Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic

Li, Yinhu; Jiang, Yiqi; Li, Zhengtu; Yu, Yonghan; Chen, Jiaxing; Jia, Wenlong; Ng, Yen Kaow; Ye, Feng; Li, Shuai Cheng; Shen, Bairong

doi:10.1016/j.csbj.2022.03.011

Cited by 8 publications

(7 citation statements)

References 60 publications

(37 reference statements)

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“…Some studies in different countries have found values ranging from 0.06 to 4.0% of co-infection and seem to be underestimated ( 15 – 20 ). Some tools based on metagenomics and bioinformatics have been proposed to identify and evaluate co-infections ( 21 – 25 ). It is unclear whether co-infections can result in more severe disease.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

et al. 2022

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Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics.

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Section: Introductionmentioning

confidence: 99%

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

et al. 2022

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“…Omicron/Delta 37 . A crucial step in confirming co-infections is the haplotype phasing of observed heterozygous mutations, which is generally limited to long-read sequencing approaches described here with PacBio ® sequencing and by others using Oxford Nanopore Technologies ®41 . In our study we observe most co-infections from the same lineage group (e.g.…”

Section: Discussionmentioning

confidence: 99%

A program for real-time surveillance of SARS-CoV-2 genetics

Brochu,

Song,

Zhang

et al. 2024

Preprint

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The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the U.S. from March 13th 2020 to July 3rd 2023. Our sequencing protocol ('Virseq') generates mutation-resistant sequencing of the entire SARS-CoV-2 genome, capturing all major lineages. We also characterize 379 clinically relevant SARS-CoV-2 multi-strain co-infections and ensure robust detection of emerging lineages via simulation. The modular infrastructure, sequencing, and analysis capabilities we describe support the U.S. Centers for Disease Control national surveillance program and serve as a model for rapid response to emerging pandemics at a national scale.

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“…A rare case of SARS‐CoV‐2 reinfection has emerged in Colombia, with two infections identified by nanopore sequencing as lineages B.1 and B.1.1.269 218 . By analyzing the variation of the SARS‐CoV‐2 genome in the GISAID database, the researchers speculated that this patient had multiple SARS‐CoV‐2 variants 219 . They then sequenced 42 COVID‐19 patients using nanopore sequencing and ultimately found that nearly half of them had SARS‐CoV‐2 variant coinfection 219 .…”

Section: Application Of Nanopore Sequencing Technology During the Cov...mentioning

confidence: 99%

Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third‐generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID‐19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus‐2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID‐19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID‐19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

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Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic

Cited by 8 publications

References 60 publications

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

A program for real-time surveillance of SARS-CoV-2 genetics

Nanopore sequencing technology and its applications

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