Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program

Goswami, Chirayu; Sheldon, Michael; Bixby, Christian; Keddache, Mehdi; Bogdanowicz, Alexander; Wang, Yihe; Schultz, Jonathan; McDevitt, Jessica; LaPorta, James; Kwon, Elaine; Buyske, Steven; Garbolino, Dana; Biloholowski, Glenys; Pastuszak, Alex; Storella, Mary; Bhalla, Amit; Charlier-Rodriguez, Florence; Hager, Russ; Grimwood, Robin; Nahas, Shareef

doi:10.1186/s12879-022-07374-7

Cited by 26 publications

(19 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In our study, the RT-LAMP method was able to differentiate samples with Ct up to ≤ 22.93. Samples with lower Ct are preferred for sequencing as they correlate with higher coverages, thus allowing better identification of samples 36 . Therefore, the RT-LAMP presented in this study could be used as a screening method in places with a low sequencing capacity.…”

Section: Discussionmentioning

confidence: 99%

Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers

Santos

Silva

Júnior

et al. 2022

Sci Rep

View full text Add to dashboard Cite

Despite the advance of vaccination worldwide, epidemic waves caused by more transmissible and immune evasive genetic variants of SARS-CoV-2 have sustained the ongoing pandemic of COVID-19. Monitoring such variants is expensive, as it usually relies on whole-genome sequencing methods. Therefore, it is necessary to develop alternatives that could help identify samples from specific variants. Reverse transcription loop-mediated isothermal amplification is a method that has been increasingly used for nucleic acid amplification, as it is cheaper and easier to perform when compared to other molecular techniques. As a proof of concept that can help distinguish variants, we present an RT-LAMP assay capable of detecting samples carrying a group of mutations that can be related to specific SARS-CoV-2 lineages, here demonstrated for the Variant of Concern Gamma. We tested 60 SARS-CoV-2 RNA samples extracted from swab samples and the reaction showed a sensitivity of 93.33%, a specificity of 88.89% and a kappa value of 0.822 for samples with a Ct ≤ 22.93. The RT-LAMP assay demonstrated to be useful to distinguish VOC Gamma and may be of particular interest as a screening approach for variants in countries with poor sequencing coverage.

show abstract

Section: Discussionmentioning

confidence: 99%

Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers

Santos

Silva

Júnior

et al. 2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Metagenomic NGS was used to sequence the complete SARS‐CoV‐2 genome early in the pandemic. 15 Since then, multiplex amplicon or hybrid capture‐based methods have been developed to run on the Illumina 16 , 17 , 18 , 19 and ONT platforms. 16 , 20 Illumina sequencing devices are commonly used; they generate accurate, high‐quality sequences.…”

Section: Introductionmentioning

confidence: 99%

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

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.

show abstract

“…The effectiveness of molecular surveillance as a tool for monitoring pandemics is dependent on continuous and consistent sampling through time and space, rapid virus genome sequencing, and rapid reporting ( 5 ). Enhancing genomic surveillance and sequencing efforts across the globe is a valuable tool to detect and understand emerging variants ( 6 ), and genomics-based SARS-CoV-2 surveillance is a helpful tool for monitoring the current and future phases of the COVID-19 pandemic ( 7 ).…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

et al. 2022

View full text Add to dashboard Cite

Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics.

show abstract

Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program

Cited by 26 publications

References 24 publications

Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers

Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers

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

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

Contact Info

Product

Resources

About