Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient

Abstract

Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but a single patient sample was analyzed, and the virus was not isolated. Here, we report the gradual creation of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. Analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the creation of new viruses.

Recombination in Coronaviruses, with a Focus on SARS-CoV-2

“…Table 1 summarizes the recombinants between VOCs detected in more than one case (generally > 50 GISAID sequences). Many more cases are likely to have occurred between non-VOCs in a pre-VOC era or within individual hosts, such as a recombinant between B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months [70]: nevertheless, those recombinant have been not fit enough to spread and outcompete the dominant strain of the moment.…”

A 21L/BA.2-21K/BA.1 “MixOmicron” SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis

“…In addition, it was deemed that up to 5% of SARS-CoV-2 that circulated in the USA and UK might have been recombinants (VanInsberghe et al, 2021), and estimated that ≈2.7% of sequenced SARS-CoV-2 genomes might have recombinant ancestry (Turkahia et al, 2021). As a matter of fact, cases of detection of recombinant genomes are increasingly reported in 2022 (Wertheim et al, 2022; Sekizuka et al, 2022; Colson et al, 2022b; Lacek et al, 2022; Bolze et al, 2022; Ou et al, 2022; Belen Pisano et al, 2022; Burel et al, 2022). Such recombinants are all the more likely to be generated when different variants co-circulate with high incidence levels.…”

“…Nasopharyngeal samples were tested for the presence of SARS-CoV-2 RNA by real-time reverse transcription-PCR (qPCR) using the BGI real-time fluorescent RT-PCR assay (BGI Genomics, Shanghai Fosun Long March Medical Science Co., Ltd., Shenzhen, China), as previously described (Burel et al, 2022). Subsequently, qPCR assays that screen for SARS-CoV-2 variants were carried out with the detection of mutations among which spike substitution K417N (Thermo Fisher Scientific, Waltham, USA) and the targeting of viral genes S (spike), N (nucleocapsid) and ORF1 with the TaqPath COVID-19 kit (Thermo Fisher Scientific), as previously reported (Colson et al, 2022a; Colson et al, 2022b).…”

“…Such genetic recombinations are extremely frequent for viruses of family Coronaviridae , and they have already been identified for endemic human coronaviruses (Lai, 1996; Zhang et al, 2015; So et al, 2019; Gribble et al, 2020). Regarding SARS-CoV-2, the occurrence of recombinations has been reported or suspected (Yi, 2019; Yeh and Contreras, 2020; Haddad et al, 2021; Ignatieva et al, 2021; Jackson et al, 2021; Taghizadeh et al, 2021; Varabyou et al, 2021; Kreier, 2022; Wertheim et al, 2022; He et al, 2022; Sekizuka et al, 2022; Colson et al, 2022b; Lacek et al, 2022; Lohrasbi-Nejad, 2022; Bolze et al, 2022; Ou et al, 2022; Belen Pisano et al, 2022; Burel et al, 2022). Very recently, we described the identification and culture of two SARS-CoV-2 recombinants, one between the B.1.160 and Alpha/20I variants in a patient chronically-infected with SARS-CoV-2 (Burel et al, 2022), and another between the Delta/21J AY.4 and Omicron 21K/BA.1 variants in patients infected approximately 10 weeks after the start of the period of co-detection of these two variants in our geographical area (Colson et al, 2022b).…”

A 21L/BA.2-21K/BA.1 “MixOmicron” SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis

“…Such genetic recombinations are extremely frequent for viruses of family Coronaviridae , and they have already been identified for endemic human coronaviruses ( Lai, 1996 ; Zhang et al, 2015 ; So et al, 2019 ; Gribble et al, 2021 ). Regarding SARS-CoV-2, the occurrence of recombinations has been reported or suspected ( Yi, 2020 ; Yeh and Contreras, 2020 ; Haddad et al, 2021 ; Ignatieva et al, 2022 ; Jackson et al, 2021 ; Taghizadeh et al, 2021 ; Varabyou et al, 2021 ; Kreier, 2022 ; Wertheim et al, 2022 ; He et al, 2022 ; Sekizuka et al, 2022 ; Colson et al, 2022b ; Lacek et al, 2022 ; Lohrasbi-Nejad, 2022 ; Bolze et al, 2022 ; Ou et al, 2022 ; Belén Pisano et al, 2022 ; Burel et al, 2022 ). Very recently, we described the identification and culture of two SARS-CoV-2 recombinants, one between the B.1.160 and Alpha/20I variants in a patient chronically-infected with SARS-CoV-2 ( Burel et al, 2022 ), and another between the Delta/21J AY.4 and Omicron 21K/BA.1 variants in patients infected approximately 10 weeks after the start of the period of co-detection of these two variants in our geographical area ( Colson et al, 2022b ).…”