3rd July - the COVID-19 coronavirus compendium

Deaths from other causes are up during the pandemic, infection protects from re-infection in monkeys, and more data on asymptomatic infections

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This week we learnt that the US has seen an increase in deaths from diabetes, heart disease, and Alzheimer's disease during the pandemic, that monkeys infected with the virus are protected from re-infection, and read another study showing that a high proportion of infections are asymptomatic.

Transmission

A detailed analysis of the outbreak in Vo’, a small town near Padua, Italy, found that 43% of infections were asymptomatic, with similar viral load as those with symptoms. More than 70% of the population was tested, two weeks apart, with the outbreak successfully controlled by lockdown. No infections were found in children under 10, even where they lived with infected contacts, and the average infectiousness period was 3-7 days. This test and trace model, combined with lockdown, has been adopted by the Veneto region.

Apparently healthy truck drivers are a source of SARS-CoV-2 importation into Uganda, and so are being tested at their entry points from Kenya, Tanzania, and South Sudan. At least 6 lineages of virus are circulating in the country, which has had 1500 laboratory confirmed cases.

Children with mild or no COVID-19 disease can still shed live virus, according to a study of 23 infected children in Geneva.

Vaccines

An immunogen made from a dimer of the MERS-CoV spike receptor binding domain showed immunogenicity in mice, and protected them from a MERS virus infection. This strategy was then used to create immunogens at high yields for both SARS and SARS-CoV-2.

A vaccine was designed based on expression of the coronavirus spike protein in bacteria, although it has not yet been tested in animals or humans.

Fatality rate

More than half of the excess deaths during the coronavirus pandemic in some US states were due to causes other than COVID-19. These were mainly deaths due to diabetes, heart disease, or Alzheimer’s disease. So far there have been 87K excess deaths, of which 56K were attributed to COVID-19. This suggests that the pandemic may be exacerbating other conditions, perhaps due to lack of access to healthcare. Another study found that there were 122K excess deaths from March to May in the US, of which 95K were officially attributed to COVID-19.

At risk groups

Black Brazilians and those of mixed ethnicity had increased mortality from COVID-19. A higher fatality rate was also seen in the north of Brazil, which is poorer, as well as in the city of Rio de Janeiro. The effect is likely due to lack of access to health care and the prevalence of pre-existing conditions, which are themselves associated with poverty, such as obesity and diabetes. 

The lack of black doctors, scientists, and engineers in the US has exacerbated the disproportionate impact of COVID-19 on black people, Latinx and native populations, according to a letter from the members of a National Academies of Sciences roundtable on this issue.

A hospital in rural Arizona that cares for 18,000 Native Americans has had a fatality rate of 1.1%, half that seen in the rest of the state, through effective community engagement activities and partnerships with tribal leaders. More than 1600 cases have been identified on the reservation, where intergenerational living is common, with 400 people transported to other hospitals for higher level care.

Multiple sclerosis patients with the most severe disabilities were more likely to have severe COVID-19 disease, with disability a greater predictor than age, in this group of more than 300 MS patients in the US.

Virology

A quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells showed how the virus alters phosphorylation, and identified potential drug targets.

Genetics

A mutation in the SARS-CoV-2 spike protein, D614G has become prevalent worldwide. The mutated virus grows faster in cell culture, when grown as a pseudovirus, and patients infected with this virus appear to have higher titres, although there was no effect on disease severity.

Immunology

Rhesus macaques infected with SARS-CoV-2 are protected from a subsequent re-infection with the same virus, suggesting that immunity can be achieved, although the duration is unclear, and the finding may not apply to humans.

A database of more than 14 million B and T cell receptor sequences from the blood of convalescent COVID-19 patients was developed to understand adaptive immunity to the virus.

Levels of antibodies against the spike protein, as measured by ELISA, correlated well with neutralising antibodies against the virus. T and B cell epitopes were also identified from convalescent sera.

Two separate labs independently developed a vesicular stomatitis virus pseudotyped with the spike protein of SARS-CoV-2, and used it in neutralisation assays with sera from convalescent patients, as a safe alternative to using live virus.

Interactions between epithelial cells and immune cells may contribute to the immune hyperactivation seen during severe COVID-19 disease, and could be targeted by inhibition of CCR1 and CCR5, according to a study of cells from infected humans.

11 more neutralising antibodies have been isolated from convalescent patients, one of which also neutralised SARS virus, and another which appeared to enhance the activity of other antibodies.

Mental health

A survey of 57,000 people in China found that almost one third had depression, anxiety, insomnia or acute stress. Participants with confirmed or suspected COVID-19, or with friends or family with the disease, had an increased risk.

Social distancing

Two thirds of US teenagers do not practice social distancing, according to a survey of 770, recruited via social media. However, they do monitor the news and practice disinfecting. Social distancing was associated with a belief that COVID-19 is severe, as was more hoarding.

Masks

Countries that recommend the use of face masks also explain the importance of their proper use, along with other hygiene practices. The authors suggest that microbiological knowledge should be promoted alongside mask wearing.

N95 respirators can be decontaminated using steam generated by a microwave oven, allowing their re-use.

Clinical findings

15% of children with COVID-19 paediatric multisystem inflammatory syndrome also had new-onset neurological symptoms and splenium signal changes, according to a study from Great Ormond Street Children’s Hospital.

Rhabdomyelosis, a breakdown of skeletal muscle and release of myoglobin, has been seen in some COVID-19 patients.

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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