Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic

“Outlaw” mutations in quasispecies of SARS-CoV-2 inhibit replication

“…SARS-CoV-2 genomes from our centre are available from sequence databases including GenBank ( https://www.ncbi.nlm.nih.gov/genbank/ , [ 11 ]) and GISAID ( https://gisaid.org/ ) [ 12 ], from the university hospital institute (IHU) Méditerranée Infection website at the following URL: https://www.mediterranee-infection.com/acces-ressources/donnees-pour-articles/60000-genomes/ , and in Supplementary Table S1. As previously reported [ 1 , 10 , 13 , 14 ], these genomes had been obtained by NGS from respiratory samples collected from patients to diagnose SARS-CoV-2 infection and sent to our centre’s clinical diagnosis laboratory (IHU Méditerranée Infection, public and university hospitals of Marseille, southeastern France). In addition, the CoV-Spectrum web application ( https://cov-spectrum.org/ ) [ 15 ] was used that allows determining mutations’ frequencies within SARS-CoV-2 genomes of the GISAID databases ( https://gisaid.org/ ) [ 12 ].…”

“…We classified the mutations according to their frequencies among quasispecies as well as among consensus, or “democratic,” genomes. We gave the name “outlaw” to the mutations that were the most frequent among quasispecies, as defined by their presence with a prevalence of ≥4% in ≥20% of the genomes analysed [ 13 ], by their absence among “democratic” genomes from the 90 nasopharyngeal samples [ 1 ], and by their complete or almost complete absence among “democratic” genomes from our centre as defined by a presence in ≤50 (0.1%) of 61,397 genomes [ 1 ], and among “democratic” genomes from the GISAID database as assessed through the Cov-Spectrum web application ( https://cov-spectrum.org/ ) [ 15 ] and defined by a presence in ≤3000 (0.02%) of 15,396,904 genomes ( Figure 1 ).

Figure 1.

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“…We have recently been able to identify “hyperfertile” mutations associated with the evolution of SARS-CoV-2 [ 1 ]. We have defined these mutations in this way because they are at the origin of phylogenetic nodes that have each generated more than 835 descendants.…”

“…For SARS-CoV-2, “hyperfertile” mutations appeared in viruses that circulated in Europe and are found at several notable positions [ 1 ]. The first amino acid substitution (P323L) is located in the NSP12 gene that encodes the RNA-dependent RNA polymerase (RdRp) and occurred in viruses that caused the pandemic onset after the Wuhan virus came into Europe [ 5 ].…”

“…Paradoxically, several other favourable mutations were identified in so-called accessory genes, including ORF8, where they generated stop codons [ 9 , 10 ]. Thus, we described that these mutations in ORF8 obeyed the “Mistigri” rule as the loss of this gene led to a major rebound of virus incidence and spread, which in several cases was at the origin of a “hyperfertile” phylogenetic node [ 1 ]. In our present work, we wanted to identify the missing mutations that could be at the origin of abortive forms of the virus, which we called “outlaw” mutations.…”