ArticleViruses2021
Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Wastewater-Based Epidemiology of Hepatitis A in Mexico: Temporal Association with Hospital Admissions and Clinical-Environmental Phylogenetic Relatedness.Food and environmental virology · 2026Article
- Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples.Journal of medical virology · 2025Article
- Hepatitis A virus infection.Nature reviews. Disease primers · 2023Review
- SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing.Microbiology spectrum · 2023Article
- Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.Archives of Iranian medicine · 2023Article
- Can the COVID-19 Pandemic Improve the Management of Solid Organ Transplant Recipients?Viruses · 2022Review
- Comparative effects of mRNA vaccine booster and natural Omicron infection on the neutralizing antibody response.The Journal of infection · 2022Article
- Influence of vaccination and prior immunity on the dynamics of Omicron BA.1 and BA.2 sub-variants.The Journal of infection · 2022Article
- Antibody titers and breakthrough infections with Omicron SARS-CoV-2.The Journal of infection · 2022Article
- Impact of Casirivimab-Imdevimab on Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Nasopharyngeal Virus Load and Spike Quasispecies.Open forum infectious diseases · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (
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Registered trials
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