@article{fdi:010057172,
  title = {{M}olecular evolutionary analysis of {PH}1{N}1 2009 influenza virus in {R}eunion {I}sland, south west {I}ndian {O}cean region : a cohort study},
  author = {{P}ascalis, {H}erv{\'e} and {T}emmam, {S}. and {W}ilkinson, {D}. {A}. and {D}souli, {N}. and {T}urpin, {M}. and {D}e {L}amballerie, {X}avier and {D}ellagi, {K}oussay},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground/{O}bjectives: {M}olecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. {L}ittle is known about the p{H}1{N}1 molecular dynamics in general population. {A} prospective study ({C}o{P}an{F}lu-{RUN}) was carried out in {R}eunion {I}sland to characterize p{H}1{N}1 genetic variability and molecular evolution occurring in population during the p{H}1{N}1 {I}nfluenza pandemic in 2009. {M}ethodology: {W}e directly amplified p{H}1{N}1 genomes from 28 different nasal swabs (26 individuals from 21 households). {F}ifteen strains were fully sequenced and 13 partially. {T}his includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. {W}e assessed the molecular evolution of p{H}1{N}1 by genetic variability and phylogenetic analyses. {P}rincipal {F}indings: {W}e found that i) {R}eunion p{H}1{N}1 sequences stemmed from global "clade 7' but shaped two phylogenetic sub-clades; ii) {D}239{E} mutation was identified in the hemagglutinin protein of all {R}eunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract p{H}1{N}1 infecting strains; iii) {D}ate estimates from molecular phylogenies predicted clade emergence some time before the first detection of p{H}1{N}1 by the epidemiological surveillance system; iv) {P}hylogenetic relatedness was observed between {R}eunion p{H}1{N}1 viruses and those from other countries in {S}outh-western {I}ndian {O}cean area; v) {Q}uasispecies populations were observed within households and individuals of the cohort-study. {C}onclusions: {S}urveillance and/or prevention systems presently based on {I}nfluenza virus sequence variation should take into account that the majority of studies of p{H}1{N}1 {I}nfluenza 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. {O}ur observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.},
  keywords = {},
  booktitle = {},
  journal = {{P}los {O}ne},
  volume = {7},
  numero = {8},
  pages = {e43742},
  ISSN = {1932-6203},
  year = {2012},
  DOI = {10.1371/journal.pone.0043742},
  URL = {https://www.documentation.ird.fr/hor/fdi:010057172},
}