Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Сен. 23, 2022

ABSTRACT Wastewater SARS-CoV-2 surveillance has been deployed since the beginning of COVID-19 pandemic to monitor dynamics in virus burden local communities. Genomic wastewater, particularly efforts for whole genome sequencing variant tracking or identification, are comparatively challenging due low target concentration, complex microbial and chemical background, lack robust nucleic acid recovery experimental procedures. The intrinsic sample limitations inherent wastewater. In this study, we evaluated impacts from types, certain features, processing methods on outcomes with a specific focus breadth coverage. We collected 184 composite grab wastewater samples Chicago area between March October 2021 quantification genomic surveillance. Samples were processed using mixture reflecting different homogenization intensities (HA+Zymo beads, HA+glass Nanotrap), sequenced two library preparation kits (the Illumina COVIDseq kit QIAseq DIRECT kit). A synthetic RNA experiment was performed validate potential outcomes. Our findings suggested that 1) associated types 2) less intensive method (HA+glass beads), higher coverage (over 80%) N1 concentration > 10 5 cp/L, while qPCR results inconsistent outcomes, 3) kits, rather than extraction features samples, played important roles amplicon sequencing. Overall, extra attention should be paid (e.g., homogenization) sufficient, good quality yield downstream

Язык: Английский

Monitoring SARS-CoV-2 in Municipal Wastewater and Correlation of Results with Covid-19 Cases from Five Municipalities in Ontario, Canada

Опубликована: Янв. 1, 2023

This study investigated the wastewater SARS-CoV-2 RNA signal correlations with community COVID-19 cases and compared results from five municipal treatment plants in Ontario, Canada, monitored October 2021 to April 2022. 24-hour composite samples were collected three times a week at each site analyzed for SARS-CoV-2, using pepper mild mottle virus (PMMoV) as main inhibition control. Viral copies quantified RT-qPCR. Temperature, pH, turbidity, TS, VS, UV-Vis scans measured all samples. was normalized by PMMoV, TS VS. Correlations between case numbers statistically significant sites, showing stronger when comparing data. Results sites ranked based on strength of their statistical correlations, differences potentially attributed sewer characteristics such populations, sizes or types (combined separate).

Язык: Английский

SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron

Biomedicines, Год журнала: 2022, Номер 10(9), С. 2080 - 2080

Опубликована: Авг. 25, 2022

The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. aim this work was characterize genetic variability during the Delta-Omicron shift in patients and a neighboring wastewater treatment plant (WWTP) same urban area. surveillance performed by routine screening positive samples single nucleotide polymorphism analysis within S gene. Moreover, additionally national systematic whole genome sequencing (WGS) once week SARS-CoV-2-positive patients, WGS also applied when mutational profiles were difficult interpret screening. Thus, on 414 respiratory four samples, northeastern France. This allowed us report (i) temporally concordant Delta Omicron wastewaters; (ii) characterization 21J (Delta) 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) mapping composite mutations predicted impact immune properties Spike protein.

Язык: Английский