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COVID-19 GPH|COVID-19 Genomics and Precision Public Health Weekly Update|PHGKB
Publication Date: Jun 29, 2022
Pathogen and Human Genomics Studies

Interim Recommendations of the Advisory Committee on Immunization Practices for Use of Moderna and Pfizer-BioNTech COVID-19 Vaccines in Children Aged 6 Months–5 Years — United States, June 2022
KE Fleming-Dutra et al, MMWR, June 28, 2022

On June 17, 2022, the Food and Drug Administration granted Emergency Use Authorization for the Moderna and Pfizer-BioNTech COVID-19 vaccines for children aged 6 months–5 years and 6 months–4 years, respectively. On June 18, 2022, the Advisory Committee on Immunization Practices (ACIP) issued interim recommendations for the use of the Moderna COVID-19 vaccine for children aged 6 months–5 years and for the Pfizer-BioNTech COVID-19 vaccine for children aged 6 months–4 years in the United States for prevention of COVID-19. ACIP determined that the benefits of vaccination outweigh risks for this population.
SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters.
Barbé Laure et al. Frontiers in microbiology 2022 6 889811
Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance.
Fast-evolving COVID variants complicate vaccine updates.
Callaway Ewen et al. Nature 2022 6
As countries brace for another Omicron wave driven by the variants BA.4 and BA.5, calls to update COVID-19 vaccines are growing louder. Existing vaccines based on the version of the virus SARS-CoV-2 that emerged in Wuhan, China, in late 2019 are a poor match to current Omicron strains. As a result, the vaccines now offer only short-lived protection from infection — although they seem to be holding up against severe disease.
Within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong
DC Adam et al, MEDRXIV, June 27, 2022
Coupling Wastewater-Based Epidemiological Surveillance and Modelling of SARS-COV-2/COVID-19: Practical Applications at the Public Health Agency of Canada
MJ Joung et al, MEDRXIV, June 27, 2022
Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic control
D Lou et al, MEDRXIV, June 27, 2022
We describe the set-up of an alternative testing platform, which allows scalable surveillance testing as an acute pandemic response tool and for pandemic preparedness purposes, exemplified by SARS-CoV-2 diagnostics in an academic environment. The testing strategy involves self-sampling based on gargling saline, pseudonymized sample handling, automated 96-well plate-based RNA extraction, and viral RNA detection using a semi-quantitative multiplexed colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with an analytical sensitivity comparable to RT-quantitative polymerase chain reaction (RT-qPCR).
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.
Tegally Houriiyah et al. Nature medicine 2022 6
Three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern predominantly drove South Africa’s fourth COVID-19 wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild type amino acid at Q493.The two lineages only differ outside of the spike region.
Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children.
Dewald Felix et al. Nature communications 2022 6 (1) 3640
Systematic SARS-CoV-2 testing is a valuable tool for infection control and surveillance. However, broad application of high sensitive RT-qPCR testing in children is often hampered due to unpleasant sample collection, limited RT-qPCR capacities and high costs. Here, we developed a high-throughput approach ('Lolli-Method') for SARS-CoV-2 detection in children, combining non-invasive sample collection with an RT-qPCR-pool testing strategy. SARS-CoV-2 infections were diagnosed with sensitivities of 100% and 93.9% when viral loads were >106 copies/ml and >103 copies/ml in corresponding Naso-/Oropharyngeal-swabs, respectively.
Contribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong.
Chen Lin-Lei et al. Nature communications 2022 6 (1) 3618
Our study suggests that this BA.2 outbreak and the exceptionally high case-fatality rate in the =80 year-old age group (9.2%) could be attributed to the lack of protective immunity in the population, especially among the vulnerable older adults, and that ongoing sero-surveillance is essential.
Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct.
Mykytyn Anna Z et al. Science immunology 2022 6 eabq4450
The antigenic maps revealed a central cluster of SARS-CoV-2 variants, which grouped based on mutual spike mutations. Whereas these early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape vaccine-induced antibody responses as a result of different antigenic characteristics.
Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID-19.
López-Rodríguez Rosario et al. Scientific reports 2022 6 (1) 10369
We report the presence of rare genetic variants in certain genes, by using whole exome sequencing, in a selected group of COVID-19 patients under 65 years who required intubation or resulting in death (n = 44). To this end, different etiopathogenic mechanisms were explored using gene prioritization-based analysis in which genes involved in immune response, immunodeficiencies or blood coagulation were studied. We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic and were located in genes mainly involved in immune response. A network analysis, including the 42 genes with candidate variants, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks composed by genes enriched in carbohydrate metabolism and in DNA metabolism and repair processes.

Non-Genomics Precision Health Studiess

The effect of notification window length on the epidemiological impact of COVID-19 contact tracing mobile applications
T Leng et al, Communications Medicine, June 27, 2022

We use an epidemiological model of SARS-CoV-2 transmission that captures the profile of infection to consider the trade-off between notification window length and active app use. We focus on 5-day and 2-day windows, the notification windows of the NHS COVID-19 app in England and Wales before and after 2nd August 2021, respectively. Our analyses show that at the same level of active app use, 5-day windows result in larger reductions in transmission than 2-day windows. However, short notification windows can be more effective at reducing transmission if they are associated with higher levels of active app use and adherence to isolation upon notification.
Global impact of the first year of COVID-19 vaccination: a mathematical modelling study.
Watson Oliver J et al. The Lancet. Infectious diseases 2022 6

News, Reviews and Commentaries

The genetic and evolutionary determinants of COVID-19 susceptibility

G Kerner et al, EJHG, June 28, 2022

We discuss recent findings relating to human genetic predisposition to infectious disease, from an immunological or population genetic perspective, and show how these and other innovative approaches have been applied to deciphering the genetic basis of human susceptibility to COVID-19 and the severity of this disease. From an evolutionary perspective, we show how past demographic and selection events characterizing the history of our species, including admixture with archaic humans, such as Neanderthals, facilitated modern human adaptation to the threats imposed by ancient pathogens.
F.D.A. May Move Toward Updating Vaccines

S LaFraniere, NY Times, June 27, 2022

Scientists had high hopes for a new coronavirus vaccine that combines the existing formulation with one targeting Omicron, but many are not impressed by the results. The federal government is hoping to improve the vaccine to better boost people’s immunity before a likely resurgence of the virus this winter. But to move that quickly, it may need to abandon the lengthy human trials that have been used to test coronavirus vaccines over the past two years in favor of a faster process that relies more on laboratory tests and animal trials.
The BA.5 story The takeover by this Omicron sub-variant is not pretty

E Topol, Ground Truths Blog, June 27, 2022

The Omicron sub-variant BA.5 is the worst version of the virus that we’ve seen. It takes immune escape, already extensive, to the next level, and, as a function of that, enhanced transmissibility, well beyond Omicron (BA.1) and other Omicron family variants that we’ve seen (including BA.1.1, BA.2, BA.2.12.1, and BA.4). Here I will review (1) what we know about its biology; (2) its current status around the world; and (3) the ways we can defend against it.
China’s first mRNA vaccine is close — will that solve its COVID woes?

Y Ye, Nature, June 27, 2022

The experimental jab, called ArCoV, is a strong candidate to become China’s first approved mRNA vaccine. But what it would mean for the government’s handling of the pandemic is hard to know, say researchers. A highly effective mRNA vaccine would reduce the chances of widespread serious infections that could overwhelm hospitals. However, it is unlikely to bring an end to the country’s strict ‘zero COVID’ strategy, which uses mass testing and lockdowns to quash all infections.
What Omicron's BA.4 and BA.5 variants mean for the pandemic.

Callaway Ewen et al. Nature 2022 6
How COVID has deepened inequality — in six stark graphics

SM Sidick, Nature, June 23, 2022

Troubling data show how the pandemic has exacted an unequal toll, pushing tens of millions into poverty and having the greatest effects on already-disadvantaged groups. The shock waves of the COVID-19 pandemic have reverberated throughout the world. But the latest data reveal that the burden of COVID and its aftermath does not rest equally. In six graphics, Nature details how the pandemic has worsened existing inequalities and exposed others in terms of income, health, safety and more.

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.