Rapid Repeat Infection of SARS-CoV-2 by Two Highly Distinct Delta-Sub-Lineage Viruses

Gorzalski, Andrew; Boyles, Christina; Sepcic, Victoria; Verma, Subhash C.; Sevinsky, Joel; Libuit, Kevin; Hooser, Stephanie Van; Pandori, Mark

doi:10.2139/ssrn.3940720

Cited by 2 publications

(3 citation statements)

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“…Briefly, genomic RNA from the specimens were reverse transcribed to cDNA followed by PCR amplification of specific regions (target capture) of the SARS-CoV-2 cDNA. A modified version of the ARTIC v3 primer panel (98 tiled primers in two pools) was used to capture target regions of roughly 400 bp through PCR reactions, as described previously 18 . Before the solid phase reversible immobilization (SPRI) bead cleanup, the resulting amplicons were pooled together to remove unused PCR components and amplicons outside the expected size range.…”

Section: Covid-19 Clinical Specimen Collectionmentioning

confidence: 99%

“…Bioinformatics pipeline for data analysis. FASTQ files generated from the Clear Dx (ClearLabs Inc., Carlos, CA, USA) were analyzed through cloud computing implemented in Terra with pipelines for lineage determination (pangolin), which is updated every 24 to 48 h to accommodate updated lineage defining mutations 18 . FASTQ files generated from the Illumina sequencing were analyzed using SARS-CoV-2 mutations analysis tool of the QIAGEN CLC Genomics Workbench (QIAGEN, Inc., Germantown, MD, USA).…”

Section: Covid-19 Clinical Specimen Collectionmentioning

confidence: 99%

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Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities

Uppal

Hartley

et al. 2022

Sci Rep

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Detection of SARS-CoV-2 viral load in wastewater has been highly informative in estimating the approximate number of infected individuals in the surrounding communities. Recent developments in wastewater monitoring to determine community prevalence of COVID-19 further extends into identifying SARS-CoV-2 variants, including those being monitored for having enhanced transmissibility. We sequenced genomic RNA derived from wastewater to determine the variants of coronaviruses circulating in the communities. Wastewater samples were collected from Truckee Meadows Water Reclamation Facility (TMWRF) from November 2020 to June 2021. SARS-CoV-2 variants resulting from wastewater were compared with the variants detected in infected individuals' clinical specimens (nasal/nasopharyngeal swabs) during the same period and found conclusively in agreement. Therefore, wastewater monitoring for SARS-CoV-2 variants in the community is a feasible strategy as a complementary tool to clinical specimen testing in the latter's absence.

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Section: Covid-19 Clinical Specimen Collectionmentioning

confidence: 99%

Section: Covid-19 Clinical Specimen Collectionmentioning

confidence: 99%

Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities

Uppal

Hartley

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Bioinformatics pipeline for data analysis FASTQ les generated from the Clear Dx (ClearLabs Inc., Carlos, CA, USA) were analyzed through cloud computing implemented in Terra with pipelines for lineage determination (pangolin), which is updated every 24 to 48 h to accommodate updated lineage de ning mutations (Gorzalski et al, 2021). FASTQ les generated from the Illumina sequencing were analyzed using SARS-CoV-2 mutations analysis tool of the QIAGEN CLC Genomics Workbench (QIAGEN, Inc., Germantown, MD, USA).…”

Section: Covid-19 Clinical Specimen Collectionmentioning

confidence: 99%

Detecting SARS-CoV-2 Variants in Wastewater and Their Correlation With Circulating Variants in the Communities

Uppal

Hartley

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Detection of SARS-CoV-2 viral load in wastewater has been highly informative in estimating the approximate number of infected individuals in the surrounding communities. Recent developments in wastewater monitoring to determine community prevalence of COVID-19 further extends into identifying SARS-CoV-2 variants, including those being monitored for having enhanced transmissibility. We sequenced genomic RNA derived from wastewater to determine the variants of coronaviruses circulating in the communities. Wastewater samples were collected from Truckee Meadows Water Reclamation Facility (TMWRF) from November 2021 to June 2021 were analyzed for SARS-CoV-2 variants and were compared with the variants detected in the clinical specimens (nasal/nasopharyngeal swabs) of infected individuals during the same period. The comparison was found to be conclusively in agreement. Therefore, wastewater monitoring for SARS-CoV-2 variants in the community is a feasible strategy both as a complementary tool to clinical specimen testing and in the latter's absence.

show abstract

Rapid Repeat Infection of SARS-CoV-2 by Two Highly Distinct Delta-Sub-Lineage Viruses

Cited by 2 publications

References 0 publications

Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities

Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities

Detecting SARS-CoV-2 Variants in Wastewater and Their Correlation With Circulating Variants in the Communities

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