Determining Gaps in Publicly Shared SARS-CoV-2 Genomic Surveillance Data by Analysis of Global Submissions

Ohlsen, Elizabeth C; Hawksworth, Anthony W.; Wong, Kimberly; Guagliardo, Sarah Anne J.; Fuller, James A.; Sloan, Michelle L.; O’Laughlin, Kevin

doi:10.3201/eid2813.220780

Cited by 9 publications

(8 citation statements)

References 10 publications

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“…We restricted our analysis to HICs because more accessible testing in those countries likely provides a more accurate assessment of the case and death burdens ( 15 , 16 ). We included HICs that reported > 200 SARS-CoV-2 sequences during the full period of interest (April 1, 2020–November 30, 2021) and > 20 Delta sequences in the first month of Delta dominance.…”

Section: Methodsmentioning

confidence: 99%

COVID-19 Epidemiology during Delta Variant Dominance Period in 45 High-Income Countries, 2020–2021

Atherstone¹,

Guagliardo²,

Hawksworth³

et al. 2023

Emerg. Infect. Dis.

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The SARS-CoV-2 Delta variant, first identified in October 2020, quickly became the dominant variant worldwide. We used publicly available data to explore the relationship between illness and death (peak case rates, death rates, case-fatality rates) and selected predictors (percentage vaccinated, percentage of the population >65 years, population density, testing volume, index of mitigation policies) in 45 high-income countries during the Delta wave using rank-order correlation and ordinal regression. During the Delta-dominant period, most countries reported higher peak case rates (57%) and lower peak case-fatality rates (98%). Higher vaccination coverage was protective against peak case rates (odds ratio 0.95, 95% CI 0.91–0.99) and against peak death rates (odds ratio 0.96, 95% CI 0.91–0.99). Vaccination coverage was vital to preventing infection and death from COVID-19 during the Delta wave. As new variants emerge, public health authorities should encourage the uptake of COVID-19 vaccination and boosters.

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Section: Methodsmentioning

confidence: 99%

COVID-19 Epidemiology during Delta Variant Dominance Period in 45 High-Income Countries, 2020–2021

Atherstone¹,

Guagliardo²,

Hawksworth³

et al. 2023

Emerg. Infect. Dis.

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“…This proved particularly problematic in low-income settings, for example in many parts of Africa, where a lack of existing sequencing infrastructure and expertise in genome analyses hindered the management and initial response to COVID-19 (22). Global analysis of viral sequence data deposited in public repositories has allowed quantitative assessments of national SARS-CoV-2 genomic surveillance programs in terms of case coverage, timeliness of reporting, and completeness of data sharing, broken down by sampling strategies and sequencing technology (28)(29)(30). The analysis has shown that, during the first 2 years of the pandemic, the SARS-CoV-2 genomic surveillance landscape displayed marked heterogeneity of outputs by country and economic income level.…”

Section: Weaknessesmentioning

confidence: 99%

“…The analysis has shown that, during the first 2 years of the pandemic, the SARS-CoV-2 genomic surveillance landscape displayed marked heterogeneity of outputs by country and economic income level. While 78% of high-income countries (HICs) sequenced >0.5% of reported COVID-19 cases, only 42% of low-and middle-income countries (LMICs) achieved that coverage level (29). The mean sequencing coverage ranged by region, from 0.1% in the Eastern Mediterranean region to 3.4% in Europe (28).…”

Section: Weaknessesmentioning

confidence: 99%

Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

Struelens,

Ludden,

Werner

et al. 2024

Front. Sci.

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This article advocates for mobilizing pathogen genomic surveillance to contain and mitigate health threats from infectious diseases and antimicrobial resistance (AMR), building upon successes achieved by large-scale genome sequencing analysis of SARS-CoV-2 variants in guiding COVID-19 monitoring and public health responses and adopting a One Health approach. Capabilities of laboratory-based surveillance and epidemic alert systems should be enhanced by fostering (i) universal access to real-time whole genome sequence (WGS) data of pathogens to inform clinical practice, infection control, public health policies, and vaccine and antimicrobial drug research and development; (ii) integration of diagnostic microbiology data, data from testing asymptomatic individuals, pathogen sequence data, clinical data, and epidemiological data into surveillance programs; (iii) stronger cross-sectorial collaborations between healthcare, public health, animal health, and environmental surveillance and research using One Health approaches, toward understanding the ecology and transmission pathways of pathogens and AMR across ecosystems; (iv) international collaboration and interconnection of surveillance networks, harmonization of laboratory methods, and standardization of surveillance methods for global reporting, including on pathogen genomic variant or strain nomenclature; (v) responsible data sharing between surveillance networks, databases, and platforms according to FAIR (findability, accessibility, interoperability, and reusability) principles; and (vi) research on genomic surveillance system implementation and its cost-effectiveness for different pathogens and AMR threats across different settings. Regional and global One Health policies and governance initiatives should foster the concerted development and efficient utilization of pathogen genomic surveillance to protect the health of humans, animals, and the environment.

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“…Surveys provided key data on SARS-CoV-2 cases in Pakistan ( 8 ) and Malawi ( 9 ). Ohlsen et al found international disparities in SARS-CoV-2 sequencing capacity and timeliness while viral genomic surveillance coverage increased globally ( 10 ). Smith-Sreen et al compared 3 waves of the pandemic in 10 countries in southern Africa ( 11 ).…”

Section: Surveillance Information and Laboratory Systemsmentioning

confidence: 99%

Global Responses to the COVID-19 Pandemic

Cassell¹,

Raghunathan²,

Henao³

et al. 2022

Emerg. Infect. Dis.

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Determining Gaps in Publicly Shared SARS-CoV-2 Genomic Surveillance Data by Analysis of Global Submissions

Cited by 9 publications

References 10 publications

COVID-19 Epidemiology during Delta Variant Dominance Period in 45 High-Income Countries, 2020–2021

COVID-19 Epidemiology during Delta Variant Dominance Period in 45 High-Income Countries, 2020–2021

Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

Global Responses to the COVID-19 Pandemic

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