Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand

Abstract

Background Recent studies have revealed the existence of genetic diversity in swine influenza viruses (SIVs) in the world. In Thailand, there has been a little information on the molecular characteristics of the SIVs since the first isolation of viruses of H1N1 and H3N2 subtypes in the late 1970s. Our previous study demonstrated that Thai H1N1 SIVs possessed the classical swine H1 and avian‐like swine N1 genes (Takemae et al., Proceedings of the Options for the Control of Influenza VI.2007;350–353). Objectives In the present study, we genetically characterized 12 SIVs including those of H1N1, H1N2 and H3N2 subtypes isolated between 2000 and 2005. Methods We determined the entire nucleotide sequences of the eight gene segments of those isolates. Results Phylogenetic analysis revealed the existence of nine distinct genotypes amongst the Thai SIVs. These genotypes arose from multiple introductions of classical swine, avian‐like swine and human viruses. The existence of two distinct sublineages within classical swine H1 and NS, avian‐like swine PA and M and human H3 and N2 genes of the Thai SIVs suggested that introduction of viruses of classical swine, avian‐like swine and human origins occurred twice respectively into the Thai pig population. The predominance of avian‐like swine genes amongst the Thai SIVs was evident. In particular, three polymerase (PB1, PB2 and PA) and matrix genes of avian‐like swine origin were retained in all the Thai SIVs examined. Conclusions These observations may suggest that genes of avian‐like swine lineages have some advantages to be maintained in pigs as seen in the SIVs established through multiple introductions in other regions.

Retrospective swine influenza serological surveillance in the four highest pig density provinces of Thailand before the introduction of the 2009 pandemic Influenza A virus subtype H1N1 using various antibody detection assays

“…Thai SIV subtype H1 can be further divided into 3 clusters (clusters I-III). 30,31,34 Therefore, whole genome characterization of previous and current Thai SIV isolates is necessary because it could provide essential epidemiologic data and diagnostic and disease preparedness of the current viruses. Currently in Thailand, there are only 16 whole genomes of 2000-2005 (6 H1N1, 9 H3N2, and 1 H1N2), 8 H1N1 whole genomes of 2009-2010, 20,31,34 and 38 HA genes available in the public database.…”

“…2 Interestingly, in Thailand, the reassortant H1N1 SIV between the North American and Eurasian lineage has been reported as swine breeds have been continuingly imported from both continents. 30,34 Similarly, antigenic and genetic diversity of swine H1N1 and H1N2 viruses in Europe have been documented. 19 This indicates that a constant update of the representative filed strain virus within different regions of the world is required to reflect true SIV serologic data.…”

“…1,29 Previous SIV genetic data in Thailand showed that H1 and H3 SIVs circulating between the years 2000-2005 formed at least 2 clusters within each subtype. 34 Data published in 2010 showed that the pandemic H1N1 2009 (pH1N1) virus is now circulating in Thai swine herds. 31 It should be noted that before the introduction of pH1N1 in Thailand, SIV HI test antigens and serological data had not yet been evaluated.…”

“…Three major subtypes including H1N1, H3N2, and H1N2 are currently circulating worldwide in swine populations, 2 including Thailand. 4,30,34 Swine influenza virus (SIV) infection causes acute respiratory syndrome including cough, dyspnea, fever, and prostration with rapid recovery. 30 The morbidity rate of SIV is high and may increase up to 100% in immunologically naïve pig populations whereas the mortality rate can be as low as 1%.…”

Single-step multiplex reverse transcription polymerase chain reaction assay for detection and differentiation of the 2009 H1N1 Influenza A virus pandemic in Thai swine populations

“…The internal genes of the first cluster include the polymerases (PB1, PB2, and PA), matrix (M), nucleoprotein (NP), and nonstructural protein (NS) of Eurasian swine origin, while in the second cluster, the NS genes are of classical swine origin. 15 The emergence of the novel swine origin H1N1 Influenza A virus (pandemic H1N1 [pH1N1]) in April of 2009 initiated the first human pandemic of the 21st century. 9 Implementation of effective control strategies, rapid diagnosis, and identification of newly emerged influenza A viruses in both the human and swine populations were required.…”