Post by Admin on Mar 13, 2022 1:16:41 GMT
Discussion
It is increasingly demonstrated that the genomes of most biological entities, whatever their level of complexity, are mosaics of sequences from various origins (Raoult, 2011; Merhej and Raoult, 2012; Feschotte et al., 2012; Roux et al., 2013; Jacobs et al., 2019). The present observations show us in real life the recombination potential of SARS-CoV-2, already largely established for other coronaviruses (Liu et al., 2013; Xiao et al., 2017; Lai, 1996; Zhang et al., 2015; Gribble et al., 2021) and reported or suspected for SARS-CoV-2 (Yi, 2020; Yeh and Contreras, 2020; VanInsberghe et al., 2020; Gallaher, 2020; Jackson et al., 2021; Haddad et al., 2021; Varabyou et al., 2021; Leary et al., 2021; Taghizadeh et al., 2021; Lohrasbi-Nejad, 2022; Kreier, 2022; Ignatieva et al., 2022). SARS-CoV-2 recombinations were difficult to spot when only genetically very similar viruses were circulating, as was the case in Europe during the first epidemic episode with mutants derived from the Wuhan-Hu-1 virus. The increasing genetic diversity of SARS-CoV-2, the tremendous number of infections at global and national levels, and the unprecedented global effort of genomic sequencing (https://covariants.org/per-country) (Aksamentov et al., 2022; Hodcroft et al., 2021; Alm et al., 2020; Colson et al., 2022b), raised the probability of detecting recombinants. Such observations will probably make it possible in the short or medium term to assess the recombination rate of SARS-CoV-2, whether there are recombination hotspots, and to what extent recombinations between different variants can generate new viable, and epidemic variants. This questions on the impact of recombinations on viral replication and transmissibility, and on clinical severity, as well as on the virus ability to escape neutralizing antibodies elicited by vaccines or a previous infection. In this view, culture isolation of SARS-CoV-2 recombinants as was carried out here for the first time to our knowledge is of primary importance. This will allow studying their phenotypic properties, among which their replicative capacity in various cell lines, their sensitivity to antibodies, or their genetic evolution in vitro. Concurrently, a high level of genomic surveillance must be maintained in order to detect and characterize all recombination events and circulating recombinants, which is a critical scientific and public health issue.
Data Availability
The dataset generated and analyzed during the current study is available in the GISAID database (https://www.gisaid.org/).
www.gisaid.org/
Author contributions
Study conception and design: Philippe Colson, Pierre-Edouard Fournier, Jacques Fantini, Didier Raoult, Bernard La Scola. Materials, data and analysis tools: Philippe Colson, Pierre-Edouard Fournier, Jeremy Delerce, Matthieu Million, Marielle Bedotto, Linda Houhamdi, Nouara Yahi, Jeremy Bayette, Jacques Fantini. Data analyses: Philippe Colson, Pierre-Edouard Fournier, Jeremy Delerce, Marielle Bedotto, Anthony Levasseur, Jacques Fantini, Didier Raoult, Bernard La Scola. Writing of the first draft of the manuscript: Philippe Colson, Jacques Fantini, and Pierre-Edouard Fournier. All authors read, commented on, and approved the final manuscript.
It is increasingly demonstrated that the genomes of most biological entities, whatever their level of complexity, are mosaics of sequences from various origins (Raoult, 2011; Merhej and Raoult, 2012; Feschotte et al., 2012; Roux et al., 2013; Jacobs et al., 2019). The present observations show us in real life the recombination potential of SARS-CoV-2, already largely established for other coronaviruses (Liu et al., 2013; Xiao et al., 2017; Lai, 1996; Zhang et al., 2015; Gribble et al., 2021) and reported or suspected for SARS-CoV-2 (Yi, 2020; Yeh and Contreras, 2020; VanInsberghe et al., 2020; Gallaher, 2020; Jackson et al., 2021; Haddad et al., 2021; Varabyou et al., 2021; Leary et al., 2021; Taghizadeh et al., 2021; Lohrasbi-Nejad, 2022; Kreier, 2022; Ignatieva et al., 2022). SARS-CoV-2 recombinations were difficult to spot when only genetically very similar viruses were circulating, as was the case in Europe during the first epidemic episode with mutants derived from the Wuhan-Hu-1 virus. The increasing genetic diversity of SARS-CoV-2, the tremendous number of infections at global and national levels, and the unprecedented global effort of genomic sequencing (https://covariants.org/per-country) (Aksamentov et al., 2022; Hodcroft et al., 2021; Alm et al., 2020; Colson et al., 2022b), raised the probability of detecting recombinants. Such observations will probably make it possible in the short or medium term to assess the recombination rate of SARS-CoV-2, whether there are recombination hotspots, and to what extent recombinations between different variants can generate new viable, and epidemic variants. This questions on the impact of recombinations on viral replication and transmissibility, and on clinical severity, as well as on the virus ability to escape neutralizing antibodies elicited by vaccines or a previous infection. In this view, culture isolation of SARS-CoV-2 recombinants as was carried out here for the first time to our knowledge is of primary importance. This will allow studying their phenotypic properties, among which their replicative capacity in various cell lines, their sensitivity to antibodies, or their genetic evolution in vitro. Concurrently, a high level of genomic surveillance must be maintained in order to detect and characterize all recombination events and circulating recombinants, which is a critical scientific and public health issue.
Data Availability
The dataset generated and analyzed during the current study is available in the GISAID database (https://www.gisaid.org/).
www.gisaid.org/
Author contributions
Study conception and design: Philippe Colson, Pierre-Edouard Fournier, Jacques Fantini, Didier Raoult, Bernard La Scola. Materials, data and analysis tools: Philippe Colson, Pierre-Edouard Fournier, Jeremy Delerce, Matthieu Million, Marielle Bedotto, Linda Houhamdi, Nouara Yahi, Jeremy Bayette, Jacques Fantini. Data analyses: Philippe Colson, Pierre-Edouard Fournier, Jeremy Delerce, Marielle Bedotto, Anthony Levasseur, Jacques Fantini, Didier Raoult, Bernard La Scola. Writing of the first draft of the manuscript: Philippe Colson, Jacques Fantini, and Pierre-Edouard Fournier. All authors read, commented on, and approved the final manuscript.