SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues

Journal of Virology, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

ABSTRACT Defective genomes are part of SARS-CoV-2 quasispecies. High-resolution, ultra-deep sequencing bulk RNA from viral populations does not distinguish mutations, insertions, and deletions in viable those defective genomes. To quantify infectious variant progeny, virus four individual plaques (biological clones) a preparation isolate USA-WA1/2020, formed on Vero E6 cell monolayers, was subjected to further biological cloning yield 9 second-generation 15 third-generation sub-clones. Consensus genomic sequences the clones sub-clones included an average 2.8 variations per genome, relative consensus sequence parental USA-WA1/2020 virus. This value is 6.5-fold lower than estimates for other viruses such as bacteriophage Qβ, foot-and-mouth disease virus, or hepatitis C culture. The mutant spectrum complexity nsp12 (polymerase)- spike (S)-coding region unique progeny each 10 sub-clones; they shared 2.4% total 164 different mutations scored 3,719 residues that were screened. presence minority out-of-frame revealed ease genome production genome. Several low-frequency point clade-discordant typical but served define future clades. Implications adaptability COVID-19 control heterogeneity generation complex spectra discussed. IMPORTANCE Sequencing means identify located distinction particularly important populations, SARS-CoV-2, contain large proportions By sub-clones, we quantified complement be exhibited by viruses. difference may due reduced mutation rate limited tolerance coronavirus incorporate remain functional combination both influences. suggests limitations occupation space SARS-CoV-2. However, rapidly generated suggest aptness confront selective constraints.

Language: Английский

Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Due to the continuous genetic diversification of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) over time, co-circulation two different lineages in same region may lead co-infections within a host, situation known contribute emergence hybrid viral populations through genomic recombination. The aim this study was use genomics-based approach identify distinct SARS-CoV-2 patients with disease 2019 (COVID-19), as an indicator potential and recombination events. cohort included 41,224 serial nasopharyngeal swabs positive for RNA, prospectively collected between January 2021 April 2022 part French national surveillance program. Full-length genomes were sequenced by next-generation sequencing (COVIDseq). Intra-host single nucleotide variants (iSNVs) identified, synthetic generated establish thresholds co-infection detection. Eight hundred sixty-one samples iSNV ratios above threshold considered "potential co-infections." Peaks prevalence occurred during periods variants. Co-infection Variants Concern (VoC) confirmed 103 cases, including Alpha-Beta 12 Alpha-Delta 15 Gamma-Delta 4 Delta-Omicron 35 Omicron BA.1-BA.2 37 cases. In conclusion, our suggests higher variant/subvariant events than that previously reported using conventional approaches, particularly characterized multiple lineages, creating increased risk Our results support premise importance approaches detect virus-infected populations, closely related lineages. We implement innovative monitor diversity human population, circulation VOCs. This focused on detecting highly diverse which are facilitate can potentially new recombinant novel characteristics. Monitoring characterizing cases outbreak is key strategy better understanding evolution, especially epidemic periods. However, challenging, their often underestimated. study, we developed be implemented programs applied large datasets. Concern.

Language: Английский

Design, synthesis, and evaluation of in-house Covid-19 real-time PCR diagnostic kit

Deleted Journal, Journal Year: 2024, Volume and Issue: 29(4), P. 497 - 511

Published: July 1, 2024

Language: Английский