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Isolations of influenza A viruses from passerine birds in Malaysia

Ibrahim HM, Awang IP, Alexander DJ, Manvell RJ, Aini I, Ibrahim AL

Vet Rec, 1990 Nov 24;127(21):528.
PMID: 2281590
Matched MeSH terms: Influenza A virus/classification
Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16

Khan A, Mushtaq MH, Ahmad MUD, Nazir J, Farooqi SH, Khan A

Virus Res, 2017 08 15;240:56-63.
PMID: 28757141 DOI: 10.1016/j.virusres.2017.07.022

BACKGROUND: A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber Pakhtunkhwa Province of Pakistan during 2015-2016.
OBJECTIVES AND METHODS: An epidemiological surveillance study was conducted from Oct 2015 to April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and nucleoprotein (NP) genes nucleotide and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species.
RESULTS: HA and NA genes amino acid sequences were very similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes.
CONCLUSION: Epidemiological data analysis indicated the potential chance of mixed, and management such as mixed farming system by keeping equine, canine and backyard poultry together in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.

Matched MeSH terms: Influenza A virus/classification
Diversity of influenza A viruses retrieved from respiratory disease outbreaks and subclinically infected herds in Spain (2017-2019)

Sosa Portugal S, Cortey M, Tello M, Casanovas C, Mesonero-Escuredo S, Barrabés S, et al.

Transbound Emerg Dis, 2021 Mar;68(2):519-530.
PMID: 32619306 DOI: 10.1111/tbed.13709

The present study was aimed to assess the diversity of influenza A viruses (IAV) circulating in pig farms in the Iberian Peninsula. The study included two different situations: farms suffering respiratory disease outbreaks compatible with IAV (n = 211) and randomly selected farms without overt respiratory disease (n = 19). Initially, the presence of IAV and lineage determination was assessed by qRT-PCR using nasal swabs. IAV was confirmed in 145 outbreaks (68.7%), mostly in nurseries (53/145; 36.5%). Subtyping by RT-qPCR was possible in 94 of those cases being H1avN2hu (33.6%), H1avN1av (24.3%) and H1huN2hu (18.7%), the most common lineages. H3huN2hu and H1pdmN1pdm represented 7.5% and 6.5% of the cases, respectively. As for the randomly selected farms, 15/19 (78.9%) were positive for IAV. Again, the virus was mostly found in nurseries and H1avN2hu was the predominant lineage. Virus isolation in MDCK cells was attempted from positive cases. Sixty of the isolates were fully sequenced with Illumina MiSeq®. Within those 60 isolates, the most frequent genotypes had internal genes of avian origin, and these were D (19/60; 31.7%) and A (11/60; 18.3%), H1avN2hu and H1avN1av, respectively. In addition, seven previously unreported genotypes were identified. In two samples, more than one H or N were found and it was not possible to precisely establish their genotypes. A great diversity was observed in the phylogenetic analysis. Notably, four H3 sequences clustered with human isolates from 2004-05 (Malaysia and Denmark) that were considered uncommon in pigs. Overall, this study indicates that IAV is a very common agent in respiratory disease outbreaks in Spanish pig farms. The genetic diversity of this virus is continuously expanding with clear changes in the predominant subtypes and lineages in relatively short periods of time. The current genotyping scheme has to be enlarged to include the new genotypes that could be found in the future.

Matched MeSH terms: Influenza A virus/classification*
Intercontinental circulation of human influenza A(H1N2) reassortant viruses during the 2001-2002 influenza season

Xu X, Smith CB, Mungall BA, Lindstrom SE, Hall HE, Subbarao K, et al.

J Infect Dis, 2002 Nov 15;186(10):1490-3.
PMID: 12404167

Reassortant influenza A viruses bearing the H1 subtype of hemagglutinin (HA) and the N2 subtype of neuraminidase (NA) were isolated from humans in the United States, Canada, Singapore, Malaysia, India, Oman, Egypt, and several countries in Europe during the 2001-2002 influenza season. The HAs of these H1N2 viruses were similar to that of the A/New Caledonia/20/99(H1N1) vaccine strain both antigenically and genetically, and the NAs were antigenically and genetically related to those of recent human H3N2 reference strains, such as A/Moscow/10/99(H3N2). All 6 internal genes of the H1N2 reassortants examined originated from an H3N2 virus. This article documents the first widespread circulation of H1N2 reassortants on 4 continents. The current influenza vaccine is expected to provide good protection against H1N2 viruses, because it contains the A/New Caledonia/20/99(H1N1) and A/Moscow/10/99(H3N2)-like viruses, which have H1 and N2 antigens that are similar to those of recent H1N2 viruses.

Matched MeSH terms: Influenza A virus/classification
Seroprevalence and risk factors for influenza A viruses in pigs in Peninsular Malaysia

Suriya R, Hassan L, Omar AR, Aini I, Tan CG, Lim YS, et al.

Zoonoses Public Health, 2008 Sep;55(7):342-51.
PMID: 18667027 DOI: 10.1111/j.1863-2378.2008.01138.x

Following a series of H5N1 cases in chickens and birds in a few states in Malaysia, there was much interest in the influenza A viruses subtypes that circulate among the local pig populations. Pigs may act as a mixing vessel for avian and mammal influenza viruses, resulting in new reassorted viruses. This study investigated the presence of antibodies against influenza H1N1 and H3N2 viruses in pigs from Peninsular Malaysia using Herdcheck Swine Influenza H1N1 and H3N2 Antibody Test Kits. At the same time, the presence of influenza virus was examined from the nasal swabs of seropositive pigs by virus isolation and real time RT-PCR. The list of pig farms was obtained from the headquarters of the Department of Veterinary Services, Malaysia, and pig herds were selected randomly from six of 11 states in Peninsular Malaysia. A total of 727 serum and nasal swab samples were collected from 4- to 6-month-old pigs between May and August 2005. By ELISA, the seroprevalences of swine influenza H1N1 and H3N2 among pigs were 12.2% and 12.1% respectively. Seropositivity for either of the virus subtypes was detected in less than half of the 41 sampled farms (41.4%). Combination of both subtypes was detected in 4% of all pigs and in 22% of sampled farms. However, no virus or viral nucleic acid was detected from nasal samples. This study identified that the seropositivity of pigs to H1N1 and H3N2 based on ELISA was significantly associated with factors such as size of farm, importation or purchase of pigs, proximity of farm to other pig farms and the presence of mammalian pets within the farm.

Matched MeSH terms: Influenza A virus/classification
Molecular characterization of influenza viruses circulating in Northern Italy during two seasons (2005/2006 and 2006/2007) of low influenza activity

Pariani E, Amendola A, Zappa A, Bianchi S, Colzani D, Anselmi G, et al.

J Med Virol, 2008 Nov;80(11):1984-91.
PMID: 18814246 DOI: 10.1002/jmv.21323

The influenza activity and circulation of influenza viruses in Lombardy (the most populous Italian region) were observed during two consecutive seasons (2005/2006 and 2006/2007) characterized by low influenza activity by the Italian Influenza Surveillance Network. The molecular characteristics of circulating viruses were analyzed to evaluate the introduction of new variants and emergence of vaccine-escape viruses. In both seasons, the epidemic in Lombardy was sustained almost exclusively by influenza A viruses, accounting for 80.5% and 93.6% of total detections, respectively, and the co-circulation of A/H3 viruses belonging to distinct phylogenetic groups was observed. The A/H1N1 viruses isolated during the 2005/2006 season were closely related to A/New Caledonia/20/99, while the hemagglutinin (HA) sequences of the A/H1N1 viruses from the 2006/2007 season exhibited a greater diversity. These viruses were A/Solomon Islands/3/2006-like and showed several variants. All B isolates were similar to B/Malaysia/2506/2004 belonging to the B/Victoria/2/87-lineage. Influenza B virus was the dominant virus in Europe in the 2005/2006 season and accounted for the 20% of total detections in Lombardy. Overall, the viruses studied presented heterogeneity in their HA sequences suggesting the circulation of a miscellaneous set of variants during the two seasons notwithstanding the medium-low activity of influenza. The importance of virological surveillance of influenza viruses is recognized widely and the molecular characterization of the viruses, especially in vaccinated subjects, is of particular importance to evaluate the introduction and circulation of new variants.

Matched MeSH terms: Influenza A virus/classification*