ArticleInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases2021
Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays.
Article in International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
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Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it, 31 citations in OpenAlex.
- Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review.European journal of medical research · 2021Pooled it
- The Spike of SARS-CoV-2: Uniqueness and Applications.Frontiers in immunology · 2021Pooled it
- Examining self-described policy-relevant evidence base for policymaking: an evidence map of COVID-19 literature.BMJ public health · 2024Article
- Article
- Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens.International journal of molecular sciences · 2023Article
- Evaluation of immunoprotection against coronavirus disease 2019: Novel variants, vaccine inoculation, and complications.Journal of pharmaceutical analysis · 2023Review
- Rapid Detection of SARS-CoV-2 Variants of Concern by Genomic Surveillance Techniques.Advances in experimental medicine and biology · 2023Article
- Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern.Journal of proteome research · 2022Article
- Review
- A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic.Frontiers in microbiology · 2022Article
- The Emergence of SARS-CoV-2 Variants With a Lower Antibody Response: A Genomic and Clinical Perspective.Frontiers in medicine · 2022Review
- Article
- SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond.Frontiers in cellular and infection microbiology · 2022Review
- Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol.Frontiers in medicine · 2022Article
- Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019-2022.PloS one · 2022Article
- CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers.Genomics · 2021Article
- Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19.Pathogens (Basel, Switzerland) · 2021Review
- Emerging SARS-CoV-2 variants of concern and potential intervention approaches.Critical care (London, England) · 2021Review
- Evaluation of Strategies to Fight COVID-19: The French Paradigm.Journal of clinical medicine · 2021Article
- Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants.Genes · 2021Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus diseases (C0VID-19) initially reported in Wuhan, China has rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of the disease. Since the virus evolves by accumulating base substitutions, mutations in the viral genome could possibly affect the accuracy of RT-PCR-based detection assays. The recent availability of genomes of SARS-CoV-2 isolates motivated us to assess the presence and potential impact of variations in target sites of the oligonucleotide primers and probes used in molecular diagnosis. We catalogued a total of 132 primer or probe sequences from literature and data available in the public domain. Our analysis revealed that a total of 5862 unique genetic variants mapped to at least one of the 132 primer or probe binding sites in the genome. A total of 29 unique variants were present in ≥ 1% of genomes from at least one of the continents (Asia, Africa, Australia, Europe, North America, and South America) that mapped to 36 unique primers or probes binding sites. Similarly, a total of 27 primer or probe binding sites had cumulative variants frequency of ≥ 1% in the global SARS-CoV-2 genomes. These included primers or probes sites which are used worldwide for molecular diagnosis as well as approved by national and international agencies. We also found 286 SARS-CoV-2 genomic regions with low variability at a continuous stretch of ≥ 20bps that could be potentially used for primer designing. This highlights the need for sequencing genomes of emerging pathogens to enable evidence-based policies for development and approval of diagnostics.
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