COVID news and trends @ 27 November

The numbers

Global

As at 19:03 CET on Wednesday 25 November, cases confirmed worldwide by national authorities stood at 59,481,313 (527,326 of them reported in the preceding 24 hours). 1,404,542 deaths have been recorded (9989). (Source: WHO Coronavirus Disease Dashboard)

Johns Hopkins University’s Centre of Systems Science and Engineering (CSSE) reported (at 16:00 AEST on Thursday 26 November) 60,346,970 confirmed cases and 1,420,721 deaths.

Australia

The Department of Health reported on 25 November that national confirmed cases stood at 27,854, a rise of 6 in 24 hours. 907 deaths have been recorded; none have been reported since 28 October.

State by state: ACT 115 total cases (first case reported 12 March); NSW 4552 (25 January); NT 47 (20 March); Qld 1197 (29 January); SA 558 (2 February); Tas 230 (2 March); Vic 20,345 (25 January); WA 810 (21 February).

Research

Virus mutations don’t increase transmissibility

None of the mutations currently documented in the SARS-CoV-2 virus appears to increase its transmissibility in humans, according to a new study in Nature Communications.

A research team from University College London (UCL), Cirad, Université de la Réunion, and University of Oxford analysed a dataset of virus genomes from 46,723 people in 99 countries collected up to the end of July. They have so far identified 12,706 mutations in SARS-CoV-2.

“The number of SARS-CoV-2 genomes being generated for scientific research is staggering,” says UCL’s Lucy van Dorp, the study’s first author. “We realised early on in the pandemic that we needed new approaches to analyse enormous amounts of data in close to real time to flag new mutations in the virus that could affect its transmission or symptom severity.

“Fortunately, we found that none of these mutations [is] making COVID-19 spread more rapidly, but we need to remain vigilant and continue monitoring new mutations, particularly as vaccines get rolled out.”

Coronaviruses, a type of RNA virus, can develop mutations in three ways: by mistake from copying errors during viral replication, through interactions with other viruses infecting the same cell, or by being induced by host RNA modification systems which are part of host immunity (e.g. a person’s own immune system).

Most mutations are neutral, while others can be advantageous or detrimental to the virus. Both neutral and advantageous mutations can become more common as they get passed down to descendant viruses.

To test if the mutations increase transmission of the virus, the researchers modelled the virus’s evolutionary tree and analysed whether a particular mutation was becoming increasingly common within a given branch of the tree. They found that most of the common mutations appear to have been induced by the human immune system, rather than being the result of the virus adapting to its novel human host.

“The virus seems well adapted to transmission among humans, and it may have already reached its fitness optimum in the human host by the time it was identified as a novel virus,” van Dorp says.

X-rays may provide first line check

Researchers at Northwestern University in the US have developed an algorithm they say can detect COVID-19 from X-ray images of the lungs – and do it much faster than specialist thoracic radiologists.

Writing in the journal Radiology, they say the DeepCOVID-XR platform could be used to rapidly screen people admitted to hospital for reasons other than COVID-19 and potentially flag patients for isolation and testing.

It’s still in the research phase and isn’t designed to replace actual testing, they stress, but a routine X-ray could screen patients in seconds and determine if they need to be isolated.

“AI doesn’t confirm whether or not someone has the virus,” says researcher Ramsey Wehbe, “but if we can flag a patient with this algorithm, we could speed up triage before the test results come back.”

Pneumonia, heart failure and other illnesses in the lungs can look similar on X-rays and it takes a trained eye to tell the difference between COVID-19 and something less contagious.

To develop and train the new algorithm, the researchers used 17,002 images – the largest published clinical dataset of chest X-rays from the COVID-19 era used to train an AI system.

They then tested it against five experienced radiologists on 300 random test images. Each radiologist took 150-210 minutes to examine the set of images, whereas the AI system took about 18. The radiologists’ accuracy was 76-81%; DeepCOVID-XR’s was 82%.

“These are experts who are sub-specialty trained in reading chest imaging,” Wehbe says, “whereas the majority of chest X-rays are read by general radiologists or initially interpreted by non-radiologists, such as the treating clinician. A lot of times decisions are made based off that initial interpretation.”

“Radiologists are expensive and not always available,” adds senior author Aggelos Katsaggelos. “X-rays are inexpensive and already a common element of routine care.”

Analysing the mask analysis

Many studies have explored the physics of face mask design and use during COVID-19, and a new paper attempts to summarise what we do and don’t know about how they filter or block the virus.

Sanjay Kumar and Heow Pueh Lee, from the National University of Singapore, write in Physics of Fluids that a key aspect is the size of fluid droplets expelled from the nose and mouth when a person talks, sings, sneezes, coughs or simply breathes.

Even the larger droplets are relatively small, and the smaller ones (below five microns) are particularly dangerous as they can remain suspended in air for long periods. Only N95 masks can filter out aerosol-sized droplets, the researchers report.

The performance of masks worn for many hours affects how effective overall mask wearing can be. Thermal comfort is an important issue, especially in hot and humid environments.

The investigators found masks made of hybrid polymer materials could filter particles at high efficiency while simultaneously cooling the face. The fibres are transparent to infrared radiation, allowing heat to escape from beneath the mask.

“There could be some relation between breathing resistance and the flow resistance of the face mask which will need to be studied for a face mask-wearing interval,” says Lee. “Also, the environmental condition in the compartmental space within the face mask will need to be more accurately quantified using miniaturised sensors and the development of human replicas for such studies.”

The pair also reviewed epidemiological studies looking at whether masks reduce the effective reproduction number. One study from the US suggests that the consistent use of efficient masks could lead to the eradication of the pandemic if at least 70% of the residents use them in public consistently. “Even less efficient cloth masks could also slow the spread if worn consistently,” Kumar says.

How the virus survives on surfaces

There is just as much interest in how the virus behaves when it lands, and Indian researchers have revealed that a nanofilm of liquid persists for long periods on surfaces contaminated with droplets containing COVID-19, helping it to survive.

Also writing in Physics of Fluids, Rajneesh Bhardwaj and Amit Agrawal at IIT Bombay report that while the drying time of typical respiratory droplets is a matter of seconds, for COVID-19 on different surfaces in recent experiments it was in the order of hours.

The nanometres-thick liquid film clings to the surface due to London-van der Waals forces. The film is assumed to be like a pancake deposited onto a surface. The researchers briefly examined changes in drying time as a function of contact angle and surface type.

“To describe this thin film, we used tools that are otherwise seldom used by researchers within the engineering realm,” says Bhardwaj.

The drying time suggests, he adds, that the surface isn’t completely dry, and “the slowly evaporating nanometric film is providing the medium required for the survival of the coronavirus”.

As well as regularly disinfecting surfaces, the researchers recommend heating them, as this can help evaporate the nanometric film and destroy the virus.

An eye to the future

Researchers led by Australia’s University of Sydney have identified where in the world a future pandemic is most likely to emerge by analysing where wildlife-human interfaces intersect with areas of poor human health outcomes and highly globalised cities.

The findings are sobering. Almost half the world’s most connected cities straddle animal-human spillover hotspots, and 14-20% of them are in areas with poor health infrastructure, meaning infections resulting from spillovers are likely to go unreported. South and Southeast Asia and Sub-Saharan Africa have the most cities at greatest risk.

The study’s methodology builds on understanding sources of pathogen transmission at wildlife-human interfaces by locating the most connected airports adjacent to these interfaces, where infections can spread quickly globally. It is described in a paper in the journal One Health.

“This is the first time this three-staged geography has been identified and mapped, and we want this to be able to inform the development of multi-tiered surveillance of infections in humans and animals to help prevent the next pandemic,” Michael Walsh and colleagues from Australia, the UK, India and Ethiopia write.

In brief

Data from 22,445 people presenting to 70 EDs in the UK with suspected COVID-19 infection highlight great differences in symptoms and outcome based on age, sex and ethnicity. Compared to children aged 16 years and under, adults were sicker and had higher rates of hospital admission (67.1% vs 24.7%), COVID positivity (31.2% vs 1.2%) and death (15.9% vs 0.3%). Men were more likely to be admitted than women (72.9% vs 61.4%), required more organ support (12.2% vs 7.7%) and were more likely to die (18.7% vs 13.3%). Black and Asian adults tended to be younger than white adults and, while less likely to be admitted to the hospital (Black 60.8%, Asian 57.3%, white 69.6%), were more likely to require organ support (15.9%, 14.3%, 8.9%) and have a positive COVID-19 test (40.8%, 42.1%, 30.0%). The findings are published in PLOS ONE.

The largest US study of its kind also provides more evidence that children tend to be less affected by COVID-19. Only 4% of the 135,000 paediatric patients tested at seven hospitals in Philadelphia since March have been positive and most infections were mild. However, as with adults, children from ethnic minorities and with some chronic medical conditions were more likely to test positive. The research was led by the Children’s Hospital of Philadelphia and is published in JAMA Paediatrics.

People suffering the chilblain-like condition “COVID toes” have characteristics which indicate an overactive immune response called a type I interferonopathy, according to French research. The team at Centre Hospitalier Universitaire de Nice saw 40 cases in less than two weeks, which they say is unusual in their temperate region and corresponded with the spread of SARS-CoV-2. All patients had signs of an overactive immune response but had negative PCR test results for COVID-19. Only about 30% developed antibodies against the virus. The researchers say the results suggest that the type of immune response is a key factor explaining the range of symptoms observed in COVID-19 infection. Their findings are published in JAMA Dermatology.