Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 15, 2024

Abstract Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis more than 2 million raw read datasets submitted to European COVID-19 Data Portal identify recombination. Co-infection was observed in 0.35% investigated cases. Two independent procedures were implemented detect We show that sensitivity is predominantly determined by density lineage-defining mutations along genome, thus used an expanded list mutually exclusive defining specific variant combinations increase statistical power. call attention multiple challenges rendering detection difficult provide guidelines reduction false positives arising from chimeric sequences produced during PCR amplification. Additionally, three recombination hotspots Delta – Omicron BA.1 recombinants.

Language: Английский

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Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(24), P. 17184 - 17184

Published: Dec. 6, 2023

Shortly after the beginning of SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor circulation virus in population. A fundamental part these surveillance programs is variant tracking through sequencing approaches and identify new variants or mutations that may be importance. Two main platforms are Illumina Oxford Nanopore Technologies. Here, we compare performance MiSeq (Illumina) MinION (Oxford Technologies), as well two different data processing pipelines, determine effect they have on results. showed higher coverage, lower error rate, better capacity detect accurately estimate abundances than R9.4.1 flow cell data. The use callers (LoFreq iVar) calculate proportions had a remarkable impact results generated from wastewater samples. Freyja, coupled with iVar, more sensitive accurate LoFreq, especially data, but it comes at cost having rate. analysis R10.4.1 using Freyja combined iVar narrows gap terms read quality, accuracy, sensitivity, number detected mutations. Although should still considered standard method for tracking, MinION's versatility rapid turnaround time represent clear advantage during ongoing pandemic.

Language: Английский

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Hybrid sequencing for detailed genetic characterization of human adenoviruses

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 27, 2024

Human adenoviruses (HAdVs) are highly contagious and have significant clinical implications in the pediatric population. In present study, we employed a combination of long-read sequencing short-read to accurately reconstruct 32 genomes HAdVs. The phylogenetic analyses based on whole genome genes revealed distinct sub-clusters within HAdV-B -E. For HAdV-C, trees constructed from hexon, fiber, E3 gene sequences consistently matched whole-genome phylogeny, reflecting high sequence diversity these regions. Notably, regions with diversity, observed higher number recombination breakpoints lower GC content. Additionally, E4 region HAdV-C exhibited Ka/Ks ratio > 1, indicating that positive selection may be driving fixation advantageous mutations. These genetic characterization crucial for enhancing future surveillance HAdVs, facilitating more strategic proactive approach monitoring their evolution, epidemiological trends.

Language: Английский

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From viral democratic genomes to viral wild bunch of quasispecies

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(11)

Published: Nov. 1, 2023

The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the most frequently found clinical samples patients but do not account for huge genetic diversity coexisting genomes, which is better described as quasispecies. A viral quasispecies defined dynamic distribution nonidentical closely related mutants, variants, recombinant, reassortant Viral have collective behavior dynamics subject internal interactions that comprise interference, complementation, cooperation. In setting SARS-CoV-2 infection, intrahost was recently notably reported immunocompromised, chronically infected patients, treated with monoclonal antibodies targeting spike protein, different body compartments a single patient. question deserves attention whether such generated postinfection clonal genome response to selection pressure already present at time infection review, we summarize data supporting hosts by "wild bunch" rather than multiple virions sharing same genome. Each virion may virulence tissue tropisms. As number replicated during host infections huge, any wide also influenced host-specific after accounts difficulty deciphering predicting appearance more fit variants evolution epidemics novel viruses.

Language: Английский

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