Skip to content
1887

Microbial Genomics logo Microbial Genomics

Volume 10, Issue 1

Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections Open Access

Abstract

Recombination events between Delta and Omicron SARS-CoV-2 lineages highlight the need for co-infection research. Existing studies focus on late-phase co-infections, with few examining earlier pandemic stages. This new study aims to globally identify and characterize co-infections using a bioinformatic pipeline to analyse genomic data from diverse locations and pandemic phases. Among 26988 high-quality SARS-CoV-2 isolates from 11 diverse project databases, we identified 141 potential co-infection cases (0.52%), surpassing previous prevalence estimates. These co-infections were observed throughout the pandemic timeline, with an increase noted after the emergence of the Omicron variant. Co-infections involving the Omicron variant were the most prevalent, potentially influenced by the high level of diversity within this lineage and its impact on the viral landscape. Additionally, we found co-infections involving the pre-Alpha/Alpha lineages, which have been rarely described, raising possibilities of contributing to new lineage emergence through recombination events. The analysis revealed co-infection cases involving both different and the same lineages/sublineages. Our study showcases the potential of our pipeline to leverage valuable information stored in global sequence repositories, advancing our understanding of SARS-CoV-2 co-infections. The prevalence of co-infections highlights the importance of monitoring viral diversity and its potential implications on disease dynamics. Integrating clinical data with genomic findings can further shed light on the clinical implications and outcomes of co-infections.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): co-infection , pipeline , repository and SARS-CoV-2
Funding
This study was supported by the:
  • Instituto de Investigación Sanitaria Gregorio Marañón (Award 2022-II-PREDOC-IA-01)
    • Principle Award Recipient: DanielPeñas-Utrilla
  • Miguel Servet (Award CPII20/00001)
    • Principle Award Recipient: LauraPérez-Lago
  • European Centre for Disease Prevention and Control (Award 2021/PHF/23776)
    • Principle Award Recipient: DaríoGarcía de Viedma
  • Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (Award CB06/06/0058)
    • Principle Award Recipient: DaríoGarcía de Viedma
  • Instituto de Salud Carlos III (Award PI21/01823)
    • Principle Award Recipient: DaríoGarcía de Viedma
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.001158
2024-01-16
2025-04-20
Loading full text...

Full text loading...

/deliver/fulltext/mgen/10/1/mgen001158.html?itemId=/content/journal/mgen/10.1099/mgen.0.001158&mimeType=html&fmt=ahah

References

  1. Bal A, Simon B, Destras G, Chalvignac R, Semanas Q et al. Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France. Nat Commun 2022; 13:6316 [View Article] [PubMed]
     [Google Scholar]
  2. Gu H, Ng DYM, Liu GYZ, Cheng SSM, Krishnan P et al. Recombinant BA.1/BA.2 SARS-CoV-2 virus in arriving travelers, Hong Kong, February 2022. Emerg Infect Dis 2022; 28: [View Article]
     [Google Scholar]
  3. Simon-Loriere E. Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe. [cited 2022 Dec 27]. n.d https://orcid.org/0000-0003-2862-9751
  4. Perez-Florido J, Casimiro-Soriguer CS, Ortuño F, Fernandez-Rueda JL, Aguado A et al. Detection of high level of co-infection and the emergence of novel SARS CoV-2 delta-omicron and omicron-omicron recombinants in the epidemiological surveillance of Andalusia. Int J Mol Sci 2023; 24:2419 [View Article] [PubMed]
     [Google Scholar]
  5. Pedro N, Silva CN, Magalhães AC, Cavadas B, Rocha AM et al. Dynamics of a dual SARS-CoV-2 lineage co-infection on a prolonged viral shedding COVID-19 case: insights into clinical severity and disease duration. Microorganisms 2021; 9:300 [View Article] [PubMed]
     [Google Scholar]
  6. Liu R, Wu P, Ogrodzki P, Mahmoud S, Liang K et al. Publisher correction: genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response. Sci Rep 2021; 11:18728 [View Article] [PubMed]
     [Google Scholar]
  7. Gutierrez B, Castelán Sánchez HG, Candido D da S, Jackson B, Fleishon S et al. Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America. Cell Host Microbe 2022; 30:1112–1123 [View Article] [PubMed]
     [Google Scholar]
  8. Combes P, Bisseux M, Bal A, Marin P, Latour J et al. Evidence of co-infections during delta and omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing. Clin Microbiol Infect 2022; 28:1503 [View Article] [PubMed]
     [Google Scholar]
  9. Peñas-Utrilla D, Pérez-Lago L, Molero-Salinas A, Estévez A, Sanz A et al. Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved. Genome Med 2023; 15:57 [View Article] [PubMed]
     [Google Scholar]
  10. Musuuza JS, Watson L, Parmasad V, Putman-Buehler N, Christensen L et al. Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: a systematic review and meta-analysis. PLoS One 2021; 16:e0251170 [View Article] [PubMed]
     [Google Scholar]
  11. Garcia-Vidal C, Sanjuan G, Moreno-García E, Puerta-Alcalde P, Garcia-Pouton N et al. Incidence of co-infections and superinfections in hospitalized patients with COVID-19: a retrospective cohort study. Clin Microbiol Infect 2021; 27:83–88 [View Article] [PubMed]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001158
Loading
Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections
M Gen 10, 001158 (2024); https://doi.org/10.1099/mgen.0.001158
/content/journal/mgen/10.1099/mgen.0.001158
/content/journal/mgen/10.1099/mgen.0.001158
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error