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Article
Environmental Sciences
Jessica L. Kevill et al.
Summary: Wastewater-based epidemiology (WBE) is a useful tool in monitoring SARS-CoV-2 during the pandemic. This study compared three viral concentration methods and found that there was no major difference in viral recovery using these methods. However, factors such as sample turbidity, storage temperature, and surfactant load did affect viral recovery, emphasizing the importance of considering these factors when working with wastewater samples.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Davida S. Smyth et al.
Summary: Tracking the genetic diversity of SARS-CoV-2 is important to monitor the emergence of novel variants resistant to immunity. The researchers detected increasing frequencies of novel cryptic SARS-CoV-2 lineages in the New York City wastewater, containing mutations rarely observed in clinical samples. These lineages share mutations with the Omicron variant and have expanded tropism and resistance to neutralizing antibodies.
NATURE COMMUNICATIONS
(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
Infectious Diseases
Janet Robishaw et al.
Summary: While vaccines offer hope for recovery from the COVID-19 pandemic, genomic surveillance is crucial in detecting and responding to virus variants in a timely manner to mitigate and contain outbreaks effectively.
Article
Multidisciplinary Sciences
Houriiyah Tegally et al.
Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.
Article
Multidisciplinary Sciences
Nicholas G. Davies et al.
Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.
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
Biology
Petr Danecek et al.
Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.
Article
Medicine, General & Internal
Thomas Ward et al.
Summary: This study analyzed the transmission patterns of new variants of SARS-CoV-2 in England from October 2020 to July 2021, taking into account different age groups, geographic locations, and ethnicities. The B.1.617.2 variant showed a clear transmission advantage over the B.1.1.7 variant, with exponential growth observed in all age groups. Early interventions were effective in reducing the growth of the B.1.617.2 variant in specific ethnic groups.
Article
Engineering, Environmental
Luke S. Hillary et al.
Summary: The study demonstrates that SARS-CoV-2 RNA levels in wastewater generally corresponded with the number of clinical cases in large urban centers, decreasing significantly after lockdown measures were implemented. Genetic sequencing of the virus in wastewater revealed multiple distinct clusters circulating in the local population, reflecting similarities with SNPs found in clinical samples. The findings suggest that wastewater-based epidemiology can be a valuable tool for monitoring and tracking the prevalence of SARS-CoV-2 and other viruses in the community, aiding in public health policy decisions.
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
Medicine, General & Internal
Marta Garcia-Finana et al.
Summary: The study revealed that the sensitivity of LFT compared to RT-qPCR was low but with high specificity in asymptomatic adults. LFT may have better detection rates for individuals with high viral loads. However, the potential for missing cases, even at high viral loads, should be considered when using a single LFT in high-risk settings.
BMJ-BRITISH MEDICAL JOURNAL
(2021)
Article
Microbiology
Sarah Cherian et al.
Summary: Genomic epidemiology and whole genome sequencing were used to investigate the transmission and evolution of the SARS-CoV-2 virus during the global pandemic. The study identified new variants B.1.617.1 and B.1.617.2 in India, responsible for the second wave of COVID-19 in Maharashtra, with B.1.617.2 designated as a VOC delta and B.1.617.1 as a variant of interest kappa. Monitoring of these and emerging variants in India is crucial for public health.
Article
Medicine, General & Internal
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.
Article
Biotechnology & Applied Microbiology
Christopher Quince et al.
Summary: STRONG is a novel method that identifies strains de novo from multiple metagenome samples by using assembly graphs to extract coverages of SCGs in each MAG and determine the number of strains, their haplotypes or sequences, and abundances. The method is validated using synthetic communities and real samples.
Article
Biochemical Research Methods
Kata Farkas et al.
Summary: Wastewater-based epidemiology is a vital tool for monitoring SARS-CoV-2 outbreaks, but the detection of viruses in sewage is challenging. A simple concentration method using PEG precipitation enables efficient detection of various viruses in wastewater, offering a comprehensive assessment of viral diseases in a community.
METHODS AND PROTOCOLS
(2021)
Article
Multidisciplinary Sciences
Fan Wu et al.
Article
Medicine, General & Internal
Na Zhu et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2020)
Article
Biotechnology & Applied Microbiology
Jordan Peccia et al.
NATURE BIOTECHNOLOGY
(2020)
Review
Environmental Sciences
Paola Foladori et al.
SCIENCE OF THE TOTAL ENVIRONMENT
(2020)
Article
Engineering, Environmental
David Polo et al.
Article
Biotechnology & Applied Microbiology
Nathan D. Grubaugh et al.
Article
Multidisciplinary Sciences
Stefan Elbe et al.
Article
Statistics & Probability
Francisco Cribari-Neto et al.
Journal of Statistical Software
(2015)
Article
Biochemistry & Molecular Biology
Daniel C. Koboldt et al.
Article
Biochemical Research Methods
Christopher Quince et al.
BMC BIOINFORMATICS
(2011)
Article
Biochemical Research Methods
Heng Li et al.
