scholarly journals Phylogenetic Analysis of HA and NA Genes of Swine Influenza Viruses in Serbia in 2016-2018

2020 ◽  
Vol 70 (1) ◽  
pp. 110-125
Author(s):  
Jelena Maksimović Zorić ◽  
Vesna Milićević ◽  
Ognjen Stevančević ◽  
Chiara Chiapponi ◽  
Aleksandar Potkonjak ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza A Virus ◽  
Influenza A ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
H3n2 Virus ◽  
Research Database ◽  
Influenza A Viruses ◽  
Tissue Samples ◽  
Commercial Farms

AbstractPigs are very important for the epidemiology of influenza A viruses, being commonly infected with the lineages of most adapted H1N1, H3N2, H1N2 swine subtypes. Epidemiological complexity of swine influenza is increasing by a periodic spillover of human or avian viruses in the pig population when genetic shifts can occur. The objectives of this research were to determine the presence of the influenza A virus in nasal and tracheobronchial swabs and lung tissue samples of ill and dead pigs on commercial farms, to determine circulating subtypes and characterize them through the phylogenetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes. A total of 255 samples collected from 13 farms were analyzed by means of real-time RTPCR. The genome of influenza A virus was detected in 24 samples, which represented a 61.5% prevalence at the farms level (influenza A virus was confirmed in 8 out of 13 farms included in this study). Based on HA and NA gene sequences of 8 viruses, the circulation of H1N1 and H3N2 subtypes of influenza A viruses were determined. In addition, one farm exhibited a time separated circulation of H1N1 and H3N2 virus subtypes. Using Influenza Research Database, our viruses of the H1 subtype were classified into 1C.2.1 and 1A.3.3.2. clade. Based on the nucleotide sequences of HA genes, three viruses of the H1N1 subtype belong to the H1N1pdm09 lineage, and the other four to Eurasian “avian-like” H1avN1 lineage; while based on NA genes sequences, these seven viruses belong to Eurasian “avian-like” H1avN1 lineage. Both HA and NA genes of the virus of the H3N2 subtype belonged to the A/swine/ Gent/1/1984-like H3N2 lineage.

Molecular Characterization of Influenza A Viruses Detected in Children Attending Yangon Children’s Hospital, 2016

2019 ◽  
Vol 31 (1) ◽  
pp. 72-80
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza A Virus ◽  
Influenza A ◽  
Epidemiological Studies ◽  
Influenza Viruses ◽  
Influenza B Virus ◽  
Influenza B ◽  
Influenza A Viruses ◽  
B Virus ◽  
Na Gene

Sequence analysis of the influenza virus strains is important for molecular epidemiological studies and evolutional studies of influenza viruses as well as for the assessment of vaccine effectiveness. The aim of this study was to determine and characterize predominant subtype of influenza A viruses among children attending Yangon Children’s Hospital (YCH). It was a cross-sectional descriptive study conducted at YCH. Nasopharyngeal swabs were collected from 153 children who attended the hospital due to influenza-like illness (ILI) during January-December, 2016. Viral RNA was extracted by QIAamp® Viral Mini Kit. Matrix genes of influenza A and influenza B virus were detected by multiplex Reverse TranscriptionPolymerase Chain Reaction (RT-PCR). Influenza A virus matrix gene positive samples were subjected to subtyping. Predominant subtypes were subjected to sequencing and phylogenetic analysis of their HA gene and neuraminidase (NA) gene. Influenza viruses were detected in about 14% of children with ILI. Among them, 55% showed influenza A virus positive and 45% showed influenza B virus positive. Influenza A (H3N2) virus was found to be predominant among influenza A virus positive children accounting for 83.4%. There was one case (8.3%) of influenza A (H1N1) pdm09 virus and one case (8.3%) of unsubtyped influenza A virus. Phylogenetic analysis of HA and NA gene of two Myanmar strains of H3N2 subtype revealed that they belonged to clade 3C.2a1. They had 99.3-99.4% nucleotide identity with A/Hong Kong/ 4801/2014, vaccine strain of H3N2 subtype, that was contained in southern hemisphere influenza vaccine for 2016 and northern hemisphere vaccine for 2016-2017 season. This study generated information useful for the assessment of influenza outbreaks, selection of upcoming vaccine strains and further evolutionary and epidemiological studies on influenza viruses.

Swine influenza vaccines: current status and future perspectives

2010 ◽  
Vol 11 (1) ◽  
pp. 81-96 ◽  
Author(s):  
Wenjun Ma ◽  
Jürgen A. Richt
Keyword(s):  
Influenza A ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Current Status ◽  
Economic Losses ◽  
Influenza A Viruses ◽  
Swine Industry ◽  
Effective Strategies ◽  
Swine Disease ◽  
And Control

AbstractSwine influenza is an important contagious disease in pigs caused by influenza A viruses. Although only three subtypes of influenza A viruses, H1N1, H1N2 and H3N2, predominantly infect pigs worldwide, it is still a big challenge for vaccine manufacturers to produce efficacious vaccines for the prevention and control of swine influenza. Swine influenza viruses not only cause significant economic losses for the swine industry, but are also important zoonotic pathogens. Vaccination is still one of the most important and effective strategies to prevent and control influenza for both the animal and human population. In this review, we will discuss the current status of swine influenza worldwide as well as current and future options to control this economically important swine disease.

scholarly journals Unseasonal Transmission of H3N2 Influenza A Virus During the Swine-Origin H1N1 Pandemic

2010 ◽  
Vol 84 (11) ◽  
pp. 5715-5718 ◽  
Author(s):  
Elodie Ghedin ◽  
David E. Wentworth ◽  
Rebecca A. Halpin ◽  
Xudong Lin ◽  
Jayati Bera ◽  
...  
Keyword(s):  
New York ◽  
Influenza A Virus ◽  
Influenza A ◽  
New York State ◽  
The United States ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
York State ◽  
Low Incidence ◽  
H3n2 Influenza

ABSTRACT The initial wave of swine-origin influenza A virus (pandemic H1N1/09) in the United States during the spring and summer of 2009 also resulted in an increased vigilance and sampling of seasonal influenza viruses (H1N1 and H3N2), even though they are normally characterized by very low incidence outside of the winter months. To explore the nature of virus evolution during this influenza “off-season,” we conducted a phylogenetic analysis of H1N1 and H3N2 sequences sampled during April to June 2009 in New York State. Our analysis revealed that multiple lineages of both viruses were introduced and cocirculated during this time, as is typical of influenza virus during the winter. Strikingly, however, we also found strong evidence for the presence of a large transmission chain of H3N2 viruses centered on the south-east of New York State and which continued until at least 1 June 2009. These results suggest that the unseasonal transmission of influenza A viruses may be more widespread than is usually supposed.

scholarly journals Influenza A Virus Inhibits RSV Infection via a Two-Wave Expression of IFIT Proteins

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1171
Author(s):  
Yaron Drori ◽  
Jasmine Jacob-Hirsch ◽  
Rakefet Pando ◽  
Aharona Glatman-Freedman ◽  
Nehemya Friedman ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Influenza Viruses ◽  
Mass Spectrometry Analysis ◽  
Influenza A Viruses ◽  
Rsv Infection ◽  
Syncytial Virus ◽  
Mouse Lungs

Influenza viruses and respiratory syncytial virus (RSV) are respiratory viruses that primarily circulate worldwide during the autumn and winter seasons. Seasonal surveillance has shown that RSV infection generally precedes influenza. However, in the last four winter seasons (2016–2020) an overlap of the morbidity peaks of both viruses was observed in Israel, and was paralleled by significantly lower RSV infection rates. To investigate whether the influenza A virus inhibits RSV, human cervical carcinoma (HEp2) cells or mice were co-infected with influenza A and RSV. Influenza A inhibited RSV growth, both in vitro and in vivo. Mass spectrometry analysis of mouse lungs infected with influenza A identified a two-wave pattern of protein expression upregulation, which included members of the interferon-induced protein with the tetratricopeptide (IFITs) family. Interestingly, in the second wave, influenza A viruses were no longer detectable in mouse lungs. In addition, knockdown and overexpression of IFITs in HEp2 cells affected RSV multiplicity. In conclusion, influenza A infection inhibits RSV infectivity via upregulation of IFIT proteins in a two-wave modality. Understanding the immune system involvement in the interaction between influenza A and RSV viruses will contribute to the development of future treatment strategies against these viruses.

IFN-κ suppresses the replication of influenza A viruses through the IFNAR-MAPK-Fos-CHD6 axis

2020 ◽  
Vol 13 (626) ◽  
pp. eaaz3381 ◽  
Author(s):  
Yongquan He ◽  
Weihui Fu ◽  
Kangli Cao ◽  
Qian He ◽  
Xiangqing Ding ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Influenza Viruses ◽  
Mitogen Activated Protein Kinase ◽  
Type I Interferons ◽  
Type I ◽  
Influenza A Viruses ◽  
Human Lung Cells ◽  
Avian Influenza A Virus ◽  
Factor C

Type I interferons (IFNs) are the first line of defense against viral infection. Using a mouse model of influenza A virus infection, we found that IFN-κ was one of the earliest responding type I IFNs after infection with H9N2, a low-pathogenic avian influenza A virus, whereas this early induction did not occur upon infection with the epidemic-causing H7N9 virus. IFN-κ efficiently suppressed the replication of various influenza viruses in cultured human lung cells, and chromodomain helicase DNA binding protein 6 (CHD6) was the major effector for the antiviral activity of IFN-κ, but not for that of IFN-α or IFN-β. The induction of CHD6 required both of the type I IFN receptor subunits IFNAR1 and IFNAR2, the mitogen-activated protein kinase (MAPK) p38, and the transcription factor c-Fos but was independent of signal transducer and activator of transcription 1 (STAT1) activity. In addition, we showed that pretreatment with IFN-κ protected mice from lethal influenza viral challenge. Together, our findings identify an IFN-κ–specific pathway that constrains influenza A virus and provide evidence that IFN-κ may have potential as a preventative and therapeutic agent against influenza A virus.

scholarly journals Detection of Antigenic Variants of Subtype H3 Swine Influenza A Viruses from Clinical Samples

2017 ◽  
Vol 55 (4) ◽  
pp. 1037-1045 ◽  
Author(s):  
Brigitte E. Martin ◽  
Andrew S. Bowman ◽  
Lei Li ◽  
Jacqueline M. Nolting ◽  
David R. Smith ◽  
...  
Keyword(s):  
Influenza A ◽  
Large Population ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Proximity Ligation Assay ◽  
Clinical Samples ◽  
Influenza Surveillance ◽  
Influenza A Viruses ◽  
Virus Propagation ◽  
Vaccination Programs

ABSTRACT A large population of genetically and antigenically diverse influenza A viruses (IAVs) are circulating among the swine population, playing an important role in influenza ecology. Swine IAVs not only cause outbreaks among swine but also can be transmitted to humans, causing sporadic infections and even pandemic outbreaks. Antigenic characterizations of swine IAVs are key to understanding the natural history of these viruses in swine and to selecting strains for effective vaccines. However, influenza outbreaks generally spread rapidly among swine, and the conventional methods for antigenic characterization require virus propagation, a time-consuming process that can significantly reduce the effectiveness of vaccination programs. We developed and validated a rapid, sensitive, and robust method, the polyclonal serum-based proximity ligation assay (polyPLA), to identify antigenic variants of subtype H3N2 swine IAVs. This method utilizes oligonucleotide-conjugated polyclonal antibodies and quantifies antibody-antigen binding affinities by quantitative reverse transcription-PCR (RT-PCR). Results showed the assay can rapidly detect H3N2 IAVs directly from nasal wash or nasal swab samples collected from laboratory-challenged animals or during influenza surveillance at county fairs. In addition, polyPLA can accurately separate the viruses at two contemporary swine IAV antigenic clusters (H3N2 swine IAV-α and H3N2 swine IAV-ß) with a sensitivity of 84.9% and a specificity of 100.0%. The polyPLA can be routinely used in surveillance programs to detect antigenic variants of influenza viruses and to select vaccine strains for use in controlling and preventing disease in swine.

scholarly journals Divergent Human-Origin Influenza Viruses Detected in Australian Swine Populations

2018 ◽  
Vol 92 (16) ◽  
Author(s):  
Frank Y. K. Wong ◽  
Celeste Donato ◽  
Yi-Mo Deng ◽  
Don Teng ◽  
Naomi Komadina ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Influenza A ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
Human Origin ◽  
Human Influenza ◽  
Influenza A Viruses ◽  
Data Set ◽  
Antigenic Properties

ABSTRACTGlobal swine populations infected with influenza A viruses pose a persistent pandemic risk. With the exception of a few countries, our understanding of the genetic diversity of swine influenza viruses is limited, hampering control measures and pandemic risk assessment. Here we report the genomic characteristics and evolutionary history of influenza A viruses isolated in Australia from 2012 to 2016 from two geographically isolated swine populations in the states of Queensland and Western Australia. Phylogenetic analysis with an expansive human and swine influenza virus data set comprising >40,000 sequences sampled globally revealed evidence of the pervasive introduction and long-term establishment of gene segments derived from several human influenza viruses of past seasons, including the H1N1/1977, H1N1/1995, H3N2/1968, and H3N2/2003, and the H1N1 2009 pandemic (H1N1pdm09) influenza A viruses, and a genotype that contained gene segments derived from the past three pandemics (1968, reemerged 1977, and 2009). Of the six human-derived gene lineages, only one, comprising two viruses isolated in Queensland during 2012, was closely related to swine viruses detected from other regions, indicating a previously undetected circulation of Australian swine lineages for approximately 3 to 44 years. Although the date of introduction of these lineages into Australian swine populations could not be accurately ascertained, we found evidence of sustained transmission of two lineages in swine from 2012 to 2016. The continued detection of human-origin influenza virus lineages in swine over several decades with little or unpredictable antigenic drift indicates that isolated swine populations can act as antigenic archives of human influenza viruses, raising the risk of reemergence in humans when sufficient susceptible populations arise.IMPORTANCEWe describe the evolutionary origins and antigenic properties of influenza A viruses isolated from two separate Australian swine populations from 2012 to 2016, showing that these viruses are distinct from each other and from those isolated from swine globally. Whole-genome sequencing of virus isolates revealed a high genotypic diversity that had been generated exclusively through the introduction and establishment of human influenza viruses that circulated in past seasons. We detected six reassortants with gene segments derived from human H1N1/H1N1pdm09 and various human H3N2 viruses that circulated during various periods since 1968. We also found that these swine viruses were not related to swine viruses collected elsewhere, indicating independent circulation. The detection of unique lineages and genotypes in Australia suggests that isolated swine populations that are sufficiently large can sustain influenza virus for extensive periods; we show direct evidence of a sustained transmission for at least 4 years between 2012 and 2016.

scholarly journals H5N1 Influenza A Virus PB1-F2 Relieves HAX-1-Mediated Restriction of Avian Virus Polymerase PA in Human Lung Cells

2018 ◽  
Vol 92 (11) ◽  
pp. e00425-18 ◽  
Author(s):  
B. Mazel-Sanchez ◽  
I. Boal-Carvalho ◽  
F. Silva ◽  
R. Dijkman ◽  
M. Schmolke
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Influenza Viruses ◽  
Zoonotic Transmission ◽  
Restriction Factor ◽  
Influenza A Viruses ◽  
Human Lung Cells ◽  
Enzymatic Function ◽  
H5n1 Influenza ◽  
Avian Origin

ABSTRACTHighly pathogenic influenza A viruses (IAV) from avian hosts were first reported to directly infect humans 20 years ago. However, such infections are rare events, and our understanding of factors promoting or restricting zoonotic transmission is still limited. One accessory protein of IAV, PB1-F2, was associated with pathogenicity of pandemic and zoonotic IAV. This short (90-amino-acid) peptide does not harbor an enzymatic function. We thus identified host factors interacting with H5N1 PB1-F2, which could explain its importance for virulence. PB1-F2 binds to HCLS1-associated protein X1 (HAX-1), a recently identified host restriction factor of the PA subunit of IAV polymerase complexes. We demonstrate that the PA of a mammal-adapted H1N1 IAV is resistant to HAX-1 imposed restriction, while the PA of an avian-origin H5N1 IAV remains sensitive. We also showed HAX-1 sensitivity for PAs of A/Brevig Mission/1/1918 (H1N1) and A/Shanghai/1/2013 (H7N9), two avian-origin zoonotic IAV. Inhibition of H5N1 polymerase by HAX-1 can be alleviated by its PB1-F2 through direct competition. Accordingly, replication of PB1-F2-deficient H5N1 IAV is attenuated in the presence of large amounts of HAX-1. Mammal-adapted H1N1 and H3N2 viruses do not display this dependence on PB1-F2 for efficient replication in the presence of HAX-1. We propose that PB1-F2 plays a key role in zoonotic transmission of avian H5N1 IAV into humans.IMPORTANCEAquatic and shore birds are the natural reservoir of influenza A viruses from which the virus can jump into a variety of bird and mammal host species, including humans. H5N1 influenza viruses are a good model for this process. They pose an ongoing threat to human and animal health due to their high mortality rates. However, it is currently unclear what restricts these interspecies jumps on the host side or what promotes them on the virus side. Here we show that a short viral peptide, PB1-F2, helps H5N1 bird influenza viruses to overcome a human restriction factor of the viral polymerase complex HAX-1. Interestingly, we found that human influenza A virus polymerase complexes are already adapted to HAX-1 and do not require this function of PB1-F2. We thus propose that a functional full-length PB1-F2 supports direct transmission of bird viruses into humans.

scholarly journals Respiratory Illness in a Piggery Associated with the First Identified Outbreak of Swine Influenza in Australia: Assessing the Risk to Human Health and Zoonotic Potential

2019 ◽  
Vol 4 (2) ◽  
pp. 96 ◽  
Author(s):  
David W. Smith ◽  
Ian G. Barr ◽  
Richmond Loh ◽  
Avram Levy ◽  
Simone Tempone ◽  
...  
Keyword(s):  
Influenza A ◽  
Haemagglutination Inhibition ◽  
Swine Influenza ◽  
Respiratory Illness ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
Strict Adherence ◽  
Zoonotic Infections ◽  
Zoonotic Risk ◽  
Biosecurity Practices

Australia was previously believed to be free of enzootic swine influenza viruses due strict quarantine practices and use of biosecure breeding facilities. The first proven Australian outbreak of swine influenza occurred in Western Australian in 2012, revealing an unrecognized zoonotic risk, and a potential future pandemic threat. A public health investigation was undertaken to determine whether zoonotic infections had occurred and to reduce the risk of further transmission between humans and swine. A program of monitoring, testing, treatment, and vaccination was commenced, and a serosurvey of workers was also undertaken. No acute infections with the swine influenza viruses were detected. Serosurvey results were difficult to interpret due to previous influenza infections and past and current vaccinations. However, several workers had elevated haemagglutination inhibition (HI) antibody levels to the swine influenza viruses that could not be attributed to vaccination or infection with contemporaneous seasonal influenza A viruses. However, we lacked a suitable control population, so this was inconclusive. The experience was valuable in developing better protocols for managing outbreaks at the human–animal interface. Strict adherence to biosecurity practices, and ongoing monitoring of swine and their human contacts is important to mitigate pandemic risk. Strain specific serological assays would greatly assist in identifying zoonotic transmission.

scholarly journals Reassortants of pandemic influenza A virus H1N1/2009 and endemic porcine HxN2 viruses emerge in swine populations in Germany

2012 ◽  
Vol 93 (8) ◽  
pp. 1658-1663 ◽  
Author(s):  
Elke Starick ◽  
Elke Lange ◽  
Christian Grund ◽  
Elisabeth grosse Beilage ◽  
Stefanie Döhring ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Swine Influenza ◽  
Biological Properties ◽  
Influenza Viruses ◽  
West Germany ◽  
Virus H1n1 ◽  
North West ◽  
Synonymous Mutations

The incursion of the human pandemic influenza A virus H1N1 (2009) (H1N1 pdm) into pig populations and its ongoing co-circulation with endemic swine influenza viruses (SIVs) has yielded distinct human–porcine reassortant virus lineages. The haemagglutinin (HA) gene of H1N1 pdm was detected in 41 influenza virus-positive samples from seven swine herds in north-west Germany in 2011. Eight of these samples yielded virus that carried SIV-derived neuraminidase N2 of three different porcine lineages in an H1N1 pdm backbone. The HA sequences of these viruses clustered in two distinct groups and were distinguishable from human and other porcine H1 pdm by a unique set of eight non-synonymous mutations. In contrast to the human population, where H1N1 pdm replaced seasonal H1N1, this virus seems to co-circulate and interact more intensely with endemic SIV lineages, giving rise to reassortants with as-yet-unknown biological properties and undetermined risks for public health.

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