@article{fdi:010088211,
  title = {{G}enomic epidemiology of {SARS}-{C}o{V}-2 in urban settings in {S}enegal},
  author = {{N}diaye, {A}. {J}. {S}. and {B}eye, {M}. and {L}o, {G}. {R}. and {K}acel, {I}. and {S}ow, {A}. and {L}eye, {N}. and {P}adane, {A}. and {M}boup, {A}. and {D}iop-{N}diaye, {H}. and {S}okhna, {C}heikh and {K}ane, {C}. {T}. and {C}olson, {P}. and {F}enollar, {F}. and {M}boup, {S}. and {F}ournier, {P}. {E}.},
  editor = {},
  language = {{ENG}},
  abstract = {{W}e used whole genome sequencing to identify and analyze mutations in {SARS}-{C}o{V}-2 in urban settings during the deadliest wave of the {COVID}-19 epidemic-from {M}arch to {A}pril 2021-in {S}enegal. {N}asopharyngeal samples testing positive for {SARS}-{C}o{V}-2 were sequenced on the {I}llumina {N}ova{S}eq 6000 sequencing system using the {COVIDS}eq protocol. {A} total of 291 genotypable consensus genome sequences were obtained. {P}hylogenetic analyses grouped the genomes into 16 distinct {PANGOLIN} lineages. {T}he major lineage was {B}.1.1.420, despite circulation of the {A}lpha variant of concern ({VOC}). {A} total of 1125 different {SNP}s, identified relative to the {W}uhan reference genome, were detected. {T}hese included 13 {SNP}s in non-coding regions. {A}n average density of 37.2 {SNP}s per 1000 nucleotides was found, with the highest density occurring in {ORF}10. {T}his analysis allowed, for the first time, the detection of a {S}enegalese {SARS}-{C}o{V}-2 strain belonging to the {P}.1.14 ({GR}/20{J}, {G}amma {V}3) sublineage of the {B}razilian {P}.1 lineage (or {G}amma {VOC}). {O}verall, our results highlight substantial {SARS}-{C}o{V}-2 diversification in {S}enegal during the study period.},
  keywords = {{S}enegal ; {SARS}-{C}o{V}-2 ; genomic ; epidemiology ; {SNP}s ; {COVIDS}eq ; {SENEGAL}},
  booktitle = {},
  journal = {{V}iruses},
  volume = {15},
  numero = {6},
  pages = {1233 [13 ]},
  year = {2023},
  DOI = {10.3390/v15061233},
  URL = {https://www.documentation.ird.fr/hor/fdi:010088211},
}