A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory

Mwangi, Peter N.; Mogotsi, Milton T.; Ogunbayo, Ayodeji E.; Mooko, Teboho; Maringa, Wairimu M; Sondlane, Hlengiwe; Nkwadipo, Kelebogile; Adelabu, Olusesan Adeyemi; Bester, Philip Armand; Goedhals, Dominique; Nyaga, Martin M.

doi:10.1007/s00705-022-05411-z

Cited by 3 publications

(5 citation statements)

References 14 publications

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“…As sample crossover has already been reported with sequencing protocols on the Illumina platform, 27 decontamination strategies are clearly important. 28 …”

Section: Discussionmentioning

confidence: 99%

“…Further investigations were not possible due to the low genome coverage and low read depth obtained with both protocols. As sample crossover has already been reported with sequencing protocols on the Illumina platform, 27 decontamination strategies are clearly important 28 …”

Section: Discussionmentioning

confidence: 99%

“…As sample crossover has already been reported with sequencing protocols on the Illumina platform, 27 decontamination strategies are clearly important. 28 The target capture protocol was more sensitive than the amplicon protocol. In fact, a higher number of samples were successfully sequenced on the whole genome, a higher number of sequences had a genome coverage >95% (the minimum coverage value recommended by ECDC 26 ) and a higher S gene coverage was observed for samples with C t > 17.…”

Section: Comparison Of the Spike Sequences Obtained With The Two Methodsmentioning

confidence: 99%

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Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

Nicot¹,

Trémeaux²,

Latour³

et al. 2022

Journal of Medical Virology

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Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) genome. Single‐molecule real‐time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole‐genome sequencing (WGS) of SARS‐CoV‐2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher ( p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3–99.5]) than with the amplicon protocol (99.3% [IQR: 69.9–99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for C t values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on C t values, higher S gene coverage with the target capture protocol was observed only for samples with C t > 17 ( p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS‐CoV‐2.

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“…As sample crossover has already been reported with sequencing protocols on the Illumina platform, 27 decontamination strategies are clearly important. 28 …”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Comparison Of the Spike Sequences Obtained With The Two Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

Nicot¹,

Trémeaux²,

Latour³

et al. 2022

Journal of Medical Virology

View full text Add to dashboard Cite

show abstract

“…(4) The risk of contamination during laboratory procedures also cannot be overlooked. The accidental mixing of samples (especially during the time of emergence of a new variant) prepared for sequencing can create the effect of co-infection in the resulting dataset 28 – 31 .…”

Section: Introductionmentioning

confidence: 99%

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

Pipek,

Medgyes-Horváth,

Stéger

et al. 2024

Nat Commun

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

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“…The risk of contamination during laboratory procedures also cannot be overlooked. The accidental mixing of samples (especially during the time of emergence of a new variant) prepared for sequencing can create the effect of coinfection in the resulting dataset [29][30][31][32] .…”

Section: Introductionmentioning

confidence: 99%

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

Medgyes-Horváth

Pipek

Stéger

et al. 2023

Preprint

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A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory

Cited by 3 publications

References 14 publications

Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

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

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

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