Records 1-27 (of 27 Records) |
Query Trace: Pathogen genomics[original query] |
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The next chapter for Africa's genomic initiatives P Adepoujo, Lancet Id, March 2024
From the article: " The Africa Pathogen Genomics Initiative 2.0, launched at the end of 2023, plans to strengthen laboratory systems and enhance genomic capacity across Africa. With COVID-19 no longer a Public Health Emergency of International Concern, the demand for SARS-CoV-2 genomic sequencing has reduced. In Africa, this has created an opportunity for the rapidly acquired capacity for genomics to serve other purposes. In 2019, only seven countries in Africa had functional next-generation sequencing capacity in public health laboratories according to the Africa Pathogen Genomics Initiative (Africa PGI), but this rapidly grew to 30 in 2023, with nine regarded as centres of excellence. By 2025, Africa PGI aims to increase the number to 50 through Africa PGI 2.0."
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A new era of pathogen surveillance using genomic sequencing Open Access Government, July 19, 2023
Genomic sequencing is a method scientists use to decipher the genetic material found in organisms or viruses. The significance of genomic sequencing tools was truly brought to the fore during the COVID-19 pandemic as researchers were able to observe any sudden changes (or mutations) in a virus’s genetic code which may give it an advantage over other variants of itself, for example, spreading faster or causing more harm to those it infects.
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Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet. Emily A Smith et al. Microb Genom 2023 6 (6)
The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet.
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Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK. Pacchiarini Nicole, et al. Microbial genomics 2023 0 0. (4) |
Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. Nielsen Bjarke Frost, et al. PLoS computational biology 2023 0 0. (2) e1010896 |
How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom. Killough Nicholas, et al. Microbial genomics 2023 0 0. (2) |
COVID-19 Genomics UK (COG-UK) Consortium: Final Report. Marjanovic Sonja, et al. Rand health quarterly 2022 0 0. (4) 24 |
Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada's public health laboratories. Nadon C, et al. BMC public health 2022 0 0. (1) 1817 |
Immune Heterogeneity and Epistasis Explain Punctuated Evolution of SARS-CoV-2. Nielsen Bjarke Frost, et al. medRxiv : the preprint server for health sciences 2022 0 0. |
Ethical Challenges Associated with Pathogen and Host Genetics in Infectious Disease. Milne Richard, et al. The New bioethics : a multidisciplinary journal of biotechnology and the body 2022 0 0. 1-13 |
Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea. Palou Theresa et al. Virus evolution 2022 7 (1) veac033 |
Global genomic surveillance strategy for pathogens with pandemic and epidemic potential, 2022–2032 WHO, March 2022
The Strategy provides a high-level unifying framework to leverage existing capacities, address barriers and strengthen the use of genomic surveillance in the detection, monitoring and response to public health threats. Genomic surveillance is part of the broader surveillance and laboratory system, and its implementation should reinforce end-to-end capacities including sample collection, diagnostics, data sharing and analysis. The strategy aims to facilitate the connectivity between different disease control programs and surveillance networks.
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Empowering Equitable Data Use Partnerships and Indigenous Data Sovereignties Amid Pandemic Genomics. Haring Rodney C, et al. Frontiers in public health 2021 0 0. 742467 |
Towards Equitable Access to Public Health Pathogen Genomics in the Western Pacific. Lin Chantel, et al. The Lancet regional health. Western Pacific 2021 0 0. 100321 |
Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: an IDSA/ASM Consensus Review Document. Greninger Alexander L, et al. Journal of clinical microbiology 2021 0 0. JCM0165921 |
Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: An IDSA/ASM Consensus Review Document. Greninger Alexander L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 11 |
An implementation science approach to evaluating pathogen whole genome sequencing in public health. Ferdinand Angeline S, et al. Genome medicine 2021 0 0. (1) 121 |
An implementation science approach to evaluating pathogen whole genome sequencing in public health AS Ferdinand et al, Genome Medicine, July 29, 2021
We developed the Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework to guide examination of the use of WGS in public health surveillance and disease control. We illustrate the use of this framework with three pathogens as case studies: Listeria monocytogenes, Mycobacterium tuberculosis and SARS-CoV-2.
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A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Bourassa Lori, et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 0 0. 104900 |
Protocol for the COG-UK hospital onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in United Kingdom NHS hospitals Blackstone, James et al. medRxiv April 15 2021 |
A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance Bourassa, Lori et al. medRxiv May 05 2021 |
A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa de Oliveira T, et al. krisp.org, Mar 25, 2021. |
Genomic-informed pathogen surveillance in Africa: opportunities and challenges. Inzaule Seth C et al. The Lancet. Infectious diseases 2021 Feb |
A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences Andreoletti, Jeremy et al. bioRxiv October 27 2020 |
The Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework: An Implementation Science Approach to Evaluating Pathogen Whole Genome Sequencing in Public Health Ferdinand, Angeline S et al. Research Square November 13 2020 |
Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus Somasundaram K, et al. medRxiv, Apr 29, 2020. |
Cryptic transmission of SARS-CoV-2 in Washington State. Bedford Trevor, et al. medRxiv : the preprint server for health sciences 2020 4 0. |
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