ArticleViruses2022
Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient.
Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 20 citations in OpenAlex.
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples.BMC infectious diseases · 2025Article
- Recombinant SARS-CoV-2 Delta/Omicron BA.5 emerging in an immunocompromised long-term infected COVID-19 patient.Scientific reports · 2024Article
- Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis.Viruses · 2024Article
- The immune response to SARS-CoV-2 in people with HIV.Cellular & molecular immunology · 2024Review
- Molecular Epidemiology of SARS-CoV-2 and Clinical Manifestations among Organ Transplant Recipients with COVID-19.Viruses · 2023Article
- SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis.medRxiv : the preprint server for health sciences · 2023Article
- Rapid screening of SARS-CoV-2 variants, a key tool for pandemic surveillance.Scientific reports · 2023Article
- Article
- Review
- Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.PLoS computational biology · 2023Article
- Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada.The Science of the total environment · 2023Article
- The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2.Frontiers in microbiology · 2023Review
- A 21L/BA.2-21K/BA.1 "MixOmicron" SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2022Article
- Immune Heterogeneity and Epistasis Explain Punctuated Evolution of SARS-CoV-2.medRxiv : the preprint server for health sciences · 2022Article
- Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 only a single patient's sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence 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 the 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. An 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's follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.