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Review
Microbiology
Peter V. Markov et al.
Summary: In this Review, the evolution of SARS-CoV-2, the phases of the COVID-19 pandemic, factors driving virus evolution, and potential future scenarios and their health repercussions are explored. The mechanisms generating genetic variation in SARS-CoV-2 and the selective forces driving its evolution are examined. Uncertainties are evaluated and scenarios for the future evolutionary trajectories of SARS-CoV-2 are outlined.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Environmental Sciences
Hannes Schenk et al.
Summary: Wastewater-based epidemiology has been widely used in Austria since April 2020 to monitor the SARS-CoV-2 pandemic. This study analyzed the viral concentrations in raw sewage to predict short-term hospitalization occupancy. The results showed the potential of using viral loads in sewage to forecast Covid-19 hospitalization occupancy.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Delphine Planas et al.
Summary: Convergent evolution of SARS-CoV-2 Omicron BA.2, BA.4, and BA.5 lineages have led to the emergence of several new subvariants, including BA.2.75.2, BA.4.6, and BQ.1.1. These subvariants carry additional mutations in the spike protein, potentially increasing transmissibility and evading immune responses. The study found that the efficacy of monoclonal antibodies and serum from vaccinated individuals against these subvariants varies.
NATURE COMMUNICATIONS
(2023)
Review
Virology
Dandan Tian et al.
Summary: The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Botswana in November 2021 and has since become the dominant strain in many countries. With a high number of mutations, it presents new challenges for preventing and controlling COVID-19. This review aims to provide a scientific reference by analyzing and summarizing the biological characteristics, epidemic features, immune escape, and vaccine reactivity of the Omicron variant.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Engineering, Environmental
Shelesh Agrawal et al.
Summary: For community-level monitoring, the European Commission recommends wastewater-based surveillance to track SARS-CoV-2 variants. High-coverage genome sequencing of wastewater samples has been successfully used to detect and track SARS-CoV-2 mutations, which are consistent with the variants reported in clinical data.
Article
Engineering, Environmental
Alba Perez-Cataluna et al.
Summary: Wastewater-based epidemiology is an effective tool for epidemiological surveillance of SARS-CoV-2, and when combined with high-throughput sequencing techniques, it can analyze viral diversity. The study proves the ability of sewage sequencing to anticipate mutations and assist in clinical testing for decision-making and analysis of the pandemic's evolution.
Article
Environmental Sciences
Vic-Fabienne Schumann et al.
Summary: The use of RNA sequencing from wastewater samples is a valuable method for estimating infection dynamics and circulating lineages of SARS-CoV-2. The study presents PiGx SARS-CoV-2, a reproducible computational analysis pipeline, for analyzing lineage dynamics in Berlin and New York City using wastewater sequencing. The pipeline includes steps from raw data to comprehensive reports, taxonomic analysis, deconvolution, and geospatial time series analyses.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Hossein Gorji et al.
Summary: This study evaluates the effects of a unique RNA mass testing program implemented in Canton Grisons, which targeted the local labor force. The analysis of test results from over 27,000 participants shows a significant decrease in test positivity rate and a reduction in associated incidence rate. These findings provide empirical evidence that long-term repetitive mass testing can effectively prevent the spread of COVID-19.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
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.
Article
Microbiology
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)
Article
Environmental Sciences
Alexander Mitranescu et al.
Summary: This study analyzed wastewater samples from southern Germany to assess the importance of normalization of SARS-CoV-2 biomarker concentrations, finding that performance of normalization parameters is site-specific. It is recommended to test the suitability of normalization parameters individually for specific sewage systems.
Article
Biochemical Research Methods
Susana Posada-Cespedes et al.
Summary: V-pipe is a bioinformatics pipeline designed to support viral high-throughput sequencing studies, incorporating various statistical models and computational tools. It allows for quality control, read mapping, low-frequency mutation calling, and inference of viral haplotypes. Through comparative evaluations of different pipeline configurations, the impact of different read aligners and variant callers on calling single-nucleotide variants in intra-host virus populations is demonstrated.
Article
Microbiology
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.
Article
Environmental Sciences
Subhanjan Mondal et al.
Summary: Studies have shown that SARS-CoV-2 RNA can be detected in the feces of infected individuals, prompting investigation into using wastewater-based epidemiology to monitor the virus. A direct unbiased total nucleic acid (TNA) extraction method was developed to overcome the limitations of previous methods, allowing for a simple, rapid, and modular alternative for sample concentration and purification. This method showed potential for wastewater surveillance of SARS-CoV-2 and other infectious agents in communities.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Environmental
Rafaela S. Fontenele et al.
Summary: The study analyzed 91 wastewater samples from 11 states in the USA, detecting a large number of new single-nucleotide variants of SARS-CoV-2, with half of them also being found in subsequent clinical data. The presence of more lineages in wastewater samples suggests a greater genetic diversity circulating within communities compared to clinical-derived data.
Article
Biochemistry & Molecular Biology
Darren P. Martin et al.
Summary: The emergence of the 501Y lineages of SARS-CoV-2 in 2020 coincided with a global shift in selective forces acting on various genes, leading to repeated convergent mutations at 35 genome sites known as the 501Y meta-signature. This meta-signature includes multiple mutation combinations that promote the persistence of diverse SARS-CoV-2 lineages in the face of increasing host immune recognition.
Review
Microbiology
William T. Harvey et al.
Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Nash D. Rochman et al.
Summary: The evolution of SARS-CoV-2 during the COVID-19 pandemic is primarily characterized by purifying selection, with a small number of sites evolving under positive selection. Variants in the spike protein's receptor-binding domain and the nucleocapsid protein region with NLS are enriched with positively selected amino acid replacements. These replacements form a connected network of apparent epistatic interactions and are indicators of major partitions in the SARS-CoV-2 phylogeny. The global virus diversity has been steadily increasing, with distinct periods based on phylogenetic distances and key mutations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Environmental
G. La Rosa et al.
Summary: A nested RT-PCR assay was developed to detect key mutations of SARS-CoV-2 variants, showing potential for rapid screening of clinical samples and detection of variants in sewage. The study highlights the importance of wastewater surveillance in exploring SARS-CoV-2 diversity and distribution.
Article
Microbiology
Nathalie Wurtz et al.
Summary: Monitoring SARS-CoV-2 variants in wastewater through genome sequencing provides a more accurate assessment of variant distribution in different regions compared to RT-PCR, highlighting the importance of targeted sequencing to understand the epidemiology of the virus.
Article
Environmental Sciences
Shuchen Feng et al.
Summary: Wastewater surveillance for SARS-CoV-2 can help assess infection burden, but measurement variability and its relationship to case data need to be considered. Research showed that a minimum of two samples collected per week were needed to maintain accuracy in trend analysis.
Letter
Infectious Diseases
Yang Pan et al.
LANCET INFECTIOUS DISEASES
(2020)
Article
Multidisciplinary Sciences
Peng Zhou et al.
Article
Medicine, General & Internal
Na Zhu et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2020)
Article
Multidisciplinary Sciences
Renhong Yan et al.
Article
Dentistry, Oral Surgery & Medicine
Hao Xu et al.
INTERNATIONAL JOURNAL OF ORAL SCIENCE
(2020)
Article
Microbiology
Alexander E. Gorbalenya et al.
NATURE MICROBIOLOGY
(2020)
Review
Environmental Sciences
Masaaki Kitajima et al.
SCIENCE OF THE TOTAL ENVIRONMENT
(2020)
Article
Multidisciplinary Sciences
Roman Woelfel et al.
Article
Allergy
Urszula Radzikowska et al.
Article
Infectious Diseases
Francois-Xavier Lescure et al.
LANCET INFECTIOUS DISEASES
(2020)
Article
Virology
Javier Martin et al.
Article
Environmental Sciences
Sara Giordana Rimoldi et al.
SCIENCE OF THE TOTAL ENVIRONMENT
(2020)
Article
Biochemical Research Methods
James Hadfield et al.
Editorial Material
Infectious Diseases
Yuelong Shu et al.
Article
Biochemistry & Molecular Biology
Dennis A. Benson et al.
NUCLEIC ACIDS RESEARCH
(2012)
