Global genomic surveillance strategy for pathogens with pandemic and epidemic potential 2022–2032

Carter, Lisa L.; Yu, M Anne; Sacks, Jilian A.; Barnadas, Céline; Pereyaslov, Dmitriy; Cognat, Sebastien; Briand, Sylvie; Ryan, Michael J.; Samaan, Gina

doi:10.2471/blt.22.288220

Cited by 50 publications

(30 citation statements)

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“…Our results suggest that sequencing 0.5% of total confirmed cases, with a TAT below 21 days, could provide a benchmark for genomic surveillance studies targeting SARS-CoV-2 and future emerging viruses. Alongside with the guidance provided by the WHO and other international public health authorities (see 37 , 38 , 40 , 65 – 69 ), ongoing surveys to understand barriers to virus genome sequencing and sampling selection strategies will provide valuable information for future surveillance programs. Implementation of metagenomic approaches for virus discovery followed by virus-genome specific sequencing approaches could help overcome existing limitations of molecular and syndromic surveillance strategies 70 .…”

Section: Discussionmentioning

confidence: 99%

“…Implementation of metagenomic approaches for virus discovery followed by virus-genome specific sequencing approaches could help overcome existing limitations of molecular and syndromic surveillance strategies 70 . Adoption of standardized protocols for representative genomic surveillance strategies 40 , 48 , establishment of data and minimal metadata standards, efficient and facilitated access to information, following equitable data sharing agreements 65 , and collaboration between academia, public health laboratories, private laboratories and other stakeholders will be essential to maximize cost-effectiveness and public health impact of genomic surveillance. While a random sampling strategy may provide accurate information into SARS-CoV-2 variant emergence and frequency estimation, we note that genome sampling strategies should be considered pathogen- and question-specific 48 , 65 , 66 .…”

Section: Discussionmentioning

confidence: 99%

“…Adoption of standardized protocols for representative genomic surveillance strategies 40 , 48 , establishment of data and minimal metadata standards, efficient and facilitated access to information, following equitable data sharing agreements 65 , and collaboration between academia, public health laboratories, private laboratories and other stakeholders will be essential to maximize cost-effectiveness and public health impact of genomic surveillance. While a random sampling strategy may provide accurate information into SARS-CoV-2 variant emergence and frequency estimation, we note that genome sampling strategies should be considered pathogen- and question-specific 48 , 65 , 66 . For example, non-random selection of samples stratified by disease severity may be required to identify genes or mutations associated with clinical outcomes 71 .…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Global disparities in SARS-CoV-2 genomic surveillance

Brito

Semenova²,

Dudas³

et al. 2022

Nat Commun

131

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Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Global disparities in SARS-CoV-2 genomic surveillance

Brito

Semenova²,

Dudas³

et al. 2022

Nat Commun

131

View full text Add to dashboard Cite

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“…This highlights the need for co-ordinated, harmonised, global genomic surveillance in line with the new WHO strategy in this area. 75 For example, the XDR outbreak lineage has evolved from a clade that has dominated MSM-associated shigellosis for nearly a decade, and bla CTX−M−27 on p893916 was detected in 2020, highlighting a potential opportunity to detect the emerging international spread earlier and to initiate interventions to prevent its spread.…”

Section: Discussionmentioning

confidence: 99%

The evolution and international spread of extensively drug resistant Shigella sonnei

Mason

Greig²,

Cowley

et al. 2022

Preprint

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Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common and can include resistance to the World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, natural history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a common, low fitness-cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.

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“…The organization conducted a series of stakeholder consultations to gather feedback and inform the development of the strategy. [18][19][20][21] The goal of the global genomic surveillance strategy is to improve the quality of surveillance and provide timely and appropriate response to the potential pandemic of pathogens. This strategy is carried out through the establishment of a resilient and sustainable global surveillance system.…”

mentioning

confidence: 99%