Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows

Abstract Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine surveillance of SARS-CoV-2 cases, as with all other respiratory viruses. Surveillance remains of paramount importance to prevent a...

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Published in:	Bioinformatics (Oxford, England) Vol. 41; no. 10
Main Authors:	Kogoj, Rok, Petrillo, Mauro, Zakotnik, Samo, Suljič, Alen, Korva, Miša, Leoni, Gabriele
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01.10.2025 Oxford Publishing Limited (England)
Subjects:	Bioinformatics Computational Biology - methods Conserved sequence COVID-19 COVID-19 - virology Frameshift mutation Frameshifting, Ribosomal Genome, Viral High-Throughput Nucleotide Sequencing Humans Laboratories Mutation Nucleocapsids Pandemics SARS-CoV-2 - genetics Sequences Severe acute respiratory syndrome coronavirus 2 Surveillance Viral diseases Workflow
ISSN:	1367-4803, 1367-4811, 1367-4811
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Abstract	Abstract Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine surveillance of SARS-CoV-2 cases, as with all other respiratory viruses. Surveillance remains of paramount importance to prevent a further SARS-CoV-2 surge, as the virus has been shown to mutate rapidly and can render available drugs and vaccines ineffective. During the pandemic, several bioinformatics pipelines and workflows have been developed to streamline analysis, shorten turnaround time and ensure reproducibility. As the number of samples decreases, laboratories are moving towards more flexible sequencing strategies and optimizing the cost per sample. However, workflow redesigns, even if individual steps have proven successful time and time again, can lead to challenges when changes in a bioinformatics pipeline are introduced (e.g. version updates, implementation of new features, etc.), a new combination of viral mutations emerge or a change in wet-lab procedures leads to unpredictable results. Here, we present a report of misidentified frameshift mutations in the consensus sequence of SARS-CoV-2, which led to an incorrect assumption of mutations in the spike and nucleocapsid viral proteins with the potential to affect PCR detection or even antigen testing. This investigation exemplifies the need for better awareness of the challenges that can occur even when using routinely applied protocols and analytical workflows and highlights the need for cooperation between experts of NGS, bioinformaticians and decision-makers towards more harmonized data workflows.
AbstractList	Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine surveillance of SARS-CoV-2 cases, as with all other respiratory viruses. Surveillance remains of paramount importance to prevent a further SARS-CoV-2 surge, as the virus has been shown to mutate rapidly and can render available drugs and vaccines ineffective. During the pandemic, several bioinformatics pipelines and workflows have been developed to streamline analysis, shorten turnaround time and ensure reproducibility. As the number of samples decreases, laboratories are moving towards more flexible sequencing strategies and optimizing the cost per sample. However, workflow redesigns, even if individual steps have proven successful time and time again, can lead to challenges when changes in a bioinformatics pipeline are introduced (e.g. version updates, implementation of new features, etc.), a new combination of viral mutations emerge or a change in wet-lab procedures leads to unpredictable results. Here, we present a report of misidentified frameshift mutations in the consensus sequence of SARS-CoV-2, which led to an incorrect assumption of mutations in the spike and nucleocapsid viral proteins with the potential to affect PCR detection or even antigen testing. This investigation exemplifies the need for better awareness of the challenges that can occur even when using routinely applied protocols and analytical workflows and highlights the need for cooperation between experts of NGS, bioinformaticians and decision-makers towards more harmonized data workflows. Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine surveillance of SARS-CoV-2 cases as with all other respiratory viruses. Surveillance remains of paramount importance to prevent a further SARS-CoV-2 surge, as the virus has been shown to mutate rapidly and can render available drugs and vaccines ineffective. During the pandemic, several bioinformatics pipelines and workflows have been developed to streamline analysis, shorten turn-around time and ensure reproducibility. As the number of samples decreases, laboratories are moving towards more flexible sequencing strategies and optimising the cost per sample. However, workflow redesigns, even if individual steps have proven successful time and time again, can lead to challenges when changes in a bioinformatics pipeline are introduced (e.g., version updates, implementation of new features, etc.), a new combination of viral mutations emerge or, a change in wet-lab procedures lead to unpredictable results. Here we present a report of misidentified frameshift mutations in the consensus sequence of SARS-CoV-2, which led to an incorrect assumption of mutations in the spike and nucleocapsid viral proteins with the potential to affect PCR detection or even antigen testing. This investigation exemplifies the need for better awareness of the challenges that can occur even when using routinely applied protocols and analytical workflows and highlights the need for cooperation between experts of NGS, bioinformaticians and decision-makers towards more harmonised data workflows.Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine surveillance of SARS-CoV-2 cases as with all other respiratory viruses. Surveillance remains of paramount importance to prevent a further SARS-CoV-2 surge, as the virus has been shown to mutate rapidly and can render available drugs and vaccines ineffective. During the pandemic, several bioinformatics pipelines and workflows have been developed to streamline analysis, shorten turn-around time and ensure reproducibility. As the number of samples decreases, laboratories are moving towards more flexible sequencing strategies and optimising the cost per sample. However, workflow redesigns, even if individual steps have proven successful time and time again, can lead to challenges when changes in a bioinformatics pipeline are introduced (e.g., version updates, implementation of new features, etc.), a new combination of viral mutations emerge or, a change in wet-lab procedures lead to unpredictable results. Here we present a report of misidentified frameshift mutations in the consensus sequence of SARS-CoV-2, which led to an incorrect assumption of mutations in the spike and nucleocapsid viral proteins with the potential to affect PCR detection or even antigen testing. This investigation exemplifies the need for better awareness of the challenges that can occur even when using routinely applied protocols and analytical workflows and highlights the need for cooperation between experts of NGS, bioinformaticians and decision-makers towards more harmonised data workflows. Abstract Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine surveillance of SARS-CoV-2 cases, as with all other respiratory viruses. Surveillance remains of paramount importance to prevent a further SARS-CoV-2 surge, as the virus has been shown to mutate rapidly and can render available drugs and vaccines ineffective. During the pandemic, several bioinformatics pipelines and workflows have been developed to streamline analysis, shorten turnaround time and ensure reproducibility. As the number of samples decreases, laboratories are moving towards more flexible sequencing strategies and optimizing the cost per sample. However, workflow redesigns, even if individual steps have proven successful time and time again, can lead to challenges when changes in a bioinformatics pipeline are introduced (e.g. version updates, implementation of new features, etc.), a new combination of viral mutations emerge or a change in wet-lab procedures leads to unpredictable results. Here, we present a report of misidentified frameshift mutations in the consensus sequence of SARS-CoV-2, which led to an incorrect assumption of mutations in the spike and nucleocapsid viral proteins with the potential to affect PCR detection or even antigen testing. This investigation exemplifies the need for better awareness of the challenges that can occur even when using routinely applied protocols and analytical workflows and highlights the need for cooperation between experts of NGS, bioinformaticians and decision-makers towards more harmonized data workflows.
Author	Leoni, Gabriele Suljič, Alen Korva, Miša Kogoj, Rok Zakotnik, Samo Petrillo, Mauro
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Cites_doi	10.1016/j.xgen.2021.100085 10.1038/nbt.3820 10.3389/fviro.2022.971862 10.2807/1560-7917.ES.2017.22.13.30494 10.1038/s41586-021-03402-9 10.1038/s41579-020-0421-0 10.1186/s12859-025-06091-7 10.1093/bioinformatics/btad728 10.3390/v15010206 10.1128/JVI.00119-21 10.1093/infdis/jiab368 10.1093/nar/gkae410 10.1371/journal.pcbi.1010752 10.1093/gbe/evad020 10.1016/j.sjbs.2022.103372 10.1158/0008-5472.CAN-17-0337
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References	Hagag (2025102706520654700_btaf516-B8) 2022; 2 Ferreira (2025102706520654700_btaf516-B6) 2021; 224 Marchini (2025102706520654700_btaf516-B12) 2023; 15 Constantinides (2025102706520654700_btaf516-B3) 2023; 39 Di Tommaso (2025102706520654700_btaf516-B5) 2017; 35 Lo (2025102706520654700_btaf516-B10) 2020; 18 Robinson (2025102706520654700_btaf516-B13) 2017; 77 Shu (2025102706520654700_btaf516-B15) 2017; 22 Manjunath (2025102706520654700_btaf516-B11) 2022; 29 Authority (EFSA), E.F.S (2025102706520654700_btaf516-B1) 2022; 19 Davies (2025102706520654700_btaf516-B4) 2021; 372 Chang (2025102706520654700_btaf516-B2) 2023; 15 Schatz (2025102706520654700_btaf516-B14) 2022; 2 World Health Organization (2025102706520654700_btaf516-B18) 2022 Zhang (2025102706520654700_btaf516-B19) 2025; 26 Hiltemann (2025102706520654700_btaf516-B9) 2023; 19 Tegally (2025102706520654700_btaf516-B16) 2021; 592 Galaxy Community (2025102706520654700_btaf516-B7) 2024; 52 Voloch (2025102706520654700_btaf516-B17) 2021; 95
References_xml	– volume: 2 start-page: 100085 year: 2022 ident: 2025102706520654700_btaf516-B14 article-title: Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space publication-title: Cell Genom. doi: 10.1016/j.xgen.2021.100085 – volume: 35 start-page: 316 year: 2017 ident: 2025102706520654700_btaf516-B5 article-title: Nextflow enables reproducible computational workflows publication-title: Nat Biotechnol doi: 10.1038/nbt.3820 – volume: 2 start-page: 971862 year: 2022 ident: 2025102706520654700_btaf516-B8 article-title: Mutations in SARS-CoV-2 nucleocapsid in variants of concern impair the sensitivity of SARS-CoV-2 detection by rapid antigen tests publication-title: Front Virol doi: 10.3389/fviro.2022.971862 – volume: 22 start-page: 30494 year: 2017 ident: 2025102706520654700_btaf516-B15 article-title: GISAID: global initiative on sharing all influenza data—from vision to reality publication-title: Eurosurveillance doi: 10.2807/1560-7917.ES.2017.22.13.30494 – volume: 372 start-page: eabg3055 year: 2021 ident: 2025102706520654700_btaf516-B4 article-title: Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England publication-title: Science (1979) – volume: 592 start-page: 438 year: 2021 ident: 2025102706520654700_btaf516-B16 article-title: Detection of a SARS-CoV-2 variant of concern in South Africa publication-title: Nature doi: 10.1038/s41586-021-03402-9 – volume: 18 start-page: 478 year: 2020 ident: 2025102706520654700_btaf516-B10 article-title: Genomics and epidemiological surveillance publication-title: Nat Rev Microbiol doi: 10.1038/s41579-020-0421-0 – volume: 26 start-page: 78 year: 2025 ident: 2025102706520654700_btaf516-B19 article-title: GoldPolish-target: targeted long-read genome assembly polishing publication-title: BMC Bioinformatics doi: 10.1186/s12859-025-06091-7 – volume: 39 start-page: btad728 year: 2023 ident: 2025102706520654700_btaf516-B3 article-title: Hostile: accurate decontamination of microbial host sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/btad728 – volume: 15 start-page: 206 year: 2023 ident: 2025102706520654700_btaf516-B12 article-title: New RT-PCR assay for the detection of current and future SARS-CoV-2 variants publication-title: Viruses doi: 10.3390/v15010206 – volume: 95 start-page: e00119 year: 2021 ident: 2025102706520654700_btaf516-B17 article-title: Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil publication-title: J. Virol doi: 10.1128/JVI.00119-21 – year: 2022 ident: 2025102706520654700_btaf516-B18 – volume: 224 start-page: 989 year: 2021 ident: 2025102706520654700_btaf516-B6 article-title: SARS-CoV-2 B.1.617 mutations L452R and E484Q are not synergistic for antibody evasion publication-title: J. Infect. Dis doi: 10.1093/infdis/jiab368 – volume: 52 start-page: W83 year: 2024 ident: 2025102706520654700_btaf516-B7 article-title: The galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update publication-title: Nucleic Acids Res doi: 10.1093/nar/gkae410 – volume: 19 start-page: e1010752 year: 2023 ident: 2025102706520654700_btaf516-B9 article-title: Galaxy training: a powerful framework for teaching! publication-title: PLoS Comput. Biol doi: 10.1371/journal.pcbi.1010752 – volume: 19 start-page: E200506E year: 2022 ident: 2025102706520654700_btaf516-B1 article-title: Theme (concept) paper—application of OMICS and BIOINFORMATICS approaches: towards next generation risk assessment publication-title: EFSA Support. Publ – volume: 15 start-page: evad020 year: 2023 ident: 2025102706520654700_btaf516-B2 article-title: polishCLR: a nextflow workflow for polishing PacBio CLR genome assemblies publication-title: Genome Biol Evol doi: 10.1093/gbe/evad020 – volume: 29 start-page: 103372 year: 2022 ident: 2025102706520654700_btaf516-B11 article-title: A comprehensive review on Covid-19 Omicron (B.1.1.529) variant publication-title: Saudi J Biol Sci doi: 10.1016/j.sjbs.2022.103372 – volume: 77 start-page: e31 year: 2017 ident: 2025102706520654700_btaf516-B13 article-title: Variant review with the integrative genomics viewer publication-title: Cancer Res doi: 10.1158/0008-5472.CAN-17-0337
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Snippet	Abstract Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples... Five years after the outbreak of the SARS-CoV-2 pandemic in 2020, diagnostic laboratories have moved from massive sequencing of thousands of samples to routine...
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SubjectTerms	Bioinformatics Computational Biology - methods Conserved sequence COVID-19 COVID-19 - virology Frameshift mutation Frameshifting, Ribosomal Genome, Viral High-Throughput Nucleotide Sequencing Humans Laboratories Mutation Nucleocapsids Pandemics SARS-CoV-2 - genetics Sequences Severe acute respiratory syndrome coronavirus 2 Surveillance Viral diseases Workflow
Title	Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows
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