Molecular Evolutionary Analysis of pH1N1 2009 Influenza Virus in Reunion Island, South West Indian Ocean Region: A Cohort Study

Abstract

Background/ObjectivesMolecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009.MethodologyWe directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses.Principal FindingsWe found that i) Reunion pH1N1 sequences stemmed from global “clade 7” but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study.ConclusionsSurveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.

Molecular and epidemiological analysis of pandemic and post‐pandemic influenza A(H1N1)pdm09 virus from central India

“…HA gene of influenza is under constant pressure of the host immune response and unusual in that it evolves remarkably and possesses highest variation among eight genes, thus targeted by maximum studies for molecular characterization . On the other hand, several studies recommend full genome sequencing especially to detect the mutations in PB1, PA, and M genes that have importance in severity and fatality owing to quasispecies generation …”

“…We have analyzed data from more than 7000 patients, over a period of 6 years, giving sufficient power to data for understanding meaningful demographic, seasonal, and virological patterns of A(H1N1)pdm09 infections in the region. On the other hand, it has some limitations such as not testing samples for other etiologies, typing for other influenza viruses, and not sequencing other genes of A(H1N1)pdm09 such as PB1, PA, and M . We had limited clinical data especially about underlying conditions of the patients and had no information about patients in categories A and B.…”

The influenza A (H1N1) pandemic in Reunion Island: knowledge, perceived risk and precautionary behaviour

“…This fact may explain the high participation rate observed. A further explanation may be that the respondents in our sample had been contacted regularly during the A (H1N1) epidemic as part of the CoPanFlu-RUN protocol (virological aspects) [16,21,22]. …”

“…This was done in the frame of a research programme called CoPanFlu-RUN that included three complementary components of epidemiological, virological and social science aspects. The epidemiological and virological parameters of the epidemy were assessed in a prospective study conducted from July 21 to December 23, 2009 during the outbreak of influenza A (H1N1) [16,21,22]. Shortly after passage of the epidemic wave, the social science aspects were specifically investigated in a cross-sectional study.…”

Phylogenetic analysis of HA and NA genes and clinical characteristics of the co-occurring mutations in HA and NA of influenza A(H1N1)pdm09 viruses during 2015-2017 in Beijing, China

“…New variants of HA and NA might contribute to the emergence of new clinical characteristics, for example, HA-D239E mutation was associated with mild infection, been less severe than HA-D239G and D239N [9], and NA-H275Y, NA-E119D conferred resistance to neuraminidase inhibitors [10,11]. However, the interactions between virus evolution, epidemiology and human behavior were complicated [12].…”