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COVID-19 GPH|COVID-19 Genomics and Precision Public Health Weekly Update|PHGKB
Publication Date: Feb 2, 2023
Pathogen and Human Genomics Studies

Inequities in COVID-19 vaccine and booster coverage across Massachusetts ZIP codes after the emergence of Omicron: A population-based cross-sectional study.
Jacob Bor et al. PLoS medicine 2023 1 (1) e1004167

We analyzed data on 418 ZIP codes. We observed wide geographic variation in primary series vaccination and booster rates, with marked inequities by ZIP code-level education, median household income, essential worker share, and racial/ethnic composition. In age-stratified analyses, primary series vaccine coverage was very high among the elderly. However, we found large inequities in vaccination rates among younger adults and children, and very large inequities in booster rates for all age groups.
Evaluation of a Commercially Available Rapid RT-PCR Assay's Detection of SARS-CoV-2 Novel Variants
L Back et al, MEDRXIV, February 1, 2023
The next generation of coronavirus vaccines: a graphical guide
E Callaway, Nature, February 1, 2023
Vaccine developers around the world are working on dozens of ‘next-generation’ COVID-19 vaccines: not just updates of the first versions, but ones that use new technologies and platforms. These vaccines are a diverse group, but the overarching aim is to deliver long-lasting protection that is resilient to viral change. Some could protect against broader classes of coronavirus, including ones that have yet to emerge. Others might provide more potent immunity, might do so at lower doses, or might be better at preventing infection or transmission of the virus.
The effect of previous SARS-CoV-2 infection and COVID-19 vaccination on SARS-CoV-2 Omicron infection and relation with serological response – a prospective cohort study
B de Gier et al, MEDRXIV, January 31, 2023
Our results showed that hybrid immunity is more protective against infection with SARS-CoV-2 Omicron than vaccine-induced immunity, up to at least 30 weeks after the last immunizing event. Among those with hybrid immunity, the sequence and number of immunizing events was not found to be of importance, and its protective effect was partly explained by circulating S-antibodies.
Multiomics single timepoint measurements to predict severe COVID-19.
Sina A Tegethoff et al. The Lancet. Digital health 2023 1 (2) e56
Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology.
Supaporn Wacharapluesadee et al. Research square 2023 1
A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/ µl.
The impact of cross-reactive immunity on the emergence of SARS-CoV-2 variants.
Robin N Thompson et al. Frontiers in immunology 2023 1 1049458
We find that, if cross-reactive immunity is complete (i.e. someone infected by the previously circulating virus is not susceptible to the novel variant), the novel variant must be more transmissible than the previous virus to invade the population. However, in a more realistic scenario in which cross-reactive immunity is partial, we show that it is possible for novel variants to invade, even if they are less transmissible than previously circulating viruses.
Interleukin-1 receptor antagonist gene ( IL1RN ) variants modulate the cytokine release syndrome and mortality of SARS-CoV-2.
Mukundan Attur et al. medRxiv : the preprint server for health sciences 2023 1
Mortality in the population was 15.3%, and was lower in women than men (13.1% vs.17.3%, p<0.0003). Carriers of the CTA-1/2 IL1RN haplotypes exhibited decreased inflammatory markers and increased plasma IL-1Ra relative to TTG carriers. Decreased mortality among CTA-1/2 carriers was observed in male patients between the ages of 55-74 [9.2% vs. 17.9%, p=0.001]. Evaluation of individual SNVs of the IL1RN gene (rs419598, rs315952, rs9005) indicated that carriers of the IL1RN rs419598 CC SNV exhibited lower inflammatory biomarker levels, and was associated with reduced mortality compared to the CT/TT genotype in men (OR 0.49 (0.23 - 1.00); 0.052).
Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics based on 10 million genomes.
Hsin-Chou Yang et al. PNAS nexus 2023 1 (4) pgac181
Here we developed systematic approaches based on sets of correlated single nucleotide variations (SNVs) for comprehensive subtyping and pattern recognition of transmission dynamics. The approach outperformed single-SNV and spike-centric scans. Moreover, the derived subtypes elucidate the relationship of signature SNVs and transmission dynamics. We found that different subtypes of the same variant, including Delta and Omicron exhibited distinct temporal trajectories. For example, some Delta and Omicron subtypes did not spread rapidly, while others did.
Extensive SARS-CoV-2 testing reveals BA.1/BA.2 asymptomatic rates and underreporting in school children
MM Martignoni et al, MEDRXIV, January 30, 2023
High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study
M Ghafari et al, MEDRXIV, January 30, 2023
We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus.
Omicron BA.1/BA.2 infections in triple-vaccinated individuals enhance a diverse repertoire of mucosal and blood immune responses
H Hornsby et al, MEDRXIV, January 29, 2023
We characterized mucosal and blood immunity to both spike and non-spike antigens following BA.1/BA.2 infections in triple mRNA-vaccinated individuals, with and without a history of previous SARS-CoV-2 infection. We find that the majority of individuals increase BA.1/BA.2/BA.5-specific NAb following infection, but confirm that the magnitude of increase and post-omicron titres are indeed higher in those who were infection-naive. In contrast, significant increases in nasal antibody responses are seen regardless of prior infection history.
Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases
T Sanderson et al, MEDRXIB, January 27, 2023
Early risk-assessment of pathogen genomic variants emergence
Z Susswein et al, MEDRXIV, January 27, 2023
Despite decades of use for influenza vaccine strain selection and PCR-based molecular diagnostics, data on pathogen variant prevalence and growth advantage has only risen to its current prominence during the SARS-CoV-2 pandemic. However, such data are still often sparse: novel variants are initially rare or a region has limited sequencing. To ensure real-time estimates of risk are available in these types of data-sparse conditions, we develop a hierarchical modeling approach that estimates variant fitness advantage and prevalence by pooling data across geographic regions. We apply this method to estimate SARS-CoV-2 variant dynamics at the country-level and assess its stability with retrospective validation.
Risk Factors for Reinfection with SARS-CoV-2 Omicron Variant among Previously Infected Frontline Workers.
Katherine D Ellingson et al. Emerging infectious diseases 2023 1 (3)
In a cohort of essential workers in the United States previously infected with SARS-CoV-2, risk factors for reinfection included being unvaccinated, infrequent mask use, time since first infection, and being non-Hispanic Black. Protecting workers from reinfection requires a multipronged approach including up-to-date vaccination, mask use as recommended, and reduction in underlying health disparities.
Should COVID vaccines be yearly? Proposal divides US scientists
M Kozlov, Nature, January 27, 2023
Scientists are split about a US Food and Drug Administration’s (FDA) proposal to update COVID-19 vaccines once a year, similar to the agency’s approach for annually updating influenza vaccines. At a meeting of the FDA’s vaccine advisory panel on 26 January, some researchers argued that the proposal to offer an updated vaccine every US autumn would help simplify the country’s complex COVID immunization schedule and might boost uptake as a result. But other scientists were less convinced about the timeline — or whether healthy adults should be urged to receive an annual COVID-19 jab at all.
Do bivalent boosters work against XBB.1.5? Vaccine questions, answered. New CDC data shows updated boosters are cutting risk of getting sick from covid-19 by about half
N Nerapil et al, Washington Post, January 25, 2023

Non-Genomics Precision Health Studiess

A modeling-based approach to optimize COVID-19 vaccine dosing schedules for improved protection
P Dogra et al, MEDRXIV, January 31, 2023
Influence of social deprivation index on in-hospital outcomes of COVID-19.
Parag Goyal et al. Scientific reports 2023 1 (1) 1746
Machine learning models for predicting severe COVID-19 outcomes in hospitals
P Wendland et al, MEDRXIV, January 30, 2023

The aim of this observational retrospective study is to improve early risk stratification of hospitalized Covid-19 patients by predicting in-hospital mortality, transfer to intensive care unit (ICU) and mechanical ventilation from electronic health record data of the first 24 hours after admission. Methods and Results Our machine learning model predicts in-hospital mortality (AUC=0.918), transfer to ICU (AUC=0.821) and the need for mechanical ventilation (AUC=0.654) from a few laboratory data of the first 24 hours after admission.
A large-scale machine learning study of sociodemographic factors contributing to COVID-19 severity
M Tumbas et al, MEDRXIV, January 29, 2023
We assemble 115 predictors for more than 3000 US counties and employ a well-defined COVID-19 severity measure derived from epidemiological dynamics modeling. We then use a number of advanced feature selection techniques from machine learning to determine which of these predictors significantly impact the disease severity. We obtain a surprisingly simple result, where only two variables are clearly and robustly selected - population density and proportion of African Americans.
The impact of COVID-19 lockdown on a cohort of adults with recurrent major depressive disorder from Catalonia: a decentralized longitudinal study using remote measurement technology
R Lavalle et al, MEDRXIV, January 27, 2023
From crisis to opportunity in a big data study: barriers and facilitators in a national web-based COVID-19 surveillance study.
Andrea Price et al. Annals of family medicine 2023 1 (20 Suppl 1)
Large participant enrollment and data accrual resulted in the need for creative approaches to trouble shooting "big data" challenges associated with the rapid start-up of a high enrolling COVID -19 surveillance study. Preemptive messaging and anticipating participants' needs enhanced enrollment, participation and retention.

About Weekly Scan

This weekly update contains the latest information and publications on the impact of genomics and precision health technologies on the investigation and control of COVID-19. Items are selected by staff from the CDC Office of Genomics and Precision Public Health daily from the COVID-19 GPH.

Disclaimer: Articles listed in the Public 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.