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Hot Topics of the Day|PHGKB
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08/11/2022

Hot Topics of the Day are picked by experts to capture the latest information and publications on public health genomics and precision health for various diseases and health topics. Sources include published scientific literature, reviews, blogs and popular press articles.

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Characterization of the SARS-CoV-2 B.1.621 (Mu) variant.
Halfmann Peter J et al. Science translational medicine 2022 5 (657) eabm4908

SARS-CoV-2 variants have evolved rapidly, particularly as populations develop immunity to prior variants through vaccination and infection. Hence, the ability of immunity elicited by one variant to confer protection against another requires investigation. This study characterized the B.1.621 (Mu) variant of SARS-CoV-2, which was prevalent in the fall of 2021. The authors found that serum from vaccinated individuals neutralized the Mu variant, although at reduced potency compared to ancestral SARS-CoV-2.

Context-specific emergence and growth of the SARS-CoV-2 Delta variant
JT McCrone et al, Nature, August 11, 2022

Here we analyse 52,992 virus genomes from England together with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the geographic focus of Delta’s expansion shifted from India to a more global pattern in early May 2021.

Pandemic-Scale Phylogenomics Reveals The SARS-CoV-2 Recombination Landscape
Y Turakhia et al, Nature, August 11, 2022

Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution. Here, we use a novel phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6M sample tree from May 2021, we identify 589 recombination events, which indicate that approximately 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry.

Considering Race and Ethnicity in Covid Risk Assessments - Legal Concerns and Possible Solutions.
Jost Timothy S et al. The New England journal of medicine 2022 8 (6) 481-483

It is well documented that Black, Indigenous, and Latinx people have been at high risk for poor outcomes during the Covid-19 pandemic. For example, Black people have been hospitalized at 2.3 times the rate and died at 1.7 times the rate of non-Hispanic White people, and Hispanic or Latinx people have been hospitalized at 2.2 times the rate and died at 1.8 times the rate of non-Hispanic White people. Many structural factors contribute to higher Covid-related risks in these populations than among White people. These factors include lower socioeconomic status and poorer living conditions, on average; more limited access to preventive interventions and treatment; and increased viral exposure among frontline, essential, and critical-infrastructure workers, who are disproportionately members of historically marginalized groups.

Use of eConsult to enhance genetics service delivery in primary care: A multimethod study.
Carroll June C et al. Genetics in medicine : official journal of the American College of Medical Genetics 2022 8

Electronic consultation (eConsult) is a freely-available secure online platform connecting primary care providers (PCPs) to geneticists. Our purpose was to determine whether eConsult is effective in improving genetics service delivery in primary care. eConsult offers a potential solution for receiving timely genetics advice and avoiding unnecessary patient referrals, however, greater effect on access and wait times will need systematic integration into PCP and geneticist practice.

Genetics follow up after rapid genomic sequencing in intensive care: current practices and recommendations for service delivery
F Lynch et al, EJHG, August 11, 2022

The delivery of rapid genomic sequencing (rGS) to critically unwell children in intensive care occurs at a time of immense pressure and stress for parents. Contact with families after result disclosure, particularly after hospital discharge, presents an opportunity to meet their psychological, medical and information needs as they evolve. This study explores the preferences and perspectives of health professionals and parents of genetics follow up after rGS. Semi-structured interviews were conducted with 30 parents, seven genetic counsellors (GCs) and four intensive care physicians with experience in rGS.

Integrative analysis of genomic and exposomic influences on youth mental health.
Choi Karmel W et al. Journal of child psychology and psychiatry, and allied disciplines 2022 8

Understanding complex influences on mental health problems in young people is needed to inform early prevention strategies. Both genetic and environmental factors are known to influence youth mental health, but a more comprehensive picture of their interplay, including wide-ranging environmental exposures – that is, the exposome – is needed. We perform an integrative analysis of genomic and exposomic data in relation to internalizing and externalizing symptoms in a cohort of 4,314 unrelated youth from the Adolescent Brain and Cognitive Development (ABCD) Study.

Enhanced rare disease mapping for phenome-wide genetic association in the UK Biobank.
Patrick Matthew T et al. Genome medicine 2022 8 (1) 85

Using our mapping approach, we identified and characterized 420 rare diseases affecting 23,575 individuals in the UK Biobank. Significant genetic associations included JAK2 V617F for immune thrombocytopenic purpura (p?=?1.24?×?10-13) and a novel CALR loss of function variant for essential thrombocythemia (p?=?1.59?×?10-13). We constructed an interactive resource highlighting demographic information and demonstrate transferability by applying our mapping to a medical claims database.

The cost-effectiveness of digital health interventions: A systematic review of the literature
A Gentili et al, Front Public Health, August 2022

The studies were heterogeneous by country (mostly conducted in upper and upper-middle income countries), type of eHealth intervention, method of implementation, and reporting perspectives. The qualitative analysis identified the economic and effectiveness evaluation of six different types of interventions: (1) seventeen studies on new video-monitoring service systems; (2) five studies on text messaging interventions; (3) five studies on web platforms and digital health portals; (4) two studies on telephone support; (5) three studies on new mobile phone-based systems and applications; and (6) three studies on digital technologies and innovations.

Bringing Sickle-Cell Treatments to Children in Sub-Saharan Africa.
Zhou Albert E et al. The New England journal of medicine 2022 8 (6) 488-491

A diagnosis of sickle-cell disease (SCD) portends a lifetime of crises marked by substantial pain, infections, anemia, and increased risk of stroke. Sub-Saharan Africa is home to the majority of people living with SCD. About 236,000 babies are born with SCD in sub-Saharan Africa each year (more than 80 times as many as in the United States), and up to 90% will die during childhood, typically before their fifth birthday. In the United States, by contrast, people with SCD often live into their 40s or beyond. An important contributor to this disparity is differential access to hydroxyurea, a chemotherapeutic agent that reduces the frequency of sickle-cell crises and prolongs survival.


Disclaimer: Articles listed in Hot Topics of the Day are selected by the CDC Office of Public Health Genomics to provide current awareness of the scientific 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 Clips, 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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