Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region DOI Creative Commons
Jianxian Sun, Minqing Ivy Yang, Jiaxi Peng

et al.

Water Research X, Journal Year: 2024, Volume and Issue: 22, P. 100221 - 100221

Published: Jan. 1, 2024

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between biomarkers noticed by independent studies these methods since late 2021. reason is presumed be due mutations targeted N1 probe. In this study, we systematically investigated unequivocally confirmed that underlying for was probe target, single mutation could cause significant drop signal. We first proportion related wastewater samples (Jan 2021-Dec 2022) nested PCR LC-MS. Based on relative proportions alleles, separated data into four time periods corresponding different variant waves: Period I (Alpha Delta waves with 0 mutation), II (BA.1/BA.2 found all Omicron strains), III (BA.5.2* wave mutations), IV (BQ.1* mutations). Significantly lower copies N2 from Periods II-IV compared those observed wastewater. To further pinpoint extent which each impacted quantification, response among synthetic oligomers mutations. This study highlighted impact even just one or qPCR-based SARS-CoV-2.

Language: Английский

Group A Streptococcus pyogenes in wastewater: Applicability of wastewater-based epidemiology for monitoring the prevalence of GAS pharyngitis during the late COVID-19 pandemic phase DOI Creative Commons
Sadhana Shrestha, Bikash Malla, Eiji Haramoto

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 928, P. 172447 - 172447

Published: April 14, 2024

Streptococcus pyogenes, Group A (GAS), is a human pathogen that causes spectrum of diseases from mild to severe, including GAS pharyngitis, common acute respiratory disease in developed countries. Although wastewater-based epidemiology (WBE) has been extensively used monitor viral pathogens such as severe syndrome coronavirus 2, its applicability S. pyogenes remains unexplored. This study was conducted investigate the feasibility detecting and quantifying wastewater by quantitative polymerase chain reaction (qPCR) evaluate WBE for monitoring prevalence pharyngitis. total 52 grab influent samples were collected treatment plant Japan once week between March 2023 February 2024. The centrifuged, followed nucleic acid extraction qPCR pyogenes-specific genes speB spy1258. Of samples, 90 % 81 positive spy1258 genes, respectively, indicating surveillance. However, percentage quantifiable gene significantly higher winter than spring summer. Similarly, concentrations both (speB, 4.1 ± 0.27 log

Language: Английский

Citations

5
Beyond COVID-19: Wastewater-based epidemiology for multipathogen surveillance and normalization strategies DOI Creative Commons
Bikash Malla, Sadhana Shrestha, Niva Sthapit

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 946, P. 174419 - 174419

Published: July 2, 2024

Wastewater-based epidemiology (WBE) is a critical tool for monitoring community health. Although much attention has focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of disease 2019 (COVID-19), other pathogens also pose significant health risks. This study quantified the presence SARS-CoV-2, influenza A virus (Inf-A), and noroviruses genogroups I (NoV-GI) II (NoV-GII) in wastewater samples collected weekly (n = 170) from July 2023 to February 2024 five treatment plants (WWTPs) Yamanashi Prefecture, Japan, by quantitative PCR. Inf-A RNA exhibited localized prevalence with positive ratios 59 %–82 % different WWTPs, suggesting regional outbreaks within specific areas. NoV-GI (94 %, 160/170) NoV-GII (100 170/170) were highly prevalent, (6.1 ± 0.8 log10 copies/L) consistently exceeding (5.4 0.7 concentrations. SARS-CoV-2 was detected 100 samples, mean concentrations 5.3 0.5 copies/L WWTP E 5.8 0.4 each WWTPs. Seasonal variability evident, higher all pathogenic viruses during winter. Non-normalized normalized fecal indicator bacteria (Escherichia coli total coliforms), an (pepper mild mottle (PMMoV)), turbidity revealed associations reported cases. + GII showed strong correlations gastroenteritis cases, particularly when E. (Spearman's ρ 0.70–0.81) coliforms (ρ 0.70–0.81), respectively. For non-normalized correlation 0.61, decreasing 0.31 PMMoV, that PMMoV unsuitable. Turbidity normalization yielded suboptimal results. underscored importance selecting suitable parameters tailored accurate trend using WBE, demonstrating its utility beyond COVID-19 surveillance.

Language: Английский

Citations

5
6-plex Crystal Digital PCR® for comprehensive surveillance of respiratory and foodborne bacterial pathogens in wastewater DOI Creative Commons
Sadhana Shrestha, Bikash Malla, Eiji Haramoto

et al.

Environmental Pollution, Journal Year: 2025, Volume and Issue: unknown, P. 126298 - 126298

Published: April 1, 2025

Language: Английский

Citations

0
Prevalence of hepatitis A and E viruses in wastewater in Asian countries DOI Creative Commons

Sunayana Raya,

Sarmila Tandukar,

Hari Prasad Kattel

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 951, P. 175473 - 175473

Published: Aug. 12, 2024

Hepatitis A and E viruses (HAV HEV, respectively) remain a significant global health concern despite advancements in healthcare vaccination programs. Regular monitoring vaccine efficacy of HAV are still lacking different countries. This study aimed to investigate HEV prevalence developed, developing, least-developed Asian countries using wastewater as surveillance tool. total 232 untreated samples were collected from six treatment plants, sewage plant, or an open drainage [Nepal (n = 51), Indonesia 37), Thailand 30), Vietnam 27), the Philippines 17), Japan 70)] between April October 2022. Viruses concentrated by simple centrifugation polyethylene glycol precipitation method, followed viral RNA extraction reverse transcription-quantitative polymerase chain reaction. detected Nepal (51 % for 2 HEV), (3 both viruses), (1 24 HEV). Only was found 11 Indonesia, whereas only Philippines, with positive ratio 15 12 %, respectively. These results highlighted geographic variability prevalence, underscoring need localized public strategies address specific hepatitis challenges each country.

Language: Английский

Citations

3
Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region DOI Creative Commons
Jianxian Sun, Minqing Ivy Yang, Jiaxi Peng

et al.

Water Research X, Journal Year: 2024, Volume and Issue: 22, P. 100221 - 100221

Published: Jan. 1, 2024

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between biomarkers noticed by independent studies these methods since late 2021. reason is presumed be due mutations targeted N1 probe. In this study, we systematically investigated unequivocally confirmed that underlying for was probe target, single mutation could cause significant drop signal. We first proportion related wastewater samples (Jan 2021-Dec 2022) nested PCR LC-MS. Based on relative proportions alleles, separated data into four time periods corresponding different variant waves: Period I (Alpha Delta waves with 0 mutation), II (BA.1/BA.2 found all Omicron strains), III (BA.5.2* wave mutations), IV (BQ.1* mutations). Significantly lower copies N2 from Periods II-IV compared those observed wastewater. To further pinpoint extent which each impacted quantification, response among synthetic oligomers mutations. This study highlighted impact even just one or qPCR-based SARS-CoV-2.

Language: Английский

Citations

2