COVID news and trends @ 13 November

The numbers

Election week and its globally reported aftermath in the US was accompanied by a series of record days for COVID-19 cases. The New York Times reported 139,855 new cases nationally on 10 November, a 69% increase over 14 days. There are hotspot clusters in Iowa, North and South Dakota and Kansas, among other states.

At a media briefing on 6 November, WHO director-general Tedros Adhanom Ghebreyesus announced that WHO and UNICEF were jointly launching an emergency appeal to rapidly boost measles and polio vaccination.

“In the summer, Africa was certified as wild polio free,” he said. “This marked one of the greatest public health achievements of all time.”

But, he said, the suspension of immunisation programs due to COVID-19 “left children, especially in high-risk areas, more vulnerable to killer diseases like polio, measles and pneumonia.

“And now we’re starting to see outbreaks of these diseases. We need to turn the tide quickly and ensure no child is left behind.

“While the world watches intently as scientists work to ensure safe and effective vaccines are developed for COVID-19, it is important to ensure that all children receive the lifesaving vaccines that are already available.”

Global

As at 17:52 CET on Wednesday 11 November, cases confirmed worldwide by national authorities stood at 51,251,715 (490,478 of them reported in the preceding 24 hours). 1,270, 930 deaths have been recorded (8570). (Source: WHO Coronavirus Disease Dashboard)

Johns Hopkins University’s Centre of Systems Science and Engineering (CSSE) reported (at 16:00 AEST on Thursday 12 November) 52,069,683 confirmed cases and 1,283,510 deaths.

Australia

The Department of Health reported on 11 November that national confirmed cases stood at 27,686, a rise of 8 in 24 hours. 907 deaths have been recorded; none have been reported in the past seven days.

State by state: ACT 114 total cases (first case reported 12 March); NSW 4478 (25 January); NT 41 (20 March); Qld 1179 (29 January); SA 519 (2 February); Tas 230 (2 March); Vic 20,345 (25 January); WA 780 (21 February).

Research

A strategy for using a vaccine

When we finally have a vaccine for COVID-19, who should be at the front of the queue if initial supplies are limited?

Australian researchers from Macquarie University, QUT and CSIRO have developed a theoretical model for a vaccination strategy they say would have the biggest impact – with the least amount of resources – on suppressing the spread of the virus.

It works by identifying locations visited by people most likely to become “superspreaders”, who transmit infectious diseases to an unexpectedly large number of others.

The team used anonymised location data for the movements of 600,000 people in Shanghai and Beijing who were on a messaging app called Momo, analysing 56 million location visits in just 71 days. They then calculated all the other people they would have come in direct and indirect contact with and then extrapolated these trends to develop a model to test the theoretical effectiveness of a vaccine strategy.

Using the location data, they ranked people into six classes by the number of places they’d visited. For example, Class 1 meant the person had only stayed at home or visited local shops and been in contact with up to five people. A person in Class 2 would have also gone to a coffee shop or a bus stop and been in direct and indirect contact with up to 15 people.

“Our research shows that to be effective – and realistic – it’s not about who exactly a superspreader has been in contact with 24×7 but where they’ve been that should be the focus of vaccination,” says Macquarie’s Bernard Mans.

Current theoretical vaccination strategies were not designed to capture indirect transmissions and potentially miss out on individuals’ numerous indirect links, the researchers say. Focussing on location means you can easily discover indirect contacts.

The findings are published in the journal PLOS ONE.

Measuring the physical and mental toll

Research from Michigan paints a troubling picture of how COVID-19 survivors can struggle.

Most dramatically, data from 1250 patients treated in 38 hospitals during the northern spring and summer, when the state was one of the first in the US to experience a peak in cases, show that nearly 7% died within two months and 15% ended up back in hospital.

When the researchers from the University of Michigan then interviewed 488 patients by phone around 60 days after their hospitalisation, they heard a litany of health and life woes.

More than 39% hadn’t returned to normal activities, 12% couldn’t carry out basic care for themselves anymore, or as well as before, and nearly 23% became short of breath climbing a flight of stairs. One-third had ongoing COVID-like symptoms, including many who still had problems with taste or smell.

Of those who had jobs before their illness, 40% said they couldn’t return to work: most because of their health and some because they’d lost their job. And 26% of those who had gone back to work said they had to work fewer hours or have reduced duties.

Nearly half of those interviewed said they’d been emotionally affected by their experience with COVID-19. A minority said they’d sought mental health care.

“These data suggest that the burden of COVID-19 extends far beyond the hospital and far beyond health,” says Vineet Chopra, lead author of a paper in the Annals of Internal Medicine.

Quantifying the risk to Australian healthcare workers

Healthcare workers are nearly three times more likely to get COVID-19 than other Australians, according to a study of the early pandemic period from UNSW Sydney.

A team led by the Head of Global Biosecurity at the Kirby Institute, Raina MacIntyre, searched government reports, websites and media reports to create a comprehensive line listing of healthcare worker infections and nosocomial outbreaks (those starting in hospitals) between 25 January and 8 July.

They then calculated rates of infections and odds ratios for healthcare workers per state, by comparing overall cases to estimated healthcare worker cases.

“Despite low community prevalence during the period studied, which was prior to the second wave in Victoria, we identified 536 cases of COVID-19 among Australia healthcare workers up to the beginning of July, meaning that more than one in 20 of Australia’s COVID-19 cases were potentially acquired on the job, in our health system,” MacIntyre says.

The findings are published in the International Journal of Nursing Studies.

The researchers acknowledge some limitations, including that the data were based on open-sourced reporting of healthcare worker cases, which may vary depending on each state’s data publishing policies. They also used media reports, which have not been verified.

“In most cases, however, there were multiple media reports about each outbreak, often with quotes from health officials,” MacIntyre says. “This means we have likely underestimated the true number of healthcare worker infections…”

Australia does not have a system for publicly reporting COVID-19 in healthcare workers.

Seeing the research with fresh eyes

Given the enormous amount of research being generated in the global quest to understand COVID-19 (over 60,000 articles in the medical database PubMed), it’s not surprising that someone somewhere would attempt to corral it.

Researchers at Sweden’s Karolinska Institutet employed a machine learning technique that let them map key areas of a research field and track development over time. The process is described in the Journal of Medical Internet Research and a website provides updates.

“Despite COVID-19 being a novel disease, several systematic reviews have already been published,” says co-author Andreas Älgå “However, such reviews are extremely time and resource consuming, generally lag far behind the latest published evidence, and only focus on a specific aspect of the pandemic.”

The new study included 16,670 scientific papers on COVID-19 published from 14 February to 1 June 2020, divided into 14 different topics. The most common were health care response, clinical manifestations, and psychosocial impact. Some, like health care response, declined over time, while others, such as clinical manifestations and protective measures, grew.

Protective measures, immunology and clinical manifestations were the topics published in journals with the highest average scientific ranking. The countries that accounted for the majority of publications (the US, China, Italy and the UK) were also amongst the ones hardest hit by the pandemic.

“We hope that our results, including the website, could help researchers and policy makers to form a structured view of the research on COVID-19 and direct future research efforts accordingly,” says Älgå.

Mink problems in Europe

Denmark has grabbed the headlines over plans to cull mink, but coronavirus cases have also been detected in farmed mink in the Netherlands and Spain.

In the Netherlands, whole genome sequencing of outbreaks on 16 farms has revealed virus transmission from humans to mink, as well as from mink to human. The virus was initially introduced from humans and it has since evolved, the researchers write in a paper in Science.

The analysis – led by Bas B. Oude Munnink from Erasmus University Medical Centre – combined SARS-CoV-2 diagnostics, whole-genome sequencing and in-depth interviews with farm workers.

The virus was first diagnosed on two mink farms in late April. By the end of June, 66 of 97 farm residents, employees and/or contacts tested had evidence for SARS-CoV-2 infection. Analysis of the mink virus genomes on these farms revealed a diversity of sequences.

It also revealed that some people were infected with strains of the virus with an animal sequence signature, providing evidence of animal to human transmission. Further analysis indicated no spill over to people living in close proximity to mink farms.

“Despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, transmission occurred between mink farms in three big transmission clusters with unknown modes of transmission,” the authors write.

Although several animals have been shown to be susceptible to SARS-CoV-2, the zoonotic origin of the pandemic is still unknown.

In brief

People of black or Asian ethnicity are twice and 1.5 times as likely, respectively, to be infected with COVID-19 than those of white ethnicity, according to a UK study. Researchers at the universities of Leicester and Nottingham analysed data from more than 18 million people who had taken part in 50 studies in the UK and the US. “Our findings suggest that the disproportionate impact… is mainly attributable to increased risk of infection in these communities,” says Manish Pareek, senior author of a paper in EClinical Medicine.

Self-reports of smell and taste changes provide earlier markers of the spread of infection of SARS-CoV-2 than current governmental indicators, according to an international team of researchers. They also observed a decline in self-reports of smell and taste changes as early as five days after lockdown enforcement, with faster declines reported in countries that adopted the most stringent lockdown measures. The study used data from the Global Consortium for Chemosensory Research survey, a crowd-sourced online study deployed in more than 35 languages. It is published in Nature Communications.