2nd October - the COVID-19 coronavirus compendium

Neanderthal DNA, India, and cancer patients

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This week we learnt that a genetic risk factor for severe COVID-19 was inherited from Neanderthals, that the outbreak in India is mainly in younger adults, and that the prevalence of the virus in cancer patients in New York was lower than that in the general population, suggesting that they are effectively protecting themselves from infection.

Genomics

A genetic risk factor for severe COVID-19 found on chromosome 3 was shown to be inherited from Neanderthals. The haplotype is common in people of European and South Asian ancestry, especially those from Bangladesh. Bangladeshi people in the UK are more likely to have severe COVID-19.

Transmission

A detailed analysis of the outbreak in two Indian states was described, with the majority of cases and deaths in younger adults, rather than older people as in higher-income countries. The case fatality rate ranged from 0.05% in ages 5-17 to 17% in those aged over 85.

Immunology

Deep serological profiling of the antibody response in COVID-19 patients and healthy controls identified epitopes across multiple viral proteins and was used to develop a rapid Luminex-based diagnostic assay. Pre-existing antibodies in uninfected individuals that cross reacted to SARS-CoV-2 were also identified in some people, most likely from past infection with common cold coronaviruses. The binding mode of several antibodies against SARS-CoV-2 was also measured.

T cell epitopes generated against SARS-CoV-2 were mapped from convalescent patients. T cell responses were identified even in those who did not develop antibodies, and some cross reacted with common cold seasonal coronaviruses. Those with mild disease had a more diverse T cell repertoire than those with severe illness.

At risk groups

The prevalence of COVID-19 in asymptomatic cancer patients in New York was exceedingly low, at 4% by serology and 1% by RT-PCR, compared to a prevalence of 20% in the general population in the city. This suggests that cancer patients are protecting themselves from the virus through social distancing, mask wearing, and other measures, and that chemotherapy and surgery should go ahead as planned.

Vaccines

The messenger RNA vaccine from Moderna, mRNA-1273, was tested in a phase 1 trial in older adults, with responses similar to those seen in younger adults.

A second phase 1 / 2 clinical trial of the mRNA vaccine, BNT162b1, was reported. The vaccine was immunogenic, with stronger responses than seen in convalescent sera. An Adenovirus-based vaccine encoding a stabilised spike protein induced immune responses in mice.

A survey found that the US public demonstrate a high willingness for a COVID-19 vaccine to be allocated to healthcare workers first, as well as those at risk of severe disease, although they also showed a preference for giving the vaccine first to children, despite them being at low risk.

Treatments

A complement C5 inhibitor, monoclonal antibody IFX-1 (vilobelimab), was tested in COVID-19 patients in a small clinical trial. The treatment was safe, but the study was too small to assess efficacy at reducing severe disease.

Pre-exposure prophylaxis with hydroxychloroquine did not prevent healthcare workers from catching SARS-CoV-2, in yet another study to show that this drug is not effective.

Diagnostics

A CRISPR-Cas12a RT-LAMP was developed that can detect viral RNA in 40-60 minutes.

Health

The frequency of alcohol consumption in the US increased during the pandemic, with potential health consequences.

Clinical findings

Of 60 COVID-19 patients who had cardiac arrest in a US hospital, all of them died. Normally 25% of patients who have in hospital cardiac arrest survive. The reasons for this discrepancy are not clear, but could include the use of mechanical ventilation.

A set of clinical criteria for COVID-19 related hyperinflammatory syndrome was proposed.

The hypoxia seen early on in COVID-19 patients was modelled, showing that it can be explained by pulmonary embolism and ventilation-perfusion mismatch.

Ben Johnson

Head of Communities & Engagement, Springer Nature

I gained my first degree in virology from the University of Warwick and a PhD in influenza virus immune evasion from Public Health England and the University of Reading, UK. My research interests then moved on to smallpox vaccines, viral ion channels, and cell adhesion, while a postdoc at Imperial College London. I joined open access publisher BioMed Central in 2011 as an Acquisitions Editor and then Associate Publisher, and was responsible for launching new journals, including Microbiome, Zoological Letters, and Movement Ecology. I have been Head of Communities & Engagement at Springer Nature since 2016, running our online community blogs, and a Consulting Editor at Nature Medicine since June 2020, handling COVID-19 papers. I am based in our London office.

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