Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing

Article Multidisciplinary Sciences

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

Sandile Cele et al.

Summary: The study found that the Omicron variant has reduced neutralizing effectiveness in individuals vaccinated with Pfizer BNT162b2, but those who had previously been infected with SARS-CoV-2 showed better neutralization against Omicron.

NATURE (2022)

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Review Environmental Sciences

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Warish Ahmed et al.

Summary: Monitoring pathogens like SARS-CoV-2 in wastewater using RT-PCR is effective for public health information, but there is a lack of standardized protocols for wastewater surveillance. Key strategies for improving accuracy include QA/QC measures, representative sampling, virus concentration, and clear data interpretation guidelines.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

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Article Multidisciplinary Sciences

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Smruthi Karthikeyan et al.

Summary: This study addresses the limitations of wastewater-based genomic surveillance by developing improved concentration protocols and deconvolution software. The researchers successfully detected emerging variants of SARS-CoV-2 in wastewater samples earlier than clinical genomic surveillance and identified instances of virus spread not captured by clinical testing. This scalable solution allows for early detection of variants and identification of hidden transmission.

NATURE (2022)

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Article Microbiology

Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

Katharina Jahn et al.

Summary: Genomic sequencing of wastewater samples can provide early detection and surveillance of SARS-CoV-2 variants. The COJAC bioinformatics method based on variant-specific signature mutations is a robust indicator of low-frequency variants. Analysis of multiple wastewater samples allows for estimation of variant prevalence and transmission fitness advantage.

NATURE MICROBIOLOGY (2022)

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Article Microbiology

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

Alexander Crits-Christoph et al.

Summary: Viral genome sequencing, including from wastewater, provides valuable insights into the spread and genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. By analyzing sewage samples, researchers can track specific viral strains and potential introductions of new lineages before they are identified through clinical sequencing.

MBIO (2021)

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Article Microbiology

Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021

Thomas Wilton et al.

Summary: This study highlights the importance of environmental surveillance in early detection of emerging SARS-CoV-2 variants and provides insights into the potential impact of these variants on human immune response and vaccine efficacy. The detection and rapid spread of variant B.1.1.7 in sewage samples from London serves as an early warning system for monitoring variant prevalence in the population. Additionally, this method can also detect other variants of concern carrying critical spike mutations, such as B.1.351 and P.1.

MSYSTEMS (2021)

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Article Medicine, General & Internal

Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

Swapnil Mishra et al.

Summary: Since late March 2021, the percentage of non-B.1.1.7 variants has been increasing in London and other English regions, driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. The competition between variants and the rise of non-B.1.1.7 variants underscore the importance of diverse data sources in community surveillance for early detection of new variants.

ECLINICALMEDICINE (2021)

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Article Immunology

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Ray Izquierdo-Lara et al.

Summary: This study evaluated the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium using sewage samples, identifying the presence of prevalent clades and clustering of sewage samples with clinical samples from the same region. Additionally, novel mutations in the SARS-CoV-2 genome were detected, illustrating the potential of wastewater surveillance in tracking virus diversity and new outbreaks.

EMERGING INFECTIOUS DISEASES (2021)

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Article Multidisciplinary Sciences