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COVID-19 GPH|COVID-19 Genomics and Precision Public Health Weekly Update|PHGKB
Publication Date: Jun 17, 2021
Pathogen and Human Genomics Studies

Neutralization of SARS-CoV-2 Variants B.1.429 and B.1.351
X Shen et al, NEJM, June 17, 2021 >

The modestly lower value in neutralization titers against the B.1.429 variant seen in this study is similar to that we saw previously when neutralization of the B.1.1.7 variant was tested with the same assay using serum samples obtained from recipients of the mRNA-1273 and NVX-CoV2373 vaccines.4 These results, and the high efficacy shown by these vaccines, suggest that vaccine-elicited neutralizing antibodies are likely to remain effective against the B.1.429 variant. The magnitude of resistance seen with the B.1.351 variant is of greater concern with respect to current vaccines.
Preliminary Findings of mRNA Covid-19 Vaccine Safety in Pregnant Persons
TT Shimabukuru et al, NEJM< June 17, 2021>
Among 3958 participants enrolled in the v-safe pregnancy registry, 827 had a completed pregnancy, of which 115 (13.9%) resulted in a pregnancy loss and 712 (86.1%) resulted in a live birth (mostly among participants with vaccination in the third trimester). Adverse neonatal outcomes included preterm birth (in 9.4%) and small size for gestational age (in 3.2%); no neonatal deaths were reported.
A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa
CL Althaus et al, MEDRXIV, June 15, 2021>
Predicted domination of variant Delta of SARS-CoV-2 before Tokyo Olympic games, Japan
K Ito et al, MEDRXIV, June 15, 2021>
Using nucleotide sequences of SARS-CoV-2 strains collected in Japan, the relative instantaneous reproduction numbers of the R.1, Alpha, and Delta variants with respect to other strains were estimated at 1.256, 1.449, and 1.776, respectively. The numbers can range 1.198-1.335 for R.1, 1.342-1.596 for Alpha, and 1.557-2.00 for Delta depending on the assumed serial interval distributions. The frequency of the Delta is expected to take over the Alpha in Japan around July 12, 2021.
Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis
T Nyberg et al, BMJ, June 15, 2021>
839?278 patients with laboratory confirmed covid-19, of whom 36?233 had been admitted to hospital within 14 days, tested between 23 November 2020 and 31 January 2021. The risk of hospital admission is higher for people infected with the B.1.1.7 variant compared with wild-type SARS-CoV-2, likely reflecting a more severe disease. The higher severity may be specific to adults older than 30 years.
SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness
A Sheikh et al, The Lancet, June 14, 2021>
We show that the Delta VOC in Scotland was found mainly in younger, more affluent groups. Risk of COVID-19 hospital admission was approximately doubled in those with the Delta VOC when compared to the Alpha VOC, with risk of admission particularly increased in those with five or more relevant comorbidities. Both the Oxford–AstraZeneca and Pfizer–BioNTech COVID-19 vaccines were effective in reducing the risk of SARS-CoV-2 infection and COVID-19 hospitalisation in people with the Delta VOC
Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals
T Kustin et al, Nature Medicine, June 14, 2021 >
Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.
A blood RNA transcriptome signature for COVID-19.
Kwan Philip Kam Weng et al. BMC medical genomics 2021 6 (1) 155>
We found 135 differentially-expressed genes in the patients with COVID-19 (median age 35 years; 82% male; 36% Chinese, 53% South Asian ethnicity). Of the 117 induced genes, 14 were found in datasets from RSV and 40 from influenza; 95 genes were unique to COVID-19. Protein pathways were mostly generic responses to viral infections, including apoptosis by P53-associated pathway, but also included some unique pathways such as viral carcinogenesis. There were no major qualitative differences in pathways between ethnic groups.
AI-guided discovery of the invariant host response to viral pandemics
D Sahoo et al, EBiomedicine, June 11, 2021>
Over 45,000 transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because it encodes the receptor that facilitates the entry of SARS-CoV-2 (the virus that causes COVID-19) into host cells. An AI-based approach was used to explore the utility of the signature. The 166-gene signature was conserved across all viral pandemics, including COVID-19, and a subset of 20-genes classified disease severity.
SARS-CoV-2 in wastewater from Mexico City used for irrigation in the Mezquital Valley: quantification and modelling of geographic dispersion
Y Coronado et al, MEDRXIV, June 12, 2021>
We quantified SARS-CoV-2 in rivers and irrigation canals in the Mezquital Valley, Hidalgo, an agricultural region where wastewater from Mexico City is distributed and used for irrigation. Using quantitative RT-PCR, we detected the virus in 6 out of 8 water samples from rivers, and 5 out of 8 water samples from irrigation canals. Notably, samples showed a general consistent trend of having the highest viral loads in the sites closer to Mexico City, indicating that this is the main source that contributes to detection.
Second wave of COVID-19 in India could be predicted with genomic surveillance of SARS-CoV-2 variants coupled with epidemiological data: A tool for future
A Kumar et al, MEDRXIV, June 13, 2021>
We analyzed the monthly distribution of the genomic sequence data for SARS-CoV-2 from India and correlated that with the epidemiological data for new cases and deaths, for the corresponding period of the second wave. Our analysis shows that the first indications of arrival of the second wave were observable by January, 2021, and by March, 2021 it was clearly predictable. B.1.617 lineage variants drove the wave, particularly B.1.617.2 (a.k.a. delta variant).
Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants
Wang L, et al. Innovation, Jun 7, 2021.>
SARS-CoV-2 has recently been found to have spread from humans to minks and then to have transmitted back to humans. However, it is unknown to what extent the human-to-human transmission caused by the variant has reached. Here, we used publicly available SARS-CoV-2 genomic sequences from both humans and minks collected in Denmark and Netherlands, and combined phylogenetic analysis with Bayesian inference under an epidemiological model to trace the possibility of person-to-person transmission. The results showed that at least 12.5% of all people being infected with dominated mink-derived SARS-CoV-2 variants in Denmark and Netherlands were caused by human-to-human transmission...
A year of COVID-19 GWAS results from the GRASP portal reveals potential SARS-CoV-2 modifiers
F Thibord et al, MEDRXIV, June 11, 2021>
Between May 2020 and February 2021, we used Covid-19 data from UK Biobank and performed over 400 Genome-Wide Association Studies (GWAS) of Covid-19 susceptibility (N=15,738 cases), hospitalization (N=1,916), severe outcomes (N=935) and death (N=828), We observed 2 independent signals at the chr3p21.31 locus (rs73062389-A, OR=1.22, P=7.64E-14 and rs13092887-A, OR=1.73, P=2.38E-8, in Europeans) modulating susceptibility and severity, respectively, and a signal influencing susceptibility at the ABO locus (rs9411378-A, OR=1.10, P =7.36E-10, in Europeans).
Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021
P Paul et a, CDC MMWR, June 10, 2021>
CDC’s genomic surveillance for SARS-CoV-2 variants generates population-based estimates of the proportions of variants among all SARS-CoV-2 infections in the United States. During April 11–24, 2021, the B.1.1.7 and P.1 variants represented an estimated 66.0% and 5.0% of U.S. infections, respectively, demonstrating the potential for new variants to emerge and become predominant.

Non-Genomics Precision Health Studiess

NIH study offers new evidence of early SARS-CoV-2 infections in U.S.
NIH, June 15, 2021

A new antibody testing study examining samples originally collected through the National Institutes of Health’s All of Us Research Program found evidence of SARS-CoV-2 infections in five states earlier than had initially been reported. These findings were published in the journal Clinical Infectious Diseases. The results expand on findings from a Centers for Disease Control and Prevention study that suggested SARS-CoV-2, the virus that causes COVID-19, was present in the U.S. as far back as December 2019.
Role of meteorological factors in the transmission of SARS-CoV-2 in the United States
Y MA et al, Nature Comms, June 14, 2021
We quantify the associations of daily mean temperature, specific humidity, and ultraviolet radiation with daily estimates of the SARS-CoV-2 reproduction number (Rt) and calculate the fraction of Rt attributable to these meteorological conditions. Lower air temperature (within the 20–40?°C range), lower specific humidity, and lower ultraviolet radiation were significantly associated with increased Rt. The fraction of Rt attributable to temperature, specific humidity, and ultraviolet radiation were 3.73% (95% empirical confidence interval [eCI]: 3.66–3.76%), 9.35% (95% eCI: 9.27–9.39%), and 4.44% (95% eCI: 4.38–4.47%), respectively. In total, 17.5% of Rt was attributable to meteorological factors.
Early Prediction of In-Hospital Death of COVID-19 Patients: A Machine-Learning Model Based on Age, Blood Analyses, and Chest X-Ray Score
A Garrafa et al, MEDRXIV, June 13, 2021
The final score was constructed by age (the most powerful predictor), blood analytes (the strongest predictors were lactate dehydrogenase, D-dimer, Neutrophil/Lymphocyte ratio, C-reactive protein, Lymphocyte %, Ferritin std and Monocyte %), and Brescia chest X-ray score. The areas under the receiver operating characteristic curve obtained for the three groups (training, validating and testing) were 0.98, 0.83 and 0.78, respectively.
Deaths involving COVID-19 by disability status: a retrospective analysis of 29 million adults during the first two waves of the Coronavirus pandemic in England
ML Bosworth et al, MEDRXIV, June 13, 2021
This is a cohort study of >29 million adults using data from the Office for National Statistics Public Health Data Asset. Age-adjusted analyses showed that, compared to non-disabled people, mortality involving COVID-19 was higher among both more-disabled people (HR=3.05, 95% CI: 2.98 to 3.11 in males; 3.48, 3.41 to 3.56 in females) and less-disabled people (HR=1.88, 95% CI: 1.84 to 1.92 in males; 2.03, 1.98 to 2.08 in females).

News, Reviews and Commentaries

Cases of a dangerous Covid-19 variant are 'rapidly increasing' in US, expert says

A Elamroussi, CNN, June 16, 2021
Vaccines highly effective against hospitalisation from Delta variant

Public Health England, June 14, 2021

New analysis by PHE shows for the first time that 2 doses of COVID-19 vaccines are highly effective against hospitalization from the Delta (B.1.617.2) variant. The analysis suggests: the Pfizer-BioNTech vaccine is 96% effective against hospitalisation after 2 doses; the Oxford-AstraZeneca vaccine is 92% effective against hospitalization after 2 doses.
Delta variant: What is happening with transmission, hospital admissions, and restrictions?

E Mahase, BMJ, June 15, 2021
Using ‘big data’ to disentangle aging and COVID-19

RR Montgomery et al, Nature Aging, June 14, 2021

A new study leverages different types of big data, either generated in house from cohorts of healthy aging and COVID-19, or downloaded from the ever-increasing public data archives, to disentangle the distinct cellular and proteomic mechanisms of COVID-19 and aging.
A new coronavirus variant is on the rise. Here's why experts are concerned

M Holcombe et al, CNN Health, June 14, 2021
A long-term perspective on immunity to COVID

A Radbruch et al, Nature News, June 14, 2021

Determining the duration of protective immunity to infection by SARS-CoV-2 is crucial for understanding and predicting the course of the COVID-19 pandemic. Clinical studies now indicate that immunity will be long-lasting.
RAS inhibition and COVID-19: more questions than answers?

M Kerneis et al, Lancet Respiratory Medicine, June 11, 2021

The ACEI-COVID study adds more data to the existing evidence showing that RAS blockers should not be systematically discontinued in patients with COVID-19, but it leaves us also with more questions than answers.
As more kids go down the ‘deep, dark tunnel’ of long Covid, doctors still can’t predict who is at risk

E Cooney, StatNews June 10, 2021
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse.

Konings Frank et al. Nature microbiology 2021 6
How a rampant coronavirus variant blunts our immune defences.

Mallapaty Smriti et al. Nature 2021 6
Fast-spreading SARS-CoV-2 variants: challenges to and new design strategies of COVID-19 vaccines.

Zhou Weilin et al. Signal transduction and targeted therapy 2021 6 (1) 226
Embrace the WHO's new naming system for coronavirus variants.

et al. Nature 2021 6 (7862) 149
Leveraging artificial intelligence for pandemic preparedness and response: a scoping review to identify key use cases

A Syrowatka et al, NPJ Digital Medicine, June 10, 2021

The search identified 1167 articles that reported on traditional modeling approaches, which highlighted additional areas where ML could be leveraged for improving the accuracy of estimations or projections. Important ML-based solutions have been developed in response to pandemics, and particularly for COVID-19 but few were optimized for practical application early in the pandemic.
Delta Variant and COVID-19 Vaccines: What to Know

R Ellis, Medscape, June 10, 2021

The Delta variant was first detected in India in December 2020 and has now spread to 60 nations, the CDC says. The World Health Organization has designated it the fourth global variant of concern, along with the ones first identified in the United Kingdom, South Africa, and Brazil. As the Delta coronavirus variant continues to devastate India and spread to other nations, health experts are reiterating the importance of getting the COVID-19 vaccine – both doses of the shot, that is.
More transmissible, wilier variant makes Covid-19 vaccinations even more crucial, experts say

A Joseph, Stat News, June 10, 2021

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.