Hyperplex PCR enables the next-generation of wastewater-based surveillance systems: long-term SARS-CoV-2 variant surveillance in Sweden as a case study DOI Open Access
Ruben R. G. Soares,

Javier Edo Varg,

Attila Szabó

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 11, 2024

Abstract Wastewater-based epidemiology aims at measuring pathogens in wastewater as a means of deriving unbiased epidemiological information population scale, ranging from buildings and aircrafts to entire cities or countries. After gaining significant mainstream attention during the SARS-CoV-2 pandemic, field holds promise continuous monitoring early warning system tracking emerging viral variants new with pandemic potential. To expand current toolbox analytical techniques for analysis, we explored use Hyperplex PCR (hpPCR) analyse mutations samples collected weekly up 22 sites across Sweden between October 2022 December 2023. Approximately 900 were tested using dynamic probe panel multiplexity 10-to 18-plex, continuously adapted within 1-2 weeks quantify relevant concern over time. The simultaneously covered deletions, single nucleotide substitutions, well variable regions resorting degeneracy. By analysing all parallel gold standard methods including qPCR two different NGS technologies, performance hpPCR is herein shown bridge gap these by providing (1) systematic sensitivity simple design, (2) high without re-optimization requirements (3) 4-5-week earlier mutation detection compared excellent quantitative linearity good correlation frequency (r=0.88). Based on demonstrated performance, authors propose combined routine discovery high-frequency key pathogens/variants potential alternative analysis paradigm.

Язык: Английский

Comparison of RT-ddPCR and RT-qPCR platforms for SARS-CoV-2 detection: Implications for future outbreaks of infectious diseases DOI Creative Commons
Jiahui Ding, Xiaoqing Xu, Yu Deng

и другие.

Environment International, Год журнала: 2024, Номер 183, С. 108438 - 108438

Опубликована: Янв. 1, 2024

The increased frequency of human infectious disease outbreaks caused by RNA viruses worldwide in recent years calls for enhanced public health surveillance better future preparedness. Wastewater-based epidemiology (WBE) is emerging as a valuable epidemiological tool providing timely population-wide prevention and response complementary to the current clinical system. Here, we compared analytical performance practical applications between predominant molecular detection methods RT-qPCR RT-ddPCR on SARS-CoV-2 wastewater surveillance. When pure viral was tested, exhibited superior quantification accuracy at higher concentration levels achieved more sensitive with reduced variation low levels. Furthermore, consistently demonstrated robust accurate measurement either background matrix or presence mismatches target regions consensus assay. Additionally, detecting mock variant samples, found that outperformed virus genotyping targeting specific loci signature mutations allele-specific (AS) assays, especially allele frequencies concentrations, which possibility low-prevalence population. Our study provides insights method selection WBE outbreaks.

Язык: Английский

Процитировано

15
Two-step wastewater surveillance reveals co-circulation of respiratory pathogens during the 2023–2024 influenza season in a low-resource setting DOI
Hui Li, Haifeng Li, Xin Du

и другие.

Frontiers of Environmental Science & Engineering, Год журнала: 2025, Номер 19(5)

Опубликована: Март 17, 2025

Язык: Английский

Процитировано

0
High-resolution and real-time wastewater viral surveillance by Nanopore sequencing DOI
Xiaoqing Xu, Yu Deng, Jiahui Ding

и другие.

Water Research, Год журнала: 2024, Номер 256, С. 121623 - 121623

Опубликована: Апрель 16, 2024

Язык: Английский

Процитировано

3
Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: long-term SARS-CoV-2 variant surveillance in Sweden as a case study DOI
Ruben R. G. Soares,

Javier Edo Varg,

Attila Szabó

и другие.

Water Research, Год журнала: 2025, Номер 274, С. 123154 - 123154

Опубликована: Янв. 16, 2025

Язык: Английский

Процитировано

0
Hyperplex PCR enables the next-generation of wastewater-based surveillance systems: long-term SARS-CoV-2 variant surveillance in Sweden as a case study DOI Open Access
Ruben R. G. Soares,

Javier Edo Varg,

Attila Szabó

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 11, 2024

Abstract Wastewater-based epidemiology aims at measuring pathogens in wastewater as a means of deriving unbiased epidemiological information population scale, ranging from buildings and aircrafts to entire cities or countries. After gaining significant mainstream attention during the SARS-CoV-2 pandemic, field holds promise continuous monitoring early warning system tracking emerging viral variants new with pandemic potential. To expand current toolbox analytical techniques for analysis, we explored use Hyperplex PCR (hpPCR) analyse mutations samples collected weekly up 22 sites across Sweden between October 2022 December 2023. Approximately 900 were tested using dynamic probe panel multiplexity 10-to 18-plex, continuously adapted within 1-2 weeks quantify relevant concern over time. The simultaneously covered deletions, single nucleotide substitutions, well variable regions resorting degeneracy. By analysing all parallel gold standard methods including qPCR two different NGS technologies, performance hpPCR is herein shown bridge gap these by providing (1) systematic sensitivity simple design, (2) high without re-optimization requirements (3) 4-5-week earlier mutation detection compared excellent quantitative linearity good correlation frequency (r=0.88). Based on demonstrated performance, authors propose combined routine discovery high-frequency key pathogens/variants potential alternative analysis paradigm.

Язык: Английский

Процитировано

0