@article{fdi:010080652,
  title = {{I}ntra-host diversity of {SARS}-{C}ov-2 should not be neglected : case of the {S}tate of {V}ictoria, {A}ustralia},
  author = {{A}rmero, {A}. and {B}erthet, {N}. and {A}varre, {J}ean-{C}hristophe},
  editor = {},
  language = {{ENG}},
  abstract = {{S}ince the identification of severe acute respiratory syndrome coronavirus 2 ({SARS}-{C}o{V}-2) as the etiological agent of the current {COVID}-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. {H}owever, less attention has been given to the assessment of intra-host diversity. {RNA} viruses such as {SARS}-{C}o{V}-2 inhabit the host as a population of variants called quasispecies. {W}e studied the quasispecies diversity in four of the main {SARS}-{C}o{V}-2 genes ({ORF}1a, {ORF}1b, {S} and {N} genes), using a dataset consisting of 210 next-generation sequencing ({NGS}) samples collected between {J}anuary and early {A}pril of 2020 in the {S}tate of {V}ictoria, {A}ustralia. {W}e found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike ({S}) glycoprotein and {ORF}1a genes. {A}bout one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. {Q}uasispecies diversity changed over time. {P}hylogenetic analysis showed that some of the intra-host single-nucleotide variants (i{SNV}s) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. {A} greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.},
  keywords = {{SARS}-{C}o{V}-2 ; quasispecies ; nonsynonymous i{SNV}s ; transmission ; phylogenetic ; genetic bottleneck ; {AUSTRALIE} ; {VICTORIA} {ETAT}},
  booktitle = {},
  journal = {{V}iruses},
  volume = {13},
  numero = {1},
  pages = {133 [15 ]},
  year = {2021},
  DOI = {10.3390/v13010133},
  URL = {https://www.documentation.ird.fr/hor/fdi:010080652},
}