Epidemiology and full genome sequence analysis of H1N1pdm09 from Northeast China

Abstract

Pandemic influenza A (H1N1) 2009 virus (H1N1pdm09) was a novel tri-assortment virus that emerged in Mexico and North America in 2009 and caused the first influenza pandemic in the 21st century. This study investigated the prevalence pattern and molecular characteristics of H1N1pdm09 in three continuous years from April 2009 to March 2012 in populations of Tianjin, Northeast China. Totally, 3,068 influenza viruses (25.4 %) were detected from 12,089 respiratory specimens. Among them, 41.4 % (1,269/3,068) were H1N1pdm09 positive. 15.1 % (192/1,269) severe respiratory infection cases were H1N1pdm09 positive. H1N1pdm09 was the predominant prevalence subtype in October 2009-March 2010 (69.1 %, 930/1,346) and October 2010-March 2011 (42.1 %, 220/523). Eight isolated H1N1pdm09 viruses from severe infection/death cases in three different years were selected to sequence the whole genome through splicing the sequences following 46 PCRs. HA sequences of seven H1N1pdm09 isolates from mild infection cases were detected. Phylogenetic analysis showed that HA, NA, M, NP and NS genes of H1N1pdm09 viruses gathered together with swine influenza A (H1N1), whereas PB2 and PA genes originated from avian influenza virus, and PB1 gene originated from human seasonal influenza virus. Identity analysis indicated that all the genes were highly conserved. Compared with vaccine strain A/California/07/2009(H1N1), the maximal mutation gene was HA (0.7-2.6 %), then NA (0.6-1.7 %), last one was M (mutation rate 0-0.6 %). More site substitutions were observed in 2011 isolates than in 2009 and 2010 isolates of HA (p = 0.002), NA (p = 0.003) and PA (p = 0.001) proteins. The amino acid substitution rates were varied among eight gene segments, ranging from 7.39 × 10(-4) for PB2 to 7.40 × 10(-3) for NA. The higher d N / d S rates were observed in HA, PA and NS segments in H1N1pdm09 in Tianjin. Three HA amino acid site substitutions occurred at the HA receptor-binding sites and antigenic determinant, including S179N and K180T (located at antigenic site Sa) in A/Tianjinhedong/SWL44/2011(H1) and A/Tianjinjinnan/SWL41/2011(H1), and D239N (located at antigenic site Ca) in A/Tianjinninghe/SWL49/2009(H1). Antigenic drift may have occurred in H1N1pdm09 with time. No oseltamivir-resistance site substitution was observed at 275 and 295 sites. Amino acid residue site at 31 in M2 protein was N in all 8 isolates, which suggested that H1N1pdm09 was resistant to amantadine.

Genetic Characterization of Circulating 2015 A(H1N1)pdm09 Influenza Viruses from Eastern India

“…It has also been suggested that the new H1N1 virus may not yet have completely adapted to the human population signifying that further adaptive changes will lead to more virulent and transmissible strains [23,45]. In summary, the high population density in India facilitates the person-to-person transmission, and creates ample opportunities for these mutated variants to sustain and become dominant.…”

Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A

“…Gene sequencing also provides information on genotypes, subtypes, and drug resistance in a hospital setting [3]. In recent years, whole-genome sequencing (WGS) has been widely used to conduct outbreak investigations of a wide range of infectious pathogens [8–11], with a few studies focusing on the epidemiology of the influenza virus [12, 13]. A recent study concluded that, in the hospital setting, WGS did not provide any additional information on influenza outbreaks and transmission chains, compared to HA/NA gene sequencing alone [14].…”

Full Genome Analysis of Influenza A(H1N1)pdm09 Virus Isolated from Peru, 2013

“…The hemagglutinin (HA) gene shows 97.88% amino acid identity with that in the vaccine strain, and the mutations K180Q (in the antigenic site Sa) and E391K were identified. This E391K mutation has been associated with cases of mild infection (4). Other mutations present in the HA gene included P100S, D114N, S202T, S220T, A273T, K300E, I338V, S468N, and E516K.…”