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Last Posted: Apr 08, 2024
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Concerted efforts toward genomic surveillance of viral pathogens in immunocompromised individuals.
Matheus Filgueira Bezerra et al. Lancet Microbe 2024 4

From the article: "A recent study underscores the crucial need to closely monitor immunocompromised individuals with prolonged SARS-CoV-2 infections for emerging variants and investigate their phenotypic implications. Sequencing the genomes of the viruses from these cases would marginally elevate the cost in the whole COVID-19 genomic surveillance effort, and many countries with universal health systems could effectively integrate the tracking of prolonged COVID-19 infections in people living with HIV into their primary care programmes. "

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."

Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.
Jody E Phelan et al. Genome Med 2023 11 (1) 96

From the abstract: "Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data. "

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.
Madikay Senghore et al. Nat Commun 2023 11 (1) 6397

From the abstract: "In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. "

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Disclaimer: Articles listed in the Public Health Genomics and Precision Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the update, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.

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