4.7 Article

Circulation of SARS-CoV-2 Omicron sub-lineages revealed by multiplex genotyping RT-qPCR assays for sewage surveillance

Related references

Note: Only part of the references are listed.
Article Environmental Sciences

Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA

Rafaela S. Fontenele et al.

Summary: Wastewater-based epidemiology is a non-invasive and cost-effective method for monitoring the spread of pathogens. In this study, a new distance metric and analysis tool were developed to analyze wastewater data and identify viral population changes. The findings showed that wastewater analysis can provide additional insights into viral population dynamics compared to clinical data. These methods have the potential to be applied in future viral outbreak monitoring.

SCIENCE OF THE TOTAL ENVIRONMENT (2023)

Article Virology

Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR

Jeremy A. Garson et al.

Summary: A double-mismatch allele-specific RT-PCR (DMAS-RT-PCR) method was developed to rapidly, simply, and inexpensively identify the Delta variant with high accuracy and reliability, showing concordance with sequencing results; The sensitivity of DMAS-RT-PCR matched that of traditional SARS-CoV-2 RT-qPCR screening, and it successfully genotyped samples that could not be sequenced due to limited virus; This method could be easily implemented in any PCR-capable laboratory, greatly facilitating global monitoring of the spread of the Delta variant.

JOURNAL OF CLINICAL VIROLOGY (2022)

Review Microbiology

Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks

Raphael Nyaruaba et al.

Summary: The ongoing COVID-19 pandemic caused by SARS-CoV-2 has created a global public health crisis. While RT-qPCR is the current gold standard for diagnosis, dPCR has shown to be more effective in detecting low viral loads. Understanding the applications of dPCR will help shape future diagnosis and monitoring of infectious disease outbreaks.

CLINICAL MICROBIOLOGY REVIEWS (2022)

Article Engineering, Environmental

Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance

Xiaoqing Xu et al.

Summary: To effectively control the ongoing outbreaks of fast-spreading SARS-CoV-2 variants, it is urgent to add rapid variant detection and discrimination methods to the existing sewage surveillance systems worldwide. Researchers designed eight assays based on allele-specific RT-qPCR for real-time allelic discrimination of eight SARS-CoV-2 variants in sewage. The assays demonstrated high specificity and sensitivity, and successfully identified and quantified target variants even in sewage samples containing mixtures of SARS-CoV-2 variants. Integration of this method into routine sewage surveillance in Hong Kong showed promising results in detecting the Beta and Delta variants, and also provided real-time discrimination of the emerging Omicron variant.

WATER RESEARCH (2022)

Article Multidisciplinary Sciences

Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5

Qian Wang et al.

Summary: SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 have become dominant in the United States and South Africa, raising concerns about their ability to evade neutralizing antibodies and compromise the efficacy of COVID-19 vaccines and therapeutic monoclonals. A systematic antigenic analysis reveals that BA.2.12.1 and BA.4/5 have different levels of resistance to antibodies, with BA.2.12.1 being modestly resistant and BA.4/5 being substantially resistant. Certain mutations in the spike protein facilitate antibody escape, but compromise the spike affinity for the viral receptor. Only bebtelovimab retains full potency against both subvariants.

NATURE (2022)

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)

Article Multidisciplinary Sciences

BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection

Yunlong Cao et al.

Summary: Omicron sublineages BA.2.12.1, BA.4 and BA.5 have higher transmissibility and increased evasion of neutralizing antibodies compared to the BA.2 lineage. They exhibit similar binding affinities to the ACE2 receptor as BA.2. BA.1 infection after vaccination boosts humoral immune memory against wild-type SARS-CoV-2, but these antibodies are largely evaded by BA.2 and BA.4/BA.5 variants.

NATURE (2022)

Article Environmental Sciences

Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater

Esther G. Lou et al.

Summary: Targeted amplicon sequencing and RT-ddPCR were compared for detecting SARS-CoV-2 variants in wastewater samples. The study found that sequencing had limited sensitivity and missed some mutation detections. Therefore, relying solely on sequencing results for quantitative measurements of variants in wastewater samples is not recommended.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Article Engineering, Environmental

Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Wei Lin Lee et al.

Summary: This article introduces a wastewater monitoring method for tracking the dynamics of SARS-CoV-2 variants in communities. The authors developed an RT-qPCR assay that can quantitatively detect the presence of the Omicron variant in wastewater and validated it through experiments. They found that the Omicron variant rapidly displaced the Delta variant within a short period of time, which is consistent with previous clinical studies and vaccination rates.

WATER RESEARCH (2022)

Article Immunology

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Rabia Johnson et al.

Summary: This study is one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. The research found a strong positive correlation between the viral RNA of SARS-CoV-2 in wastewater samples and clinical cases, demonstrating the importance of wastewater-based epidemiology in monitoring the spread and potential origin of new Omicron sublineages.

JOURNAL OF INFECTIOUS DISEASES (2022)

Letter Infectious Diseases

Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants

Fanchong Jian et al.

LANCET INFECTIOUS DISEASES (2022)

Article Environmental Sciences

From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater

Sebastien Wurtzer et al.

Summary: This study monitored wastewater in the greater Paris area to determine the emergence and dynamics of different variants of concern (VOC) of the SARS-CoV-2 virus. It also analyzed the impact of vaccination strategies on viral circulation and variant selection. The findings suggest a possible decorrelation between incidence and actual virus circulation, possibly due to lower severity of infection in vaccinated populations.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Article Environmental Sciences

Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities

Femi F. Oloye et al.

Summary: Monitoring the communal incidence of COVID-19 is important for decision-making, but relying on a single method may lead to inaccurate results. Wastewater surveillance provides unbiased data that can predict COVID-19 situations in smaller communities.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Article Virology

Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater

Alexander Wilhelm et al.

Summary: Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. In this study, the prevalence of SARS-CoV-2 BA.4/BA.5 was monitored at six wastewater treatment plants in Germany. The study successfully detected and confirmed the presence of BA.4/BA.5 variant using RT-qPCR, SNP-PCR, and RT-dPCR.

VIRUSES-BASEL (2022)

Article Environmental Sciences

Comparison of RT-qPCR and RT-dPCR Platforms for the Trace Detection of SARS-CoV-2 RNA in Wastewater

Warish Ahmed et al.

Summary: This study compared the performance of RT-qPCR and RT-dPCR platforms in detecting SARS-CoV-2 RNA in low-prevalence locations in Queensland, Australia. The results showed that RT-dPCR had a lower limit of detection and a higher detection rate than RT-qPCR in both eluate and pellet samples.

ACS ES&T WATER (2022)

Article Engineering, Environmental

Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Wei Lin Lee et al.

Summary: The study successfully validated a new method for detecting the Omicron variant using wastewater-based monitoring at a wastewater treatment plant in Italy, revealing a rapid displacement trend of the Omicron variant over the Delta variant in wastewater. These data support clinical studies that found the Omicron variant to have an infection advantage in vaccinated populations.

WATER RESEARCH (2022)

Article Immunology

Novel dual multiplex real-time RT-PCR assays for the rapid detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus using the BD MAX open system

Hsing-Yi Chung et al.

Summary: This study evaluated the performance of the BD MAX Open System module for identifying viral pathogens, including SARS-CoV-2, and developed a rapid total nucleic acid extraction method for simultaneous detection of common cold viral pathogens. The BD MAX Platform demonstrated high sensitivity and accuracy for detecting common cold viral pathogens.

EMERGING MICROBES & INFECTIONS (2021)

News Item Critical Care Medicine

New variant of SARS-CoV-2 in UK causes surge of COVID-19

Tony Kirby

LANCET RESPIRATORY MEDICINE (2021)

Article Environmental Sciences

SARS-CoV-2 detection in wastewater using multiplex quantitative PCR

Anna Navarro et al.

Summary: A multiplex RT-qPCR method was developed for simultaneous detection of different SARS-CoV-2 genes. The results showed that the multiplex assay was comparable to single assay in detecting SARS-CoV-2, but faster and cost-effective.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

Article Environmental Sciences

Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater

Leo Heijnen et al.

Summary: Wastewater surveillance using RT-ddPCR for specific detection of the N501Y mutation in SARS-CoV-2 variants has proven to be an effective tool in monitoring the trends and spread of COVID-19 variants in the community, supporting public health decision-making for control measures.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

Article Environmental Sciences

SARS-CoV-2 RNA monitoring in wastewater as a potential early warning system for COVID-19 transmission in the community: A temporal case study

Warish Ahmed et al.

Summary: Detection of SARS-CoV-2 RNA in wastewater can serve as an early warning system to identify viral hotspots and target localized public health responses. This method provides unique information on asymptomatic and pre-symptomatic cases that may not be captured by clinical testing, showing potential for effective disease surveillance.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

Article Engineering, Environmental

RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity

Karin Yaniv et al.

Summary: SARS-CoV-2 variants of concern, including Alpha and Delta, have different impacts on infection rates and vaccine effectiveness. The study found that the Alpha variant dominated during the second morbidity peak, while the Delta variant emerged during the third peak. It also showed that vaccines had higher neutralization efficiency towards the Alpha variant compared to the Delta variant, and that a third vaccine dose improved neutralization against the Delta variant.

WATER RESEARCH (2021)

Article Multidisciplinary Sciences

Development of multiplex real-time RT-PCR assay for the detection of SARS-CoV-2

Huseyin Tombuloglu et al.

Summary: The study developed a multiplex rRT-PCR diagnostic method targeting two viral genes and one human gene, which was validated to be highly consistent with the CDC authorized diagnostic system, providing an accurate diagnostic approach for SARS-CoV-2.

PLOS ONE (2021)

Article Biochemistry & Molecular Biology

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Chantal B. F. Vogels et al.

Summary: With the emergence of SARS-CoV-2 variants with increased transmissibility and immune escape, targeted surveillance is urgently needed. The B.1.1.7 variant can be detected by a specific deletion in the spike gene, but other variants like B.1.351 and P.1 cannot. An open-source PCR assay targeting a deletion in the ORF1a gene has been designed and validated to enhance surveillance for these variants.

PLOS BIOLOGY (2021)

Article Microbiology

Multiplex SARS-CoV-2 Genotyping Reverse Transcriptase PCR for Population-Level Variant Screening and Epidemiologic Surveillance

Hannah Wang et al.

Summary: This study developed a new nucleic acid amplification test to detect SARS-CoV-2 variants with high sensitivity and specificity. Screening a large cohort of infected individuals in the San Francisco Bay Area revealed a rapid increase in the prevalence of the L452R variant over time.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

Article Virology

Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70-and N501Y variants such as B.1.1.7

Dominik Noerz et al.

Summary: New SARS-CoV-2 variants like B.1.1.7 and B.1.351 have raised global concern, highlighting the need for rapid, sensitive, and high-throughput detection methods. This study presents a highly sensitive multiplex PCR assay capable of detecting and distinguishing SARS-CoV-2 mutations, allowing for high-throughput screening of relevant variants in clinical samples before sequencing.

JOURNAL OF CLINICAL VIROLOGY (2021)

Review Genetics & Heredity

The biological and clinical significance of emerging SARS-CoV-2 variants

Kaiming Tao et al.

Summary: The emergence of multiple SARS-CoV-2 variants has significant impacts on the epidemiological and clinical aspects of the COVID-19 pandemic, including increased virus transmission rates, heightened risk of reinfection, and reduced effectiveness of neutralizing antibodies and vaccines. These variants have introduced new challenges to COVID-19 research, necessitating additional avenues of laboratory, epidemiological, and clinical studies.

NATURE REVIEWS GENETICS (2021)

Article Engineering, Environmental

Near real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in wastewater using an allele-specific primer extension PCR strategy

Tyson E. Graber et al.

Summary: The COVID-19 pandemic caused by SARS-CoV-2 has led to the emergence of viral variants with potentially increased transmissibility and virulence. Wastewater-based epidemiology can provide a reliable proxy for monitoring the viral load of these variants in specific populations, allowing for timely assessment of community transmission.

WATER RESEARCH (2021)

Article Engineering, Environmental

Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR

Wei Lin Lee et al.

Summary: This study developed a detection method for tracking the B.1.1.7 variant in wastewater, which can reliably detect low levels of B.1.1.7 and provide rapid and inexpensive surveillance of SARS-CoV-2 variants.

ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS (2021)

Article Environmental Sciences

Within- and between-Day Variability of SARS-CoV-2 RNA in Municipal Wastewater during Periods of Varying COVID-19 Prevalence and Positivity

Aaron Bivins et al.

Summary: Wastewater surveillance using grab samples every 2 hours over 24-hour periods revealed diurnal loading patterns of SARS-CoV-2 RNA, suggesting monitoring efforts should focus on daytime periods with high fecal loading. Manual compositing may introduce bias, and concentrations in wastewater demonstrated a correlation with clinical COVID-19 positivity rather than case numbers. Large variation within and between days may limit robust quantitative analyses.

ACS ES&T WATER (2021)

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)

Article Medicine, Research & Experimental

Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection

Luca Falzone et al.

INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE (2020)

Article Biotechnology & Applied Microbiology

Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics

Jordan Peccia et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemistry & Molecular Biology

Detection of SARS-CoV-2 RNA by multiplex RT-qPCR

Eriko Kudo et al.

PLOS BIOLOGY (2020)