Immunosuppression as a Hub for SARS-CoV-2 Mutational Drift

Viruses, Journal Year: 2023, Volume and Issue: 15(4), P. 855 - 855

Published: March 27, 2023

The clinical course of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is largely determined host factors, with a wide range outcomes. Despite an extensive vaccination campaign and high rates infection worldwide, the pandemic persists, adapting to overcome antiviral immunity acquired through prior exposure. source many such major adaptations variants concern (VOCs), novel SARS-CoV-2 produced extraordinary evolutionary leaps whose origins remain mostly unknown. In this study, we tested influence factors on SARS-CoV-2. Electronic health records individuals infected were paired viral whole-genome sequences assess effects parameters intra-host evolution We found slight, albeit significant, differences in diversity, which depended as status smoking. Only one genome had significant alterations result parameters; it was immunocompromised, chronically woman her 70s. highlight unusual obtained from woman, accelerated mutational rate excess rare mutations, including near-complete truncating accessory protein ORF3a. Our findings suggest that capacity during limited unaffected characteristics. Significant seemingly exclusive small subset COVID-19 cases, typically prolong infections immunocompromised patients. these genomes accumulate impactful potentially adaptive mutations; however, transmissibility viruses remains unclear.

Language: Английский

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Traceability of SARS‐CoV‐2 transmission through quasispecies analysis

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(6)

Published: June 1, 2023

Abstract During COVID‐19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in infected host, SARS‐CoV‐2 consists an ensemble replicating and closely related viral variants so‐called quasispecies. Here we show that single nucleotide (iSNVs) represent a target contact tracing analysis. Our data indicate acute phase infection, highly likely transmission links, number particles transmitted from one host another (bottleneck size) is large enough propagate iSNVs among individuals. Furthermore, demonstrate that, during outbreaks when are identical, it possible reconstruct chains by investigations iSNVs. Specifically, found identify limiting analysis only three well‐conserved genes, namely nsp2, ORF3, ORF7.

Language: Английский

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Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 6, 2023

Abstract Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases inform design of interventions. Methods that jointly estimate reproduction number R dispersion parameter k have however mainly remained limited analysis epidemiological clusters or contact tracing data, whose collection often proves difficult. Here, we show identical sequences are imprinted pathogen offspring distribution, derive an analytical formula for distribution size these clusters. We develop evaluate a novel inference framework from sequences. then illustrate its application across range situations. Finally, hypothesis testing relying on determine whether given genetic subpopulation associated with increased reduced transmissibility. Our work provides new tools without building phylogenetic tree, thus making it easily scalable large genome datasets. Significance statement For many diseases, small fraction individuals has been documented disproportionately contribute onward spread. Characterizing extent superspreading step towards implementation efficient Despite relevance, remains difficult quantify heterogeneity. present harnessing parameter. also can be used advantage variant. This better characterize spread pathogens their control.

Language: Английский

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SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(4)

Published: June 1, 2023

Co-infection with at least 2 strains of virus is the prerequisite for recombination, one means genetic diversification. Little known about prevalence these events in SARS-CoV-2, partly because it difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology sequence whole genomes and targeted regions haplotyping. identified 17 co-infections SARS-CoV-2 belonging different clades 6829 samples sequenced between January October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron 14 Omicron/Omicron (4 cases 21K/21L, 1 case 21L/22A, 21L/22B, 4 22A/22B, 22B/22C 22B/22E). Four patients (24%) also harbored recombinant minor haplotypes, including a that was selected viral quasispecies over course his chronic infection. While remain rare among SARS-CoV-2-infected individuals, SMRT useful tool detecting them as well events, providing basis assessing their clinical impact, precise indicator epidemic evolution. IMPORTANCE variants have been responsible successive waves infection years pandemic. co-infection followed by recombination driver evolution, there few reports co-infections, mainly Delta Omicron or first 21K_BA.1 21L_BA.2. The we detected during included recent 22A, 22B, 22C, 22E; 24% variants. This study shows suited genomic surveillance.

Language: Английский

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Modelling COVID-19 mutant dynamics: understanding the interplay between viral evolution and disease transmission dynamics

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 4, 2024

Abstract Understanding virus mutations is critical for shaping public health interventions. These lead to complex multi-strain dynamics often underrepresented in models. Aiming understand the factors influencing variants’ fitness and evolution, we explore several scenarios of spreading gain qualitative insight into dictating which variants ultimately predominate at population level. To this end, propose a two-strain stochastic model that accounts asymptomatic transmission, mutations, possibility disease import. We find with milder symptoms are likely spread faster than those severe symptoms. This because can prompt affected individuals seek medical help earlier, potentially leading quicker identification isolation cases. However, or cases may more widely, making it harder control spread. Therefore, increased transmissibility still result higher hospitalizations fatalities due widespread infection. The proposed highlights interplay between viral evolution transmission dynamics. Offering nuanced view variant spread, provides foundation further investigation mitigating strategies

Language: Английский

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