ArticleComputational and structural biotechnology journal2022
Genomic evidence for divergent co-infections of co-circulating SARS-CoV-2 lineages.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 31 citations in OpenAlex.
- Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.Microbial genomics · 2026Article
- Intra-host variation and transmission dynamics of SARS-CoV-2 Omicron outbreaks in Shandong, China.mSphere · 2025Article
- Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations.Microbiology spectrum · 2025Article
- Quasi-species prevalence and clinical impact of evolving SARS-CoV-2 lineages in European COVID-19 cohorts, January 2020 to February 2022.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- A program for real-time surveillance of SARS-CoV-2 genetics.Scientific reports · 2024Article
- Review
- Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover.Microbial genomics · 2024Article
- Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.Nature communications · 2024Article
- Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic.Virus evolution · 2024Article
- SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing.Microbiology spectrum · 2023Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages.International journal of medical sciences · 2023Review
- Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021.Frontiers in public health · 2023Article
- The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus.Vaccines · 2022Review
- SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods.Pathogens (Basel, Switzerland) · 2022Review
- Genomic evidence of co-identification with Omicron and Delta SARS-CoV-2 variants: a report of two cases.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- Review
- Deltacron: Apprehending a new phase of the COVID-19 pandemic.International journal of surgery (London, England) · 2022Article
- A Review of SARS-CoV-2 Disease (COVID-19): Pandemic in Our Time.Pathogens (Basel, Switzerland) · 2022Review
- Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection.Microbial genomics · 2022Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Co-infection of RNA viruses may contribute to their recombination and cause severe clinical symptoms. However, the tracking and identification of SARS-CoV-2 co-infection persist as challenges. Due to the lack of methods for detecting co-infected samples in a large amount of deep sequencing data, the lineage composition, spatial-temporal distribution, and frequency of SARS-CoV-2 co-infection events in the population remains unclear. Here, we propose a hypergeometric distribution-based method named Cov2Coinfect with the ability to decode the lineage composition from 50,809 deep sequencing data. By resolving the mutational patterns in each sample, Cov2Coinfect can precisely determine the co-infected SARS-CoV-2 variants from deep sequencing data. Results from two independent and parallel projects in the United States achieved a similar co-infection rate of 0.3-0.5 % in SARS-CoV-2 positive samples. Notably, all co-infected variants were highly consistent with the co-circulating SARS-CoV-2 lineages in the regional epidemiology, demonstrating that the co-circulation of different variants is an essential prerequisite for co-infection. Overall, our study not only provides a robust method to identify the co-infected SARS-CoV-2 variants from sequencing samples, but also highlights the urgent need to pay more attention to co-infected patients for better disease prevention and control.
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