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. 2020 Jul;26(7):960-962.
doi: 10.1016/j.cmi.2020.03.020. Epub 2020 Mar 28.

Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)

A Bal  1 , G Destras  2 , A Gaymard  2 , M Bouscambert-Duchamp  3 , M Valette  3 , V Escuret  2 , E Frobert  2 , G Billaud  3 , S Trouillet-Assant  4 , V Cheynet  5 , K Brengel-Pesce  5 , F Morfin  2 , B Lina  2 , L Josset  6
Affiliations

Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)

A Bal et al. Clin Microbiol Infect. 2020 Jul.
No abstract available

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Figures

Fig. 1
Fig. 1
Phylogenetic analysis based on whole-genome sequencing (WGS) of SARS-CoV-2. The analysis included 571 WGS of SARS-CoV-2 (>29 000 bp) collected in humans and available on GISAID (Global Initiative on Sharing All Influenza Data) from March 17th, 2020. The following sequences were excluded from the analysis—EPI_ISL_406592, EPI_ISL_414588, EPI_ISL_412900, EPI_ISL_408487, EPI_ISL_408483 and EPI_ISL_406595 because they were outliers, and EPI_ISL_413747, EPI_ISL_413695—because of incomplete sequences in ORF1ab. The hCoV19/Wuhan/IPBCAMSWH01/2019 strain was used as an outgroup virus. Genetic distances were calculated using the Kimura's two-parameter model (K80) and pairwise deletion. The tree was constructed by the neighbour-joining method using R seqinr and ggtree packages and validated using 1000 bootstrap pseudo-replicates. Sequence from sample #2 (EPI_ISL_410486) is indicated by the black arrow. Nucleotide alignment (1601–1615) is depicted as a heatmap on the right panel with the three-nucleotide deletion shown in black. Corresponding amino acid sequence (nsp2: 266-270) for the reference sequence is indicated below the heatmap.
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