scholarly journals Virological Investigation of Avian Influenza Virus on Postglacial Species of Phasianidae and Tetraonidae in the Italian Alps

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Mauro Delogu ◽  
Giulia Ghetti ◽  
Alessandro Gugiatti ◽  
Claudia Cotti ◽  
Isabella Piredda ◽  
...  
Keyword(s):  
Wildlife Management ◽  
Influenza A ◽  
Species Conservation ◽  
Rt Pcr ◽  
Italian Alps ◽  
Influenza A Viruses ◽  
Matrix Gene ◽  
Lagopus Mutus ◽  
The Matrix ◽  
In The Wild

Land-based birds, belonging to Galliformes order are considered to be potential intermediaries in the emergence of new strains of influenza A viruses (AIVs), but the viral circulation in these birds remains largely unknown. To gain insights into the circulation of AIV in the wild Galliformes populations in Italian Alps, we conducted a virological survey on rock partridge (Alectoris graeca saxatilis) belonging to Phasianidae family and on tetraonids including rock ptarmigan (Lagopus mutus helveticus) and black grouse (Tetrao tetrix tetrix). In 2003 and 2004, during the hunting seasons, 79 wild Galliformes, categorised into age and sex classes, were hunted in the Sondrio Province (Central Alps). Cloacal swabs were collected from 11 rock partridges and from 68 tetraonids including 23 alpine rock ptarmigans and 45 black grouses. We tested cloacal swabs by a high sensitive reverse transcription- (RT-) PCR detecting the matrix gene of AIV. No AIV was detected in the investigated samples, thus, suggesting the lack of AIV circulation in these relict populations in the study period. In terms of threatened species conservation, during wildlife management activities, it is very important to exclude the introduction of AIV-carrier birds in shared territories, a fact representing a health risk for these populations.

scholarly journals Development and application of a real-time RT-PCR assay to rapidly detect H2 subtype avian influenza A viruses

2021 ◽  
pp. 104063872199481
Author(s):  
Yixin Xiao ◽  
Fan Yang ◽  
Fumin Liu ◽  
Hangping Yao ◽  
Nanping Wu ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Real Time ◽  
Influenza A ◽  
Minor Groove Binder ◽  
Rt Pcr ◽  
Influenza A Viruses ◽  
Pcr Assay ◽  
Infectious Dose ◽  
The Matrix ◽  
Taqman Minor Groove Binder

The H2 subtypes of avian influenza A viruses (avian IAVs) have been circulating in poultry, and they have the potential to infect humans. Therefore, establishing a method to quickly detect this subtype is pivotal. We developed a TaqMan minor groove binder real-time RT-PCR assay that involved probes and primers based on conserved sequences of the matrix and hemagglutinin genes. The detection limit of this assay was as low as one 50% egg infectious dose (EID50)/mL per reaction. This assay is specific, sensitive, and rapid for detecting avian IAV H2 subtypes.

scholarly journals Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes

2017 ◽  
Vol 91 (18) ◽  
Author(s):  
Andres Diaz ◽  
Douglas Marthaler ◽  
Marie Culhane ◽  
Srinand Sreevatsan ◽  
Moh Alkhamis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Influenza A ◽  
Gene Segment ◽  
Global Scale ◽  
Limited Information ◽  
Influenza A Viruses ◽  
Sequencing Technologies ◽  
Matrix Gene ◽  
Reservoir Species ◽  
The Matrix

ABSTRACT Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms for a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. Of these, 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genomes of 123 IAV isolates and found 31 H1N1, 26 H1N2, 63 H3N2, and 3 mixed IAVs. Based on the IAV hemagglutinin, seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs, although an additional viral group was identified for gene segment 3 (PA). Moreover, the codetection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs), highlighting the environment for potential IAV reassortment. Additionally, 3 out of 5 farms contained IAV isolates (n = 5) with gene segments from more than one VG, and 79% of all the IAVs sequenced contained a signature mutation (S31N) in the matrix gene that has been associated with resistance to the antiviral amantadine. Within farms, some IAVs were detected only once, while others were detected for 283 days. Our results illustrate the maintenance and subsidence of different IAVs within swine farrow-to-wean farms over time, demonstrating that pig subpopulation dynamics are important to better understand the diversity and epidemiology of swine IAVs. IMPORTANCE On a global scale, swine are one of the main reservoir species for influenza A viruses (IAVs) and play a key role in the transmission of IAVs between species. Additionally, the 2009 IAV pandemics highlighted the role of pigs in the emergence of IAVs with pandemic potential. However, limited information is available regarding the diversity and distribution of swine IAVs on farrow-to-wean farms, where novel IAVs can emerge. In this study, we studied 5 swine farrow-to-wean farms for a year and characterized the genetic diversity of IAVs among three different pig subpopulations commonly housed on this type of farm. Using next-generation-sequencing technologies, we demonstrated the complex distribution and diversity of IAVs among the pig subpopulations studied. Our results demonstrated the dynamic evolution of IAVs within farrow-to-wean farms, which is crucial to improve health interventions to reduce the risk of transmission between pigs and from pigs to people.

scholarly journals Detection of Influenza A Viruses from Different Species by PCR Amplification of Conserved Sequences in the Matrix Gene

2000 ◽  
Vol 38 (11) ◽  
pp. 4096-4101 ◽  
Author(s):  
Ron A. M. Fouchier ◽  
Theo M. Bestebroer ◽  
Sander Herfst ◽  
Liane Van Der Kemp ◽  
Guus F. Rimmelzwaan ◽  
...  
Keyword(s):  
Influenza A ◽  
Virus Isolation ◽  
Influenza Pandemic ◽  
Pcr Amplification ◽  
Cloacal Swab ◽  
Host Cells ◽  
Influenza A Viruses ◽  
Reverse Transcription Pcr ◽  
Matrix Gene ◽  
The Matrix

The recently raised awareness of the threat of a new influenza pandemic has stimulated interest in the detection of influenza A viruses in human as well as animal secretions. Virus isolation alone is unsatisfactory for this purpose because of its inherent limited sensitivity and the lack of host cells that are universally permissive to all influenza A viruses. Previously described PCR methods are more sensitive but are targeted predominantly at virus strains currently circulating in humans, since the sequences of the primer sets display considerable numbers of mismatches to the sequences of animal influenza A viruses. Therefore, a new set of primers, based on highly conserved regions of the matrix gene, was designed for single-tube reverse transcription-PCR for the detection of influenza A viruses from multiple species. This PCR proved to be fully reactive with a panel of 25 genetically diverse virus isolates that were obtained from birds, humans, pigs, horses, and seals and that included all known subtypes of influenza A virus. It was not reactive with the 11 other RNA viruses tested. Comparative tests with throat swab samples from humans and fecal and cloacal swab samples from birds confirmed that the new PCR is faster and up to 100-fold more sensitive than classical virus isolation procedures.

scholarly journals Influenza A Virus Detected in Native Bivalves in Waterfowl Habitat of the Delmarva Peninsula, USA

2019 ◽  
Vol 7 (9) ◽  
pp. 334 ◽  
Author(s):  
Christine L. Densmore ◽  
Deborah D. Iwanowicz ◽  
Shawn M. McLaughlin ◽  
Christopher A. Ottinger ◽  
Jason E. Spires ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Influenza A Virus ◽  
Natural Water ◽  
Influenza A ◽  
Macoma Balthica ◽  
Delmarva Peninsula ◽  
Tissue Samples ◽  
Matrix Gene ◽  
Waterfowl Habitat ◽  
The Matrix

We evaluated the prevalence of influenza A virus (IAV) in different species of bivalves inhabiting natural water bodies in waterfowl habitat along the Delmarva Peninsula and Chesapeake Bay in eastern Maryland. Bivalve tissue from clam and mussel specimens (Macoma balthica, Macoma phenax, Mulinia sp., Rangia cuneata, Mya arenaria, Guekensia demissa, and an undetermined mussel species) from five collection sites was analyzed for the presence of type A influenza virus by qPCR targeting the matrix gene. Of the 300 tissue samples analyzed, 13 samples (4.3%) tested positive for presence of influenza virus A matrix gene. To our knowledge, this is the first report of detection of IAV in the tissue of any bivalve mollusk from a natural water body.

scholarly journals One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples

2010 ◽  
Vol 164 (1-2) ◽  
pp. 83-87 ◽  
Author(s):  
Alessio Lorusso ◽  
Kay S. Faaberg ◽  
Mary Lea Killian ◽  
Leo Koster ◽  
Amy L. Vincent
Keyword(s):  
Real Time ◽  
Influenza A Virus ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Virus H1n1 ◽  
Rt Pcr ◽  
Gene Detection ◽  
Matrix Gene ◽  
One Step

scholarly journals Genomic Signature-Based Identification of Influenza A Viruses Using RT-PCR/Electro-Spray Ionization Mass Spectrometry (ESI-MS) Technology

PLoS ONE ◽  
2010 ◽  
Vol 5 (10) ◽  
pp. e13293 ◽  
Author(s):  
Varough M. Deyde ◽  
Rangarajan Sampath ◽  
Rebecca J. Garten ◽  
Patrick J. Blair ◽  
Christopher A. Myers ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Influenza A ◽  
Genomic Signature ◽  
Ionization Mass Spectrometry ◽  
Ionization Mass ◽  
Rt Pcr ◽  
Influenza A Viruses ◽  
Esi Ms ◽  
Electro Spray Ionization

scholarly journals Matrix Gene of Influenza A Viruses Isolated from Wild Aquatic Birds: Ecology and Emergence of Influenza A Viruses

2004 ◽  
Vol 78 (16) ◽  
pp. 8771-8779 ◽  
Author(s):  
Linda Widjaja ◽  
Scott L. Krauss ◽  
Richard J. Webby ◽  
Tao Xie ◽  
Robert G. Webster
Keyword(s):  
North American ◽  
Influenza A ◽  
Delaware Bay ◽  
Influenza Viruses ◽  
Aquatic Birds ◽  
Influenza A Viruses ◽  
M Gene ◽  
Matrix Gene ◽  
Distinct Lineage ◽  
Wild Waterfowl

ABSTRACT Wild aquatic birds are the primary reservoir of influenza A viruses, but little is known about the viruses' gene pool in wild birds. Therefore, we investigated the ecology and emergence of influenza viruses by conducting phylogenetic analysis of 70 matrix (M) genes of influenza viruses isolated from shorebirds and gulls in the Delaware Bay region and from ducks in Alberta, Canada, during >18 years of surveillance. In our analysis, we included 61 published M genes of isolates from various hosts. We showed that M genes of Canadian duck viruses and those of shorebird and gull viruses in the Delaware Bay shared ancestors with the M genes of North American poultry viruses. We found that North American and Eurasian avian-like lineages are divided into sublineages, indicating that multiple branches of virus evolution may be maintained in wild aquatic birds. The presence of non-H13 gull viruses in the gull-like lineage and of H13 gull viruses in other avian lineages suggested that gulls' M genes do not preferentially associate with the H13 subtype or segregate into a distinct lineage. Some North American avian influenza viruses contained M genes closely related to those of Eurasian avian viruses. Therefore, there may be interregional mixing of the two clades. Reassortment of shorebird M and HA genes was evident, but there was no correlation among the HA or NA subtype, M gene sequence, and isolation time. Overall, these results support the hypothesis that influenza viruses in wild waterfowl contain distinguishable lineages of M genes.

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