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COVID-19 GPH|COVID-19 Genomics and Precision Public Health Weekly Update|PHGKB
Publication Date: Sep 22, 2022
Pathogen and Human Genomics Studies

Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021.
Yakovleva Anna et al. Scientific reports 2022 9 (1) 15749

We report local sequencing of 103 SARS-CoV-2 genomes from patient samples collected in Kyiv in July-December 2021 using Oxford Nanopore technology. Together with other published Ukrainian SARS-CoV-2 genomes, our data suggest that the third wave of the epidemic in Ukraine (June-December 2021) was dominated by the Delta Variant of Concern (VOC). Our phylogeographic analysis revealed that in summer 2021 Delta VOC was introduced into Ukraine from multiple locations worldwide, with most introductions coming from Central and Eastern European countries.
A Bivalent Omicron-Containing Booster Vaccine against Covid-19.
Chalkias Spyros et al. The New England journal of medicine 2022 9
The bivalent omicron-containing vaccine mRNA-1273.214 elicited neutralizing antibody responses against omicron that were superior to those with mRNA-1273, without evident safety concerns.
Outcomes at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination in adolescents and young adults in the USA: a follow-up surveillance study
I Kracalik et al, The Lancet Infectious Diseases, September 2022
After at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination, most individuals in our cohort were considered recovered by health-care providers, and quality of life measures were comparable to those in pre-pandemic and early pandemic populations of a similar age.
Association of polymorphisms of IL-6 pathway genes (IL6, IL6R and IL6ST) with COVID-19 severity in an Amazonian population.
FBB Rodrigues et al, BIORXIV, September 21, 2022
IL-1RA Antibodies in Myocarditis after SARS-CoV-2 Vaccination
L Thurner et al, NEJM, September 21, 2022
Myocarditis was confirmed by biopsy in 40 of 61 patients. Among patients with histologically confirmed myocarditis, anti–IL-1RA antibodies were found in 9 of 12 patients (75%) younger than 21 years of age, as compared with 3 of 28 patients (11%) 21 years of age or older. Anti–IL-1RA antibodies were not detectable in the 21 patients in whom biopsy ruled out the diagnosis of myocarditis. IL-1RA antibody–positive patients with biopsy-confirmed myocarditis had an early onset of symptoms, which occurred mostly after receipt of the second vaccine dose, and a milder course of myocarditis than patients with biopsy-confirmed myocarditis but without anti–IL-1RA autoantibodies
Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method
E Segelhurst et al, MEDRXIV, September 20, 2022
The impact of cross-reactive immunity on the emergence of SARS-CoV-2 variants
RN Thompson et al, MEDRXIV, September 20, 2022
Here, we investigate the impact of cross-reactive immunity on the emergence of SARS-CoV-2 variants in a simplified scenario in which a novel SARS-CoV-2 variant is introduced after an antigenically related virus has spread in the population. We use mathematical modelling to explore the risk that the novel variant invades the population and causes a large number of cases, as opposed to fading out.
Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments
A Gupta et al, MEDRXIV, September 20, 2022
The role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored. Here, we show that patients treated with various anti-SARS-CoV-2 mAb regimens develop evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Mutations develop more frequently in immunocompromised patients and strongly correlate not only with neutralizing capacity of the therapeutic mAbs, but also with an anti-inflammatory and healing-promoting host milieu.
Improving correlation of wastewater SARS-CoV-2 gene copy numbers with COVID-19 public health cases using readily available biomarkers.
Hutchison Justin M et al. FEMS microbes 2022 9
The COVID-19 pandemic has highlighted the potential role that wastewater-based epidemiology can play in assessing aggregate community health. However, efforts to translate SARS-CoV-2 gene copy numbers obtained from wastewater samples into meaningful community health indicators are nascent. Over the course of the study, the strongest correlations were observed with a one-day case data lag. However, early measurements were strongly correlated with a five-day case data lag. This indicates that in the early stages of the pandemic, the wastewater samples may have indicated active COVID-19 cases before clinical indications.
Mortality Risk Among Patients Hospitalized Primarily for COVID-19 During the Omicron and Delta Variant Pandemic Periods - United States, April 2020-June 2022.
Adjei Stacey et al. MMWR. Morbidity and mortality weekly report 2022 9 (37) 1182-1189
Risk for severe COVID-19 increases with age, disability, and underlying medical conditions. The SARS-CoV-2 Omicron variant is more infectious but has been associated with less severe disease. In-hospital mortality among patients hospitalized primarily for COVID-19 decreased from 15.1% (Delta period) to 4.9% (later Omicron period; April–June 2022), despite high-risk patient groups representing a larger proportion of hospitalizations. During the later Omicron period, the majority of in-hospital deaths occurred among adults aged =65 years (81.9%) and persons with three or more underlying medical conditions (73.4%).
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs
AX Han et al, MEDRXIV, September 16, 2022
We simulated COVID-19 epidemics in a prototypical LMIC to investigate how testing rates, sampling strategies, and sequencing proportions jointly impact surveillance outcomes and showed that low testing rates and spatiotemporal biases delay time-to-detection of new variants by weeks-to-months and can lead to unreliable estimates of variant prevalence even when the proportion of samples sequenced is increased.
Neutralizing antibodies following three doses of BNT162b2 vaccine, breakthrough infection, and symptoms during the Omicron predominant wave
S Yamamoto et al, MEDRXIV, September 17, 2022
The third vaccine dose was effective in decreasing the risk of severe acute respiratory syndrome coronavirus 2 infection during the Omicron wave compared with the second dose. Among third–dose recipients, higher pre–infection NAb levels may not be associated with a lower risk of Omicron infection. Contrarily, they may be associated with fewer symptoms of infection.

Non-Genomics Precision Health Studiess

Bayesian Prediction of Severe Outcomes in the LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort
B Sullivan et al, MEDRXIV, September 21, 2022

News, Reviews and Commentaries

SARS-CoV-2 Genome Set Reveals Evolution, Spread in Africa

Genomeweb, September 16, 2022
Why Omicron Might Stick Around Omicron, the 13th named variant of the coronavirus, seems to have a remarkable capacity to evolve new tricks.

C Zimmer, NY Times, September 22, 2022
Recovery from mRNA COVID-19 vaccine-related myocarditis

E Ammirati et al, Lancet Child and Adolescent Health, September 21, 2022

New data help to resolve the dilemma between vaccination and no vaccination: health-care providers and individuals should be reassured by the high rate of cardiac recovery in mRNA COVID-19 vaccine-related myocarditis. Nonetheless, the psychosocial burden after a myocarditis diagnosis remains substantial and has been under-recognized.
Global distribution of ACE1 (rs4646994) and ACE2 (rs2285666) polymorphisms associated with COVID-19: A systematic review and meta-analysis.

Keikha Masoud et al. Microbial pathogenesis 2022 9 105781

Based on geographical region, the rs4646994 DD genotype may be considered as a predictive biomarker to identify the susceptibility of human to SARS-CoV-2 infection and severe COVID-19 outcomes. We also concluded that individuals with GG and TT genotypes are significantly more susceptible to severe outcomes of disease, while conversely, individuals with GA, AA, and CC genotypes are less susceptible to severe COVID-19.

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.