4.8 Article

Global landscape of SARS-CoV-2 genomic surveillance and data sharing

Related references

Note: Only part of the references are listed.
Review Immunology

Neutralizing Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Induced by Natural Infection or Vaccination: A Systematic Review and Pooled Analysis

Xinhua Chen et al.

Summary: Emerging SARS-CoV-2 variants pose a threat to immunity, with varying reductions in neutralizing antibody titers. Vaccines induce neutralizing antibodies that can effectively neutralize the newer variants, but with significant reductions in neutralizing titers.

CLINICAL INFECTIOUS DISEASES (2022)

Article Infectious Diseases

Genomic surveillance to combat COVID-19: challenges and opportunities

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.

LANCET MICROBE (2021)

Article Infectious Diseases

Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, the Netherlands, June to July 2021

Richard Molenkamp et al.

Summary: Routine testing with SARS-CoV-2 Delta variant-specific RT-PCR in regional hospital laboratories showed a good correlation with centralised national genomic surveillance data, detecting the Delta variant approximately 2 weeks earlier. Rapid identification of the relative abundance and increase of SARS-CoV-2 variants of concern could have significant benefits for implementing local public health measures.

EUROSURVEILLANCE (2021)

Article Public, Environmental & Occupational Health

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

Summer E. Galloway et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2021)

Article Medicine, General & Internal

Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study

Raphael Sonabend et al.

Summary: The study assessed the UK Government's four-step process to easing lockdown restrictions in England, taking into account the impact of the Delta variant and other factors. The findings suggest that the risk of a large wave of COVID-19 hospital admissions resulting from lifting NPIs can be mitigated but there is substantial uncertainty in the epidemic trajectory due to the emergence of the Delta variant.

LANCET (2021)

News Item Multidisciplinary Sciences

HEAVILY MUTATED OMICRON VARIANT PUTS SCIENTISTS ON ALERT

Ewen Callaway

NATURE (2021)

Article Genetics & Heredity

The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant

Mariana G. Lopez et al.

Summary: This study sequenced 2,170 samples from the first wave of the COVID-19 epidemic in Spain, identifying at least 500 introductions of SARS-CoV-2 variants from multiple international sources and documenting the early rise of two dominant Spanish epidemic clades. The research shows that public health interventions effectively reduced the reproductive number of these clades, leading to the replacement of the dominant variants by a new variant over the summer of 2020.

NATURE GENETICS (2021)

Editorial Material Multidisciplinary Sciences

Want to track pandemic variants faster? Fix the bioinformatics bottleneck Comment

Emma B. Hodcroft et al.

Summary: Researchers are in need of new approaches to control the pandemic as existing tools, rules, and incentives are struggling to cope with the flood of coronavirus genome sequences.

NATURE (2021)

Article Multidisciplinary Sciences

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Eduan Wilkinson et al.

Summary: The progression of the SARS-CoV-2 pandemic in Africa has shown heterogeneous patterns, with many countries experiencing epidemics initiated mainly by imports from Europe. The implementation of early travel restrictions helped reduce this trend. However, ongoing transmission and increasing mobility within Africa have led to the emergence and spread of various concerning variants. This highlights the importance of not neglecting Africa in the global pandemic response to prevent it from becoming a source of new variants.

SCIENCE (2021)

Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

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.

SCIENCE (2021)

Editorial Material Medicine, General & Internal

Under-reporting of deaths limits our understanding of true burden of covid-19

Charles Whittaker et al.

BMJ-BRITISH MEDICAL JOURNAL (2021)

Article Public, Environmental & Occupational Health

SARS-CoV-2 sequencing collaboration in west Africa shows best practices

Chika Kingsley Onwuamah et al.

Lancet Global Health (2021)

Letter Medicine, General & Internal

S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021

Kevin A. Brown et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

News Item Multidisciplinary Sciences

THE FLIP SIDE OF UNRESTRICTED VIRAL GENOME SHARING

Amy Maxmen

NATURE (2021)

Article Multidisciplinary Sciences

India’s neighbours race to sequence genomes as COVID surges

Smriti Mallapaty

NATURE (2021)

Article Multidisciplinary Sciences

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Erik Volz et al.

Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.

NATURE (2021)

Letter Biochemistry & Molecular Biology

Africa needs more genome sequencing to tackle new variants of SARS-CoV-2

Akaninyene Otu et al.

NATURE MEDICINE (2021)

Letter Medicine, General & Internal

Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants

Laith J. Abu-Raddad et al.

NEW ENGLAND JOURNAL OF MEDICINE (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)

Letter Medicine, General & Internal

AZD1222-induced neutralising antibody activity against SARS-CoV-2 Delta VOC

Emma C. Wall et al.

LANCET (2021)

Article Multidisciplinary Sciences

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Emma B. Hodcroft et al.

Summary: A variant of SARS-CoV-2, 20E (EU1), was identified in Spain in early summer 2020 and later spread across Europe. Despite not showing increased transmissibility, the variant's success can be attributed to rising incidence in Spain, resumption of travel, and lack of effective screening and containment measures. Travel played a significant role in introducing the variant multiple times to European countries during the summer, undermining local efforts to prevent SARS-CoV-2 infection.

NATURE (2021)

Review Biochemistry & Molecular Biology

The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

Bas B. Oude Munnink et al.

Summary: This review summarizes the current knowledge on key viral mutations and variants, emphasizing the need for a systematic approach to link global genomic surveillance with timely assessment of the phenotypic characteristics of novel variants in preparation for the next phase of the pandemic.

NATURE MEDICINE (2021)

Article Genetics & Heredity

Global variation in sequencing impedes SARS- CoV-2 surveillance

Dana C. Crawford et al.

PLOS GENETICS (2021)

Article Public, Environmental & Occupational Health

Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021

Prabasaj Paul et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2021)

Article Microbiology

Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Daniel Lule Bugembe et al.

Summary: The SARS-CoV-2 variant A.23.1 emerged and became predominant in Uganda, showing amino acid changes in both the spike protein and non-spike proteins similar to other known variants of concern. While the clinical impact of the A.23.1 variant is still unclear and it has not been designated as a variant of concern, careful monitoring and assessment of its impact on COVID-19 vaccine efficacy are advisable.

NATURE MICROBIOLOGY (2021)

Article Immunology

Effectiveness of inactivated SARS-CoV-2 vaccines against the Delta variant infection in Guangzhou: a test-negative case-control real-world study

Xiao-Ning Li et al.

Summary: The two-dose inactivated SARS-CoV-2 vaccine showed an effectiveness of 59.0% to 70.2% against the Delta variant, with higher efficacy among participants aged 40-59 years and in females compared to males in preventing COVID-19 and moderate diseases.

EMERGING MICROBES & INFECTIONS (2021)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Ten recommendations for supporting open pathogen genomic analysis in public health

Allison Black et al.

NATURE MEDICINE (2020)

Article Genetics & Heredity

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

Shuhui Song et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2020)

Article Mathematical & Computational Biology

Increased interactivity and improvements to the GigaScience database, GigaDB

Si Zhe Xiao et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2019)

Article Biochemical Research Methods

Nextstrain: real-time tracking of pathogen evolution

James Hadfield et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Virus Variation Resource - improved response to emergent viral outbreaks

Eneida L. Hatcher et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Data, disease and diplomacy: GISAID's innovative contribution to global health

Stefan Elbe et al.

GLOBAL CHALLENGES (2017)