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Article ; Online: Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology.

de Vries, Ellen M / Cogan, Noel O I / Gubala, Aneta J / Mee, Peter T / O'Riley, Kim J / Rodoni, Brendan C / Lynch, Stacey E

Scientific reports

2022 Volume 12, Issue 1, Page(s) 11886

Abstract: Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral ... ...

Abstract	Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner.
MeSH term(s)	Animals ; Australia ; Hemagglutinins ; Influenza A virus/genetics ; Influenza in Birds ; Poultry ; Technology ; Tool Use Behavior
Chemical Substances	Hemagglutinins
Language	English
Publishing date	2022-07-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16048-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: In Vitro and In Vivo Characterization of a Pigeon Paramyxovirus Type 1 Isolated from Domestic Pigeons in Victoria, Australia 2011

Shan, Songhua / Bruce, Kerri / Stevens, Vittoria / Wong, Frank Y. K / Wang, Jianning / Johnson, Dayna / Middleton, Deborah / O’Riley, Kim / McCullough, Sam / Williams, David T / Bergfeld, Jemma

Viruses. 2021 Mar. 08, v. 13, no. 3

2021

Abstract: Significant mortalities of racing pigeons occurred in Australia in late 2011 associated with a pigeon paramyxovirus serotype 1 (PPMV-1) infection. The causative agent, designated APMV-1/pigeon/Australia/3/2011 (P/Aus/3/11), was isolated from diagnostic ... ...

Abstract	Significant mortalities of racing pigeons occurred in Australia in late 2011 associated with a pigeon paramyxovirus serotype 1 (PPMV-1) infection. The causative agent, designated APMV-1/pigeon/Australia/3/2011 (P/Aus/3/11), was isolated from diagnostic specimens in specific pathogen free (SPF) embryonated eggs and was identified by a Newcastle Disease virus (NDV)-specific RT-PCR and haemagglutination inhibition (HI) test using reference polyclonal antiserum specific for NDV. The P/Aus/3/11 strain was further classified as PPMV-1 using the HI test and monoclonal antibody 617/161 by HI and phylogenetic analysis of the fusion gene sequence. The isolate P/Aus/3/11 had a slow haemagglutin-elution rate and was inactivated within 45 min at 56 °C. Cross HI tests generated an R value of 0.25, indicating a significant antigenic difference between P/Aus/3/11 and NDV V4 isolates. The mean death time (MDT) of SPF eggs infected with the P/Aus/3/11 isolate was 89.2 hr, characteristic of a mesogenic pathotype, consistent with other PPMV-1 strains. The plaque size of the P/Aus/3/11 isolate on chicken embryo fibroblast (CEF) cells was smaller than those of mesogenic and velogenic NDV reference strains, indicating a lower virulence phenotype in vitro and challenge of six-week-old SPF chickens did not induce clinical signs. However, sequence analysis of the fusion protein cleavage site demonstrated an ¹¹²RRQKRF¹¹⁷ motif, which is typical of a velogenic NDV pathotype. Phylogenetic analysis indicated that the P/Aus/3/11 isolate belongs to a distinct subgenotype within class II genotype VI of avian paramyxovirus type 1. This is the first time this genotype has been detected in Australia causing disease in domestic pigeons and is the first time since 2002 that an NDV with potential for virulence has been detected in Australia.
Keywords	Avian orthoavulavirus 1 ; Respirovirus ; chick embryos ; death ; etiological agents ; fibroblasts ; hemagglutination ; monoclonal antibodies ; nucleotide sequences ; pathotypes ; phenotype ; phylogeny ; polyclonal antibodies ; sequence analysis ; serotypes ; specific pathogen-free animals ; subgenotype ; virulence
Language	English
Dates of publication	2021-0308
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13030429
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: In Vitro and In Vivo Characterization of a Pigeon Paramyxovirus Type 1 Isolated from Domestic Pigeons in Victoria, Australia 2011.

Shan, Songhua / Bruce, Kerri / Stevens, Vittoria / Wong, Frank Y K / Wang, Jianning / Johnson, Dayna / Middleton, Deborah / O'Riley, Kim / McCullough, Sam / Williams, David T / Bergfeld, Jemma

Viruses

2021 Volume 13, Issue 3

Abstract	Significant mortalities of racing pigeons occurred in Australia in late 2011 associated with a pigeon paramyxovirus serotype 1 (PPMV-1) infection. The causative agent, designated APMV-1/pigeon/Australia/3/2011 (P/Aus/3/11), was isolated from diagnostic specimens in specific pathogen free (SPF) embryonated eggs and was identified by a Newcastle Disease virus (NDV)-specific RT-PCR and haemagglutination inhibition (HI) test using reference polyclonal antiserum specific for NDV. The P/Aus/3/11 strain was further classified as PPMV-1 using the HI test and monoclonal antibody 617/161 by HI and phylogenetic analysis of the fusion gene sequence. The isolate P/Aus/3/11 had a slow haemagglutin-elution rate and was inactivated within 45 min at 56 °C. Cross HI tests generated an R value of 0.25, indicating a significant antigenic difference between P/Aus/3/11 and NDV V4 isolates. The mean death time (MDT) of SPF eggs infected with the P/Aus/3/11 isolate was 89.2 hr, characteristic of a mesogenic pathotype, consistent with other PPMV-1 strains. The plaque size of the P/Aus/3/11 isolate on chicken embryo fibroblast (CEF) cells was smaller than those of mesogenic and velogenic NDV reference strains, indicating a lower virulence phenotype in vitro and challenge of six-week-old SPF chickens did not induce clinical signs. However, sequence analysis of the fusion protein cleavage site demonstrated an
MeSH term(s)	Animals ; Avulavirus/classification ; Avulavirus/genetics ; Avulavirus/isolation & purification ; Avulavirus/pathogenicity ; Chickens/virology ; Columbidae/virology ; Genome, Viral ; Genotype ; Hemagglutination Inhibition Tests ; Phylogeny ; Specific Pathogen-Free Organisms ; Victoria ; Viral Fusion Proteins/genetics ; Viral Fusion Proteins/immunology ; Virulence ; Zygote/virology
Chemical Substances	Viral Fusion Proteins
Language	English
Publishing date	2021-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13030429
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Article ; Online: Field Verification of an African Swine Fever Virus Loop-Mediated Isothermal Amplification (LAMP) Assay During an Outbreak in Timor-Leste.

Mee, Peter T / Wong, Shani / O'Riley, Kim J / da Conceição, Felisiano / Bendita da Costa Jong, Joanita / Phillips, Dianne E / Rodoni, Brendan C / Rawlin, Grant T / Lynch, Stacey E

Viruses

2020 Volume 12, Issue 12

Abstract: Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular ... ...

Abstract	Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular laboratories. Loop-mediated isothermal amplification (LAMP) is a rapid point of care test that can overcome a range of inhibitors. We outline further development of a real-time ASFV LAMP, including field verification during an outbreak in Timor-Leste. To increase field applicability, the extraction step was removed and an internal amplification control (IAC) was implemented. Assay performance was assessed in six different sample matrices and verified for a range of clinical samples. A LAMP detection limit of 400 copies/rxn was determined based on synthetic positive control spikes. A colourmetric LAMP assay was also assessed on serum samples. Comparison of the LAMP assay to a quantitative polymerase chain reaction (qPCR) was performed on clinical ASFV samples, using both serum and oral/rectal swabs, with a substantial level of agreement observed. The further verification of the ASFV LAMP assay, removal of extraction step, implementation of an IAC and the assessment of a range of sample matrix, further support the use of this assay for rapid in-field detection of ASFV.
MeSH term(s)	African Swine Fever/diagnosis ; African Swine Fever/epidemiology ; African Swine Fever/virology ; African Swine Fever Virus/genetics ; African Swine Fever Virus/isolation & purification ; Animals ; Disease Outbreaks ; Female ; Male ; Molecular Diagnostic Techniques/methods ; Molecular Diagnostic Techniques/standards ; Nucleic Acid Amplification Techniques/methods ; Nucleic Acid Amplification Techniques/standards ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; Swine ; Viremia
Language	English
Publishing date	2020-12-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12121444
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Article ; Online: Avian influenza infection dynamics under variable climatic conditions, viral prevalence is rainfall driven in waterfowl from temperate, south-east Australia.

Ferenczi, Marta / Beckmann, Christa / Warner, Simone / Loyn, Richard / O'Riley, Kim / Wang, Xinlong / Klaassen, Marcel

Veterinary research

2016 Volume 47, Page(s) 23

Abstract: Understanding Avian Influenza Virus (AIV) infection dynamics in wildlife is crucial because of possible virus spill over to livestock and humans. Studies from the northern hemisphere have suggested several ecological and environmental drivers of AIV ... ...

Abstract	Understanding Avian Influenza Virus (AIV) infection dynamics in wildlife is crucial because of possible virus spill over to livestock and humans. Studies from the northern hemisphere have suggested several ecological and environmental drivers of AIV prevalence in wild birds. To determine if the same drivers apply in the southern hemisphere, where more irregular environmental conditions prevail, we investigated AIV prevalence in ducks in relation to biotic and abiotic factors in south-eastern Australia. We sampled duck faeces for AIV and tested for an effect of bird numbers, rainfall anomaly, temperature anomaly and long-term ENSO (El-Niño Southern Oscillation) patterns on AIV prevalence. We demonstrate a positive long term effect of ENSO-related rainfall on AIV prevalence. We also found a more immediate response to rainfall where AIV prevalence was positively related to rainfall in the preceding 3-7 months. Additionally, for one duck species we found a positive relationship between their numbers and AIV prevalence, while prevalence was negatively or not affected by duck numbers in the remaining four species studied. In Australia largely non-seasonal rainfall patterns determine breeding opportunities and thereby influence bird numbers. Based on our findings we suggest that rainfall influences age structures within populations, producing an influx of immunologically naïve juveniles within the population, which may subsequently affect AIV infection dynamics. Our study suggests that drivers of AIV dynamics in the northern hemisphere do not have the same influence at our south-east Australian field site in the southern hemisphere due to more erratic climatological conditions.
MeSH term(s)	Animals ; Animals, Wild ; Ducks ; Feces/virology ; Influenza A virus/physiology ; Influenza in Birds/epidemiology ; Influenza in Birds/virology ; Population Density ; Prevalence ; Rain ; Seasons ; Victoria/epidemiology
Language	English
Publishing date	2016-02-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1146298-x
ISSN	1297-9716 ; 0928-4249
ISSN (online)	1297-9716
ISSN	0928-4249
DOI	10.1186/s13567-016-0308-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Molecular characterization and phylogenetic analysis of Murray Valley encephalitis virus and West Nile virus (Kunjin subtype) from an arbovirus disease outbreak in horses in Victoria, Australia, in 2011.

Mann, Rachel A / Fegan, Mark / O'Riley, Kim / Motha, Julian / Warner, Simone

Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc

2013 Volume 25, Issue 1, Page(s) 35–44

Abstract: Virus was detected in the central nervous system (CNS) tissue of 11 horses from Victoria that died displaying neurological symptoms during an outbreak of disease in Australia in 2011. Five horses were identified as being infected with Murray Valley ... ...

Abstract	Virus was detected in the central nervous system (CNS) tissue of 11 horses from Victoria that died displaying neurological symptoms during an outbreak of disease in Australia in 2011. Five horses were identified as being infected with Murray Valley encephalitis virus (MVEV) and 6 as being infected with West Nile virus subtype Kunjin (WNV(KUN)). Analysis of partial sequence information from the NS5 and E genes indicated that the MVEVs within the samples were highly homogenous and all belonged to lineage I, which is enzootic to the tropical regions of northern Australia. Likewise, analysis of partial NS5 and E gene and full genome sequences indicated that the WNV(KUN) within the samples were also highly homogenous and clustered with WNV lineage 1, clade b, which is consistent with other WNV(KUN) isolates. Full genomes of 1 MVEV isolate and 2 WNV(KUN) isolates were sequenced and characterized. The genome sequences of Victorian WNV(KUN) are almost identical (3 amino acid differences) to that of the recently sequenced WNV isolate WNV(NSW2011). Metagenome sequencing directly from CNS tissue identified the presence of WNV(KUN) and MVEV within infected CNS tissue.
MeSH term(s)	Amino Acid Sequence ; Animals ; Base Sequence ; Disease Outbreaks/veterinary ; Encephalitis Virus, Murray Valley/genetics ; Encephalitis Virus, Murray Valley/isolation & purification ; Encephalitis, Arbovirus/veterinary ; Encephalitis, Arbovirus/virology ; Horse Diseases/epidemiology ; Horse Diseases/virology ; Horses ; Molecular Sequence Data ; Phylogeny ; RNA, Viral/chemistry ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction/veterinary ; Sequence Alignment ; Sequence Analysis, DNA ; Victoria/epidemiology ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; West Nile Fever/veterinary ; West Nile Fever/virology ; West Nile virus/genetics ; West Nile virus/isolation & purification
Chemical Substances	NS5 protein, flavivirus ; RNA, Viral ; Viral Nonstructural Proteins
Language	English
Publishing date	2013-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	287603-6
ISSN	1943-4936 ; 1040-6387
ISSN (online)	1943-4936
ISSN	1040-6387
DOI	10.1177/1040638712467985
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Article ; Online: Australia as a global sink for the genetic diversity of avian influenza A virus.

Wille, Michelle / Grillo, Victoria / Ban de Gouvea Pedroso, Silvia / Burgess, Graham W / Crawley, Allison / Dickason, Celia / Hansbro, Philip M / Hoque, Md Ahasanul / Horwood, Paul F / Kirkland, Peter D / Kung, Nina Yu-Hsin / Lynch, Stacey E / Martin, Sue / McArthur, Michaela / O'Riley, Kim / Read, Andrew J / Warner, Simone / Hoye, Bethany J / Lisovski, Simeon /

Leen, Trent / Hurt, Aeron C / Butler, Jeff / Broz, Ivano / Davies, Kelly R / Mileto, Patrick / Neave, Matthew J / Stevens, Vicky / Breed, Andrew C / Lam, Tommy T Y / Holmes, Edward C / Klaassen, Marcel / Wong, Frank Y K

PLoS pathogens

2022 Volume 18, Issue 5, Page(s) e1010150

Abstract: Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant ... ...

Abstract	Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.
MeSH term(s)	Animals ; Animals, Wild ; Australia/epidemiology ; Birds ; Ducks ; Genetic Variation ; Influenza A virus/genetics ; Influenza in Birds/epidemiology ; Phylogeny
Language	English
Publishing date	2022-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010150
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Article ; Online: The recent establishment of North American H10 lineage influenza viruses in Australian wild waterfowl and the evolution of Australian avian influenza viruses.

Vijaykrishna, Dhanasekaran / Deng, Yi-Mo / Su, Yvonne C F / Fourment, Mathieu / Iannello, Pina / Arzey, George G / Hansbro, Philip M / Arzey, K Edla / Kirkland, Peter D / Warner, Simone / O'Riley, Kim / Barr, Ian G / Smith, Gavin J D / Hurt, Aeron C

Journal of virology

2013 Volume 87, Issue 18, Page(s) 10182–10189

Abstract: Influenza A H10N7 virus with a hemagglutinin gene of North American origin was detected in Australian chickens and poultry abattoir workers in New South Wales, Australia, in 2010 and in chickens in Queensland, Australia, on a mixed chicken and domestic ... ...

Abstract	Influenza A H10N7 virus with a hemagglutinin gene of North American origin was detected in Australian chickens and poultry abattoir workers in New South Wales, Australia, in 2010 and in chickens in Queensland, Australia, on a mixed chicken and domestic duck farm in 2012. We investigated their genomic origins by sequencing full and partial genomes of H10 viruses isolated from wild aquatic birds and poultry in Australia and analyzed them with all available avian influenza virus sequences from Oceania and representative viruses from North America and Eurasia. Our analysis showed that the H10N7 viruses isolated from poultry were similar to those that have been circulating since 2009 in Australian aquatic birds and that their initial transmission into Australia occurred during 2007 and 2008. The H10 viruses that appear to have developed endemicity in Australian wild aquatic birds were derived from several viruses circulating in waterfowl along various flyways. Their hemagglutinin gene was derived from aquatic birds in the western states of the United States, whereas the neuraminidase was closely related to that from viruses previously detected in waterfowl in Japan. The remaining genes were derived from Eurasian avian influenza virus lineages. Our analysis of virological data spanning 40 years in Oceania indicates that the long-term evolutionary dynamics of avian influenza viruses in Australia may be determined by climatic changes. The introduction and long-term persistence of avian influenza virus lineages were observed during periods with increased rainfall, whereas bottlenecks and extinction were observed during phases of widespread decreases in rainfall. These results extend our understanding of factors affecting the dynamics of avian influenza and provide important considerations for surveillance and disease control strategies.
MeSH term(s)	Animals ; Australia/epidemiology ; Birds ; Cluster Analysis ; Evolution, Molecular ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Influenza A virus/classification ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Influenza in Birds/epidemiology ; Influenza in Birds/virology ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Poultry ; RNA, Viral/genetics ; Sequence Analysis, DNA
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus ; RNA, Viral
Language	English
Publishing date	2013-07-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.03437-12
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Article ; Online: Surveillance and analysis of avian influenza viruses, Australia.

Hansbro, Philip M / Warner, Simone / Tracey, John P / Arzey, K Edla / Selleck, Paul / O'Riley, Kim / Beckett, Emma L / Bunn, Chris / Kirkland, Peter D / Vijaykrishna, Dhanasekaran / Olsen, Bjorn / Hurt, Aeron C

Emerging infectious diseases

2010 Volume 16, Issue 12, Page(s) 1896–1904

Abstract: We investigated carriage of avian influenza viruses by wild birds in Australia, 2005-2008, to assess the risks to poultry industries and human health. We collected 21,858 (7,357 cloacal, 14,501 fecal) samples and detected 300 viruses, representing a ... ...

Abstract	We investigated carriage of avian influenza viruses by wild birds in Australia, 2005-2008, to assess the risks to poultry industries and human health. We collected 21,858 (7,357 cloacal, 14,501 fecal) samples and detected 300 viruses, representing a detection rate of ≈1.4%. Rates were highest in autumn (March-May) and differed substantially between bird types, areas, and years. We typed 107 avian influenza viruses and identified 19 H5, 8 H7, and 16 H9 (40% of typed viruses). All were of low pathogenicity. These viruses formed clearly different phylogenetic clades to lineages from Eurasia or North America, suggesting the potential existence of Australian lineages. H7 viruses were similar to highly pathogenic H7 strains that caused outbreaks in poultry in Australia. Several periods of increased detection rates (numbers or subtypes of viruses) were identified. This study demonstrates the need for ongoing surveillance to detect emerging pathogenic strains and facilitate prevention of outbreaks.
MeSH term(s)	Animal Migration ; Animals ; Australia/epidemiology ; Birds/virology ; Cloaca/virology ; Environmental Monitoring ; Epidemiological Monitoring ; Feces/virology ; Humans ; Influenza A virus/classification ; Influenza A virus/isolation & purification ; Influenza A virus/pathogenicity ; Influenza in Birds/epidemiology ; Influenza in Birds/genetics ; Influenza in Birds/virology ; Influenza, Human/epidemiology ; Phylogeny ; RNA, Viral/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Seasons
Chemical Substances	RNA, Viral
Language	English
Publishing date	2010-11-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid1612.100776
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Article: Molecular characterization and phylogenetic analysis of Murray Valley encephalitis virus and West Nile virus (Kunjin subtype) from an arbovirus disease outbreak in horses in Victoria, Australia, in 2011

Mann, Rachel A. / Fegan, Mark / O'Riley, Kim / Motha, Julian / Warner, Simone

Journal of veterinary diagnostic investigation

Volume v. 25,, Issue no. 1

Abstract	Virus was detected in the central nervous system (CNS) tissue of 11 horses from Victoria that died displaying neurological symptoms during an outbreak of disease in Australia in 2011. Five horses were identified as being infected with Murray Valley encephalitis virus (MVEV) and 6 as being infected with West Nile virus subtype Kunjin (WNVKUN). Analysis of partial sequence information from the NS5 and E genes indicated that the MVEVs within the samples were highly homogenous and all belonged to lineage I, which is enzootic to the tropical regions of northern Australia. Likewise, analysis of partial NS5 and E gene and full genome sequences indicated that the WNVKUN within the samples were also highly homogenous and clustered with WNV lineage 1, clade b, which is consistent with other WNVKUN isolates. Full genomes of 1 MVEV isolate and 2 WNVKUN isolates were sequenced and characterized. The genome sequences of Victorian WNVKUN are almost identical (3 amino acid differences) to that of the recently sequenced WNV isolate WNVNSW2011. Metagenome sequencing directly from CNS tissue identified the presence of WNVKUN and MVEV within infected CNS tissue.
Keywords	metagenomics ; Murray Valley encephalitis virus ; horses ; phylogeny ; genes ; nucleotide sequences ; central nervous system ; viruses ; West Nile virus ; tropics
Language	English
Document type	Article
ISSN	1040-6387
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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