A includes PTV 1 - 13, 17 and 18 (Source: https://doi.org/10.1007/s00705-020-04525-6)

Demarcation criteria:

According to the ICTV, members of a species of the genus Teschovirus:

are less than 20% divergent in polyprotein aa sequence

are less than 30% divergent in P1 aa sequence

are less than 10% divergent in 2C+3CD aa sequence

share a common genome organization

share a natural host range

However, in order to differentiate the different Teschovirus A genotypes, phylogenetic comparison of the VP1 nucleotide sequence with other PTV VP1 sequences is required. (Source: WOAH)

RNA PNEUMOVIRIDAE

Metapneumovirus

Metapneumovirus avis

Also known as:

Avian metapneumovirus

Turkey rhinotracheitis virus

Abbreviation: AMPV

Disease: Turkey rhinotracheitis (swollen head syndrome)

Host: Avian - mostly turkeys, pheasants, Muscovy ducks and guinea fowls

Genome: -ssRNA, non-segmented (8 genes with 9 ORFs; gene order: N-P-M-F-M2-SH-G-L)

Size: 13.3kb

NCBI Tax ID: 38525

NCBI RefSeq: NC_039231

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.03.15_TURKEY_RHINO.pdf

CABI: https://www.cabidigitallibrary.org/doi/full/10.1079/cabicompendium.92920

ICTV: https://ictv.global/report/chapter/pneumoviridae/pneumoviridae/metapneumovirus

Genotype info: 4 subtypes (A, B, C and D)

Demarcation criteria:

Species: Metapneumovirus species are distinguished on the basis of having an avian or human host. Antigenic and sequence relatedness also distinguishes AMPV subgroups A, B, and D from human metapneumovirus (HMPV); but AMPV subgroup C is more closely related to HMPV than to AMPV A, B, and D. Thus, antigenic and sequence relatedness do not consistently distinguish between HMPV and AMPV. (Source: ICTV)

Genotype: Phylogenetic comparison of the G gene nucleotide sequence. (Source: WOAH)

RNA REOVIRIDAE

Sedoreovirinae

Orbivirus

African horse sickness virus

Abbreviation: AHSV

Disease: African horse sickness

Host: Equine - commonly horses, mules, and donkeys (transmitted by insects, incl. midges, mosquitoes and ticks)

Genome: dsRNA, 10 segments (4 non-structural proteins + 7 structural proteins)

Size: ~19kb

NCBI Tax ID: 40050

NCBI acc:

Seg1: NC_006021

Seg2: NC_005996

Seg3: NC_006017

Seg4: NC_006012

Seg5: NC_006020

Seg6: NC_006018

Seg7: NC_006011

Seg8: NC_006016

Seg9: NC_006019

Seg10: NC_006009

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1602/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.06.01_AHS.pdf

ICTV: https://ictv.global/report/chapter/sedoreoviridae/sedoreoviridae/orbivirus

Genotype info: 9 serotypes (1-9)

Demarcation criteria:

Species: In the conserved Seg3 (encoding the major subcore structural protein, VP3), viruses within the same species will normally have >76% nucleotide identity (>83% amino acid identity) while those in different species usually have <74% identity. These differences are also reflected in the amino acid sequences of the viral proteins. In segment 1, encoding the RdRP, members of a single species will normally have >78% amino acid identity. (Source: ICTV)

Genotype: Phylogenetic comparison of the Seg2 (encoding the outer viral capsid protein, VP2) nucleotide sequence. (Source: WOAH)

Bluetongue virus

Abbreviation: BTV

Disease: Bluetongue disease

Host: Ruminants - mainly sheep but also cattle, goats, deer etc. (transmitted by Culicoides spp.)

Genome: dsRNA, 10 segments (4 non-structural proteins + 7 structural proteins)

Size: ~19kb

NCBI Tax ID: 40051

NCBI acc:

Seg1: NC_006023

Seg2: NC_006013

Seg3: NC_006014

Seg4: NC_006024

Seg5: NC_006025

Seg6: NC_006010

Seg7: NC_006022

Seg8: NC_006007

Seg9: NC_006008

Seg10: NC_006015

Australian Reference Laboratory: CSIRO-ACDP (Debbie Eagles)

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1622/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.03_BLUETONGUE.pdf

ICTV: https://ictv.global/report/chapter/sedoreoviridae/sedoreoviridae/orbivirus

Genotype info:

27 serotypes (1-27)

Toggenburg orbivirus is a strain of serotype 25

Demarcation criteria:

Species: In the conserved Seg3 (encoding the major subcore structural protein, VP3), viruses within the same species will normally have >76% nucleotide identity (>83% amino acid identity) while those in different species usually have <74% identity. These differences are also reflected in the amino acid sequences of the viral proteins. In segment 1, encoding the RdRp, members of a single species will normally have >78% amino acid identity. (Source: ICTV)

Genotype: The most reliable sequence-based method of BTV serotype classification is using a whole genome approach. (Source: WOAH)

Epizootic hemorrhagic disease virus

Abbreviation: EHDV

Disease: Epizootic hemorrhagic disease

Host: Cattle, sheep, deer, camels, llamas, wild ruminants, marsupials (transmitted by Culicoides spp.)

Genome: dsRNA, 10 segments (4 non-structural proteins + 7 structural proteins)

Size: ~19kb

NCBI Tax ID: 40054

NCBI acc:

Seg1: NC_013396

Seg2: NC_013397

Seg3: NC_013398

Seg4: NC_013399

Seg5: NC_013400

Seg6: NC_013401

Seg7: NC_013402

Seg8: NC_013403

Seg9: NC_013404

Seg10: NC_013405

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.07_EHD.pdf

ICTV: https://ictv.global/report/chapter/sedoreoviridae/sedoreoviridae/orbivirus

Genotype info:

8 serotypes (1-8)

Ibaraki virus is a strain of serotype 2

Serotype 3 was regrouped as serotype 1

Demarcation criteria:

Species: In the conserved Seg3 (encoding the major subcore structural protein, VP3), viruses within the same species will normally have >76% nucleotide identity (>83% amino acid identity) while those in different species usually have <74% identity. These differences are also reflected in the amino acid sequences of the viral proteins. In segment 1, encoding the RdRp, members of a single species will normally have >78% amino acid identity. (Source: ICTV)

Genotype: Phylogenetic comparison of the Seg2 (encoding the outer viral capsid protein, VP2) nucleotide sequence. (Source: WOAH)

Equine encephalosis virus

Abbreviation: EEV

Disease: Equine encephalosis

Host: Equine (transmitted by Culicoides spp.)

Genome: dsRNA, 10 segments (4 non-structural proteins + 7 structural proteins)

Size: ~19kb

NCBI Tax ID: 201490

NCBI acc:

Seg1: NC_038574

Seg2: NC_038582

Seg3: NC_038575

Seg4: NC_038581

Seg5: NC_038576

Seg6: NC_038577

Seg7: NC_038583

Seg8: NC_038578

Seg9: NC_038579

Seg10: NC_038580

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

ICTV: https://ictv.global/report/chapter/sedoreoviridae/sedoreoviridae/orbivirus

Genotype info: 7 serotypes (1-7) (Source: https://doi.org/10.3390/v13030398)

Demarcation criteria:

Species: In the conserved Seg3 (encoding the major subcore structural protein, VP3), viruses within the same species will normally have >76% nucleotide identity (>83% amino acid identity) while those in different species usually have <74% identity. These differences are also reflected in the amino acid sequences of the viral proteins. In segment 1, encoding the RdRp, members of a single species will normally have >78% amino acid identity. (Source: ICTV)

Genotype: Phylogenetic comparison of the Seg2 (encoding the outer viral capsid protein, VP2) nucleotide sequence. (Source: https://doi.org/10.3390/v13030398)

RNA RETROVIRIDAE

Deltaretrovirus

Bovine leukaemia virus

Also known as:

Bovine leukosis virus

Bovine type C oncovirus

Abbreviation: BLV

Disease: Enzootic bovine leukosis (EBL)

Host: Cattle and buffalo (transmitted by insects)

Genome: +ssRNA (5’-gag-pro-pol-env-px-3’)

Size: 8.4kb

NCBI Tax ID: 11901

NCBI RefSeq: NC_001414

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.04.09_EBL.pdf

ICTV: https://ictv.global/report/chapter/retroviridae/retroviridae/deltaretrovirus

Genotype info: 11 genotypes (1–11)

Demarcation criteria: Phylogenetic comparison of env-gp51 gene sequences. (Source: https://doi.org/10.3390/v13112167)

Lentivirus

Equine infectious anaemia virus

Abbreviation: EIAV

Disease: Equine infectious anaemia; swamp fever

Host: Equine

Genome: +ssRNA, non-segmented with 11 proteins

Size: 8.4kb

NCBI Tax ID: 11665

NCBI RefSeq: NC_001450

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.06.06_EIA.pdf

ICTV: https://ictv.global/report/chapter/retroviridae/retroviridae/lentivirus

Genotype info: Split into 6 groups related to separate outbreaks

Demarcation criteria: Phylogenetic comparison of the pol gene or whole genome sequence. (Source: https://doi.org/10.1186%2Fs12917-021-02849-2)

Jembrana disease virus

Abbreviation: JDV

Disease: Jembrana disease

Host: Cattle

Genome: +ssRNA, non-segmented with 11 proteins

Size: 7.7 kb

NCBI Tax ID: 36370

NCBI RefSeq: NC_001654

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

ICTV: https://ictv.global/report/chapter/retroviridae/retroviridae/lentivirus

Demarcation criteria: Phylogenetic comparison of the pol gene. (Source: https://doi.org/10.1099/0022-1317-76-1-189)

Visna-maedi virus

Also known as:

Visna virus

Maedi-visna virus

Ovine lentivirus

Abbreviation: VMV

Disease: Visna–Maedi; ovine progressive pneumonia (OPP)

Visna = meningoencephalitis (central nervous system)

Maedi = chronic progressive pneumonia (respiratory system)

Host: Sheep

Genome: +ssRNA, non-segmented with 11 proteins

Size: 9.2kb

NCBI Tax ID: 2169971

NCBI RefSeq: NC_001452

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.08.02_CAE_MV.pdf

ICTV: https://ictv.global/report/chapter/retroviridae/retroviridae/lentivirus

Genotype info:

VMV belongs to the small ruminant lentiviruses (SRLVs)

SRLVs are divided into five genotypes (A–E), with VMV belonging to Genotype A

Genotype A is divided into 22 subgenotypes (A1–A22)

Demarcation criteria: Phylogenetic comparison of gag-pol gene and LTR sequences. (Source: https://doi.org/10.3389/fvets.2022.846634)

RNA RHABDOVIRIDAE

Lyssavirus

Lyssavirus australis

Also known as: Australian bat lyssavirus

Abbreviation: ABLV

Disease: Rabies

Host: Mammals

Genome: -ssRNA

Size: 11.8kb

NCBI Tax ID: 90961

NCBI RefSeq: NC_003243

AUSVETPLAN: https://animalhealthaustralia.com.au/download/5100/

WHA: https://wildlifehealthaustralia.com.au/Portals/0/ResourceCentre/FactSheets/mammals/Australian_Bat_Lyssavirus.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.18_RABIES.pdf

ICTV: https://ictv.global/report/chapter/rhabdoviridae/rhabdoviridae/lyssavirus

Genotype info: Belongs to Genotype 7 of the Lyssavirus genotypes and has two sub-lineages: the yellow-bellied sheathtail bat variant and the pteropid variant. (Source: WHA)

Demarcation criteria:

Species:

A) Genetic distances, with the threshold of 78-80% nt identity for the complete N gene, provide better quantitative resolution compared to other genes, or 80% nt identity for concatenated coding regions of N+P+M+G+L;

B) In phylogenetic trees based on the entire N, or G, or L gene sequences, or concatenated N+P+M+G+L coding sequences, the new virus does not represent a sister branch to a virus from an established species. Instead, it is placed ancestrally to a group (cluster) of phylogenetically-related viruses that belong to several established species. (Source: ICTV)

Genotype: Phylogenetic comparison of the N gene or whole genome sequences. (Source: https://doi.org/10.11134/btp.4.2022.15)

Lyssavirus rabies

Also known as:

Rabies lyssavirus

Rabies virus

Abbreviation: RABV

Disease: Rabies

Host: Mammals

Genome: -ssRNA

Size: 11.9kb

NCBI Tax ID: 11292

NCBI RefSeq: NC_001542

Australian Reference Laboratory: CSIRO-ACDP (John Bingham)

AUSVETPLAN: https://animalhealthaustralia.com.au/download/5100/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.18_RABIES.pdf

ICTV: https://ictv.global/report/chapter/rhabdoviridae/rhabdoviridae/lyssavirus

Genotype info: Belongs to Genotype 1 of the Lyssavirus genotypes

Demarcation criteria:

Species:

A) Genetic distances, with the threshold of 78-80% nt identity for the complete N gene, provide better quantitative resolution compared to other genes, or 80% nt identity for concatenated coding regions of N+P+M+G+L;

B) In phylogenetic trees based on the entire N, or G, or L gene sequences, or concatenated N+P+M+G+L coding sequences, the new virus does not represent a sister branch to a virus from an established species. Instead, it is placed ancestrally to a group (cluster) of phylogenetically-related viruses that belong to several established species. (Source: ICTV)

Genotype: Phylogenetic comparison of the N gene or whole genome sequences. (Source: https://doi.org/10.11134/btp.4.2022.15)

Vesiculovirus

Vesiculovirus alagoas

Also known as:

Alagoas virus

Alagoas vesiculovirus

Vesicular stomatitis Alagoas virus

Abbreviation: VSAV

Disease: Vesicular stomatitis

Host: cattle; equids; pigs (transmitted by insects)

Genome: -ssRNA; enveloped

Size: 11.1kb

NCBI Tax ID: 1972579

NCBI RefSeq: NC_025353

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1708/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.23_VESICULAR_STOMATITIS.pdf

ICTV: https://ictv.global/report/chapter/rhabdoviridae/rhabdoviridae/vesiculovirus

Demarcation criteria:

Species: According to ICTV:

A) minimum amino acid sequence divergence of 20% in the L protein;

B) minimum amino acid sequence divergence of 10% in the N protein;

C) minimum amino acid sequence divergence of 15% in the G protein;

D) can be distinguished in serological tests; and

E) occupy different ecological niches as evidenced by differences in hosts and or arthropod vectors.

Genotype: Phylogenetic comparison of whole genome sequences. (Source: https://doi.org/10.3389/fvets.2023.1110483)

Vesiculovirus cocal

Also known as:

Cocal virus

Cocal vesiculovirus

Vesicular stomatitis Cocal virus

Abbreviation: COCV

Disease: Vesicular stomatitis

Host: cattle; equids; pigs (transmitted by insects)

Genome: -ssRNA; enveloped

Size: 11kb

NCBI Tax ID: 1972572

NCBI RefSeq: NC_028255

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1708/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.23_VESICULAR_STOMATITIS.pdf

ICTV: https://ictv.global/report/chapter/rhabdoviridae/rhabdoviridae/vesiculovirus

Demarcation criteria:

Species: According to ICTV:

A) minimum amino acid sequence divergence of 20% in the L protein;

B) minimum amino acid sequence divergence of 10% in the N protein;

C) minimum amino acid sequence divergence of 15% in the G protein;

D) can be distinguished in serological tests; and

E) occupy different ecological niches as evidenced by differences in hosts and or arthropod vectors.

Genotype: Phylogenetic comparison of whole genome sequences. (Source: https://doi.org/10.3389/fvets.2023.1110483)

Vesiculovirus indiana

Also known as:

Indiana virus

Indiana vesiculovirus

Vesicular stomatitis Indiana virus

Abbreviation: VSIV

Disease: Vesicular stomatitis

Host: cattle; equids; pigs (transmitted by insects)

Genome: -ssRNA; enveloped

Size: 11.1kb

NCBI Tax ID: 1972577

NCBI RefSeq: NC_001560

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1708/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.23_VESICULAR_STOMATITIS.pdf

ICTV: https://ictv.global/report/chapter/rhabdoviridae/rhabdoviridae/vesiculovirus

Demarcation criteria:

Species: According to ICTV:

A) minimum amino acid sequence divergence of 20% in the L protein;

B) minimum amino acid sequence divergence of 10% in the N protein;

C) minimum amino acid sequence divergence of 15% in the G protein;

D) can be distinguished in serological tests; and

E) occupy different ecological niches as evidenced by differences in hosts and or arthropod vectors.

Genotype: Phylogenetic comparison of whole genome sequences. (Source: https://doi.org/10.3389/fvets.2023.1110483)

Vesiculovirus newjersey

Also known as:

New Jersey virus

New Jersey vesiculovirus

Vesicular stomatitis New Jersey virus

Abbreviation: VSNJV

Disease: Vesicular stomatitis

Host: cattle; equids; pigs (transmitted by insects)

Genome: -ssRNA; enveloped

Size: 11.1kb

NCBI Tax ID: 1972578

NCBI RefSeq: NC_024473

AUSVETPLAN: https://animalhealthaustralia.com.au/download/1708/

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.01.23_VESICULAR_STOMATITIS.pdf

ICTV: https://ictv.global/report/chapter/rhabdoviridae/rhabdoviridae/vesiculovirus

Demarcation criteria:

Species: According to ICTV:

A) minimum amino acid sequence divergence of 20% in the L protein;

B) minimum amino acid sequence divergence of 10% in the N protein;

C) minimum amino acid sequence divergence of 15% in the G protein;

D) can be distinguished in serological tests; and

E) occupy different ecological niches as evidenced by differences in hosts and or arthropod vectors.

Genotype: Phylogenetic comparison of whole genome sequences. (Source: https://doi.org/10.3389/fvets.2023.1110483)

RNA TOGAVIRIDAE

Alphavirus

Getah virus

Also known as: Sagiyama virus

Abbreviation: GETV

Disease: Getah virus infection

Host: Equine

Genome: +ssRNA, enveloped

Size: 11.5kb

NCBI Tax ID: 59300

NCBI RefSeq: NC_006558

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

CFSPH: https://www.cfsph.iastate.edu/Factsheets/pdfs/getah_virus.pdf

ICTV: https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/w/togaviridae/872/genus-alphavirus

Genotype info: Four genotypes (I–IV)

Demarcation criteria:

Species: According to ICTV, species demarcation criteria in the genus include:

Nucleotide and deduced amino acid sequences.

Antigenic characteristics.

Vector association.

Host association.

Disease association.

Ecological characteristics.

Species demarcation considers a combination of each of the criteria listed above. Whereas members of most species show at least 10% difference in amino acid sequence identity over entire coding regions, there is not a clear cutoff of sequence divergence to provide absolute species demarcation. For example, for Venezuelan equine encephalitis virus (VEEV), there are multiple subtypes with amino acid identities as low as 85%. However, although Everglades, Tonate, and Mucambo viruses are phylogenetically located within the VEEV cluster and have 94–97% amino acid identity with each other or the closest related VEEV strains, they are considered to belong to different individual species due to differences in several of the traits listed above.

Genotype: Phylogenetic comparison of the E2 gene or whole genome sequences. (Source: https://doi.org/10.3390%2Fpathogens11080945)

Eastern equine encephalitis virus

Abbreviation: EEEV

Disease: Equine encephalomyelitis; sleeping sickness

Host: Equine

Genome: +ssRNA, enveloped

Size: 11.4kb

NCBI Tax ID: 11021

NCBI RefSeq: NC_003899

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.06.05_EEE_WEE_VEE.pdf

CABI: https://www.cabi.org/isc/datasheet/84274

ICTV: https://ictv.global/report/chapter/togaviridae/togaviridae/alphavirus

Genotype info: There used to be four genotypes (I–IV), however, genotypes II–IV were reclassified as Madariaga virus (MADV).

Demarcation criteria:

Species: According to ICTV, species demarcation criteria in the genus include:

Nucleotide and deduced amino acid sequences.

Antigenic characteristics.

Vector association.

Host association.

Disease association.

Ecological characteristics.

Species demarcation considers a combination of each of the criteria listed above. Whereas members of most species show at least 10% difference in amino acid sequence identity over entire coding regions, there is not a clear cutoff of sequence divergence to provide absolute species demarcation. For example, for Venezuelan equine encephalitis virus (VEEV), there are multiple subtypes with amino acid identities as low as 85%. However, although Everglades, Tonate, and Mucambo viruses are phylogenetically located within the VEEV cluster and have 94–97% amino acid identity with each other or the closest related VEEV strains, they are considered to belong to different individual species due to differences in several of the traits listed above.

Genotype: Phylogenetic comparison of the E2 gene or whole genome sequences. (Source: https://doi.org/10.3201%2Feid1403.070816)

Western equine encephalitis virus

Abbreviation: WEEV

Disease: Equine encephalomyelitis; sleeping sickness

Host: Equine

Genome: +ssRNA, enveloped

Size: 11.4kb

NCBI Tax ID: 11039

NCBI RefSeq: NC_003908

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.06.05_EEE_WEE_VEE.pdf

CABI: https://www.cabi.org/isc/datasheet/60874

ICTV: https://ictv.global/report/chapter/togaviridae/togaviridae/alphavirus

Genotype info: Two lineages (A and B)

Demarcation criteria:

Species: According to ICTV, species demarcation criteria in the genus include:

Nucleotide and deduced amino acid sequences.

Antigenic characteristics.

Vector association.

Host association.

Disease association.

Ecological characteristics.

Species demarcation considers a combination of each of the criteria listed above. Whereas members of most species show at least 10% difference in amino acid sequence identity over entire coding regions, there is not a clear cutoff of sequence divergence to provide absolute species demarcation. For example, for Venezuelan equine encephalitis virus (VEEV), there are multiple subtypes with amino acid identities as low as 85%. However, although Everglades, Tonate, and Mucambo viruses are phylogenetically located within the VEEV cluster and have 94–97% amino acid identity with each other or the closest related VEEV strains, they are considered to belong to different individual species due to differences in several of the traits listed above.

Genotype: Phylogenetic comparison of the E2 gene or whole genome sequences. (Source: https://doi.org/10.1128%2FJVI.01463-14)

Venezuelan equine encephalitis virus

Abbreviation: VEEV

Disease: Equine encephalomyelitis; sleeping sickness

Host: Equine

Genome: +ssRNA, enveloped

Size: 11.4kb

NCBI Tax ID: 11036

NCBI RefSeq: NC_001449

AUSVETPLAN: https://animalhealthaustralia.com.au//wp-content/uploads/dlm_uploads/AVP_RPB_Collated_V3.6_2018-1.pdf

WOAH: https://www.woah.org/fileadmin/Home/eng/Health_standards/tahm/3.06.05_EEE_WEE_VEE.pdf

CABI: https://www.cabi.org/isc/datasheet/96519

ICTV: https://ictv.global/report/chapter/togaviridae/togaviridae/alphavirus

Genotype info:

Six subtypes (I–VI)

Subtype I includes five antigenic variants (AB–F)

Demarcation criteria:

Species: According to ICTV, species demarcation criteria in the genus include:

Nucleotide and deduced amino acid sequences.

Antigenic characteristics.

Vector association.

Host association.

Disease association.

Ecological characteristics.

Species demarcation considers a combination of each of the criteria listed above. Whereas members of most species show at least 10% difference in amino acid sequence identity over entire coding regions, there is not a clear cutoff of sequence divergence to provide absolute species demarcation. For example, for Venezuelan equine encephalitis virus (VEEV), there are multiple subtypes with amino acid identities as low as 85%. However, although Everglades, Tonate, and Mucambo viruses are phylogenetically located within the VEEV cluster and have 94–97% amino acid identity with each other or the closest related VEEV strains, they are considered to belong to different individual species due to differences in several of the traits listed above.

Genotype: Phylogenetic comparison of the E2 gene or whole genome sequences. (Source: https://doi.org/10.3390/vetsci9060258)

Australian Biosecurity Genomic Database

Licensing information

Access the database

Usage guidelines

1. Initial screening

2. Interpreting results

High confidence

Medium confidence

Low confidence

3. Further analysis

Visualisation of read mapping results

Sequence identity of mapped reads

Generating consensus sequences

De novo assembly

Contacting the Chief Veterinary Office (CVO)

Troubleshooting

References

Notifiable Virus Compendium

DNA ASFARVIRIDAE

Asfivirus

African swine fever virus

DNA CIRCOVIRIDAE

Circovirus

Circovirus porcine2

DNA ORTHOHERPESVIRIDAE

Alphaherpesvirinae

Mardivirus

Mardivirus anatidalpha1

Varicellovirus

Varicellovirus equidalpha1

Varicellovirus suidalpha1

Gammaherpesvirinae

Macavirus

Macavirus alcelaphinegamma1

DNA POXVIRIDAE

Orthopoxvirus

Camelpox virus

Capripoxvirus

Goatpox virus

Lumpy skin disease virus

Sheeppox virus

RNA ARTERIVIRIDAE

Alphaarterivirus

Alphaarterivirus equid

Betaarterivirus

Betaarterivirus suid 1

RNA ASTROVIRIDAE

Avastrovirus

Duck astrovirus

RNA BIRNAVIRIDAE

Avibirnavirus

Avibirnavirus gumboroense

RNA BORNAVIRIDAE

Orthobornavirus

Orthobornavirus bornaense

RNA CALICIVIRIDAE

Vesivirus

Vesicular exanthema of swine virus

RNA CORONAVIRIDAE

Alphacoronavirus

Alphacoronavirus 1

Porcine epidemic diarrhea virus

RNA FLAVIVIRIDAE

Orthoflavivirus

Orthoflavivirus encephalitidis

Orthoflavivirus japonicum

Orthoflavivirus loupingi

Orthoflavivirus nilense

Orthoflavivirus wesselsbronense

Pestivirus

Pestivirus australiaense

Pestivirus suis

Pestivirus tauri

RNA NAIROVIRIDAE

Orthonairovirus

Orthonairovirus haemorrhagiae

Orthonairovirus nairobiense

RNA ORTHOMYXOVIRIDAE

Influenzavirus A

Influenza A virus