Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing

Article Virology

ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

Filipe Zimmer Dezordi et al.

Summary: This study developed a workflow for processing and analyzing large-scale SARS-CoV-2 genomic sequencing data. The workflow automates all steps of reference-based genomic analysis and is efficient, versatile, and standardized.

VIRUSES-BASEL (2022)

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Article Multidisciplinary Sciences

Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater

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)

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Article Biology

ACE2 is the critical in vivo receptor for SARS-CoV-2 in a novel COVID-19 mouse model with TNF- and IFNγ-driven immunopathology

Riem Gawish et al.

Summary: Despite progress in understanding COVID-19, limited mechanistic insight into immunological factors and disease severity remains. Scientists generated a mouse-adapted SARS-CoV-2 strain, maVie16, and found that cytokine-driven immunopathology and ACE2 dependence determine disease severity. This study provides a new tool for discovering therapies.

ELIFE (2022)

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Article Public, Environmental & Occupational Health

Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater — United States, November–December 2021

Amy E. Kirby et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2022)

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Article Multidisciplinary Sciences

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Tyler N. Starr et al.

Summary: Research has found that mutations in the receptor binding domain (RBD) of SARS-CoV-2 may potentially escape the action of the REGN-COV2 cocktail, providing important information for interpreting mutations observed during viral surveillance.

SCIENCE (2021)

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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

Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

Zhuoming Liu et al.

Summary: The study found that antibodies targeting the SARS-CoV-2 spike protein have escape mutations, different monoclonal antibodies have unique resistance profiles, some mutants are resistant to multiple antibodies while some variants can escape neutralization by convalescent sera. Comparing antibody-mediated mutations with circulating SARS-CoV-2 sequences revealed substitutions that may weaken neutralizing immune responses in some individuals, warranting further investigation.

CELL HOST & MICROBE (2021)

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Article Microbiology

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

Allison J. Greaney et al.

Summary: The evolution of SARS-CoV-2 may impact the recognition of the virus by human antibody-mediated immunity, with mutations affecting antibody binding varying significantly among individuals and within the same individual over time. Despite this variability, mutations that greatly reduce antibody binding usually occur at specific sites in the RBD, with E484 being the most crucial. These findings can inform surveillance efforts for SARS-CoV-2 evolution in the future.

CELL HOST & MICROBE (2021)

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Article Multidisciplinary Sciences

Beyond Omicron: what’s next for COVID’s viral evolution

Ewen Callaway

NATURE (2021)

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Article Environmental Sciences

Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling

Candice L. Swift et al.

Summary: The study compared wastewater samples from two different wastewater treatment plants in South Carolina, USA, and found that wastewater surveillance can provide earlier community-level detection and detect specific mutations associated with variants of the SARS-CoV-2 virus.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

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Article Multidisciplinary Sciences

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Kevin R. McCarthy et al.

Summary: The translation above discusses zoonotic pandemics caused by animal viruses spilling over into highly susceptible human populations, specifically focusing on the evolution of coronaviruses in human hosts and the impact of recurrent deletions in the spike glycoprotein on antibody epitopes. These studies help understand the antigenic evolution and adaptive evolution of SARS-CoV-2.

SCIENCE (2021)

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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)

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Article Engineering, Environmental

High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants

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.

WATER RESEARCH (2021)

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Article Virology

Alternate primers for whole-genome SARS-CoV-2 sequencing

Matthew Cotten et al.

Summary: Efforts are being made globally to control the spread and evolution of SARS-CoV-2 by sequencing its genome, but a significant percentage of generated genomes each month have gaps, reducing their information content. This study identifies the frequencies and positions of these genome gaps and provides a new primer set and sequencing scheme to enhance the quality and coverage of the genomes.

VIRUS EVOLUTION (2021)

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Article Environmental Sciences

Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater

Malte Herold et al.

Summary: Monitoring SARS-CoV-2 in wastewater using RT-qPCR to track RNA levels has proven effective for epidemiological surveillance. Identifying specific signature mutations from individual lineages in wastewater samples helps estimate circulating lineages in the population, with allele frequencies of signature mutations corresponding to the occurrence of particular lineages. Additionally, regional clusters can also be discerned based on the genomic sequencing data.

WATER (2021)

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Article Microbiology

Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic Variants of SARS-CoV-2 in Municipal Wastewater

Xuan Lin et al.

Summary: Wastewater-based genomic surveillance of SARS-CoV-2 has shown promise in complementing genomic epidemiology efforts. Different multiplex primer schemes and sample matrices were assessed for targeted genome sequencing in wastewater, with the 400 bp primer scheme and influent sample matrix proving to be optimal for detecting emerging mutations associated with variants of concern. These findings provide guidance on best practices for implementing wastewater-based genomic surveillance and demonstrate its ability to inform epidemiology efforts by detecting circulating genomic variants of concern in a geographic region.

MSYSTEMS (2021)

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Article Biochemistry & Molecular Biology

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

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.

CELL (2021)

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Review Microbiology

SARS-CoV-2 variants, spike mutations and immune escape

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)

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Article Virology

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner

Devon A. Gregory et al.

Summary: Sequencing SARS-CoV-2 from wastewater is an effective tool for monitoring viral variants, and a novel computational workflow was developed to track viral populations in a Missouri sewershed, identifying two variants of concern.

VIRUSES-BASEL (2021)

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Article Multidisciplinary Sciences

Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies

Allison J. Greaney et al.

Summary: The study found that although the human immune system can produce antibodies that target diverse RBD epitopes, in practice, the polyclonal response to infection tends to be skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.

NATURE COMMUNICATIONS (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 Cell Biology

Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

Tyler N. Starr et al.

Summary: The study mapped mutations to the SARS-CoV-2 spike receptor-binding domain that escape binding by certain monoclonal antibodies. These mutations are concentrated in specific lineages of SARS-CoV-2. The authors suggest diversifying the epitopes targeted by antibodies and antibody cocktails to make them more resilient to SARS-CoV-2 antigenic evolution.

CELL REPORTS MEDICINE (2021)

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Article Virology

Alternate primers for whole-genome SARS-CoV-2 sequencing

Matthew Cotten et al.

Summary: Global efforts to sequence the SARS-CoV-2 genome are hindered by gaps in approximately 19 to 43 per cent of monthly generated sequences. This study provides an alternative primer set and sequencing scheme to improve the quality and coverage of genomes, aiding in the development of effective control measures.

VIRUS EVOLUTION (2021)

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Article Gastroenterology & Hepatology