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

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

“…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.…”

“…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).…”

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

“…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).…”