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Comment
. 2021 Apr;82(4):84-123.
doi: 10.1016/j.jinf.2020.11.011. Epub 2020 Nov 15.

Evidence of SARS-CoV-2 re-infection with a different genotype

Philippe Colson  1 , Michael Finaud  2 , Nicolas Levy  3 , Jean-Christophe Lagier  1 , Didier Raoult  4
Affiliations
Comment

Evidence of SARS-CoV-2 re-infection with a different genotype

Philippe Colson et al. J Infect. 2021 Apr.
No abstract available

Keywords: Covid-19; Genome; Genotype; Next-generation sequencing; Re-infection; SARS-CoV-2.

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Figures

Fig. 1
Fig. 1
Phylogeny reconstruction based on SARS-CoV-2 genomes recovered during the first and second infections. Phylogenetic tree was reconstructed using the MEGA X software (https://www.megasoftware.net/) based on SARS-CoV-2 genome sequences, with a total of 29,703 positions in the final dataset. This analysis incorporated the genome sequences the most similar through BLASTn searches (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch) to the two genome sequences recovered from the case-patient in April and August 2020 (indicated by a black background and a white bold font and a framed white background and a black bold font, respectively) among those obtained in our center from respiratory samples collected since end of February 2020 until end of September (indicated by a gray bold font) and those from the GISAID database (https://www.gisaid.org/) (indicated by a black bold font). Among top hit sequences from the GISAID database, a single one was kept by country. The evolutionary history was inferred by using the Maximum Likelihood method and Kimura 2-parameter model. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap greater than 50% are indicated in the tree. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All nucleotide positions with less than 80% site coverage were discarded (partial deletion option). Prior nucleotide sequence alignment was performed using Muscle.
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