Coronavirus Research Tracking - 5 June

Wastewater testing, seasonality effects and viral origins.

In this week’s Research Tracker we focus on some recent papers with environmental themes - testing for the virus in wastewater, the effect of season on spread, and the origins of the virus. But first, the Tracker notes the retraction of a paper we highlighted last week.

The Research Tracker is prepared by Dr Robert Hickson for the Science Media Centre. As this is a new service, please don’t hesitate to provide feedback.

Hydroxychloroquine paper retracted

Earlier this week the Editors of The Lancet issued an “Expression of Concern” for a paper examining potential risks of hydroxychloroquine for Covid-19 patients that we highlighted last week. Other researchers had concerns that some of the data used in the paper could not be trusted. Today the lead authors retracted the paper after a co-author failed to submit all the data to an independent review.

This does not mean that hydroxychloroquine is an effective treatment for Covid-19 patients. An editorial in the New England Journal of Medicine about another hydroxychloroquine paper notes that its potential benefits as a Covid-19 prophylactic have not yet been satisfactorily demonstrated.

A paper in the New England Journal of Medicine on cardiovascular disease risks associated with Covid-19, published by some of the same authors as The Lancet paper, has also been retracted. The Guardian provides some background on the co-author responsible for much of the data in these two studies.

Retraction of the two research papers is also raising concerns about the processes that the journals used to peer review them. An open letter from over 200 clinicians and scientists to the authors and The Lancet emphasises the need for greater transparency about the data and data sharing agreements, and the peer reviewers comments on The Lancet paper.

Other scientists reactions to the retractions are available on the Science Media Centre website.

In the New York Times the science writer Carl Zimmer provides some tips on how to read a scientific paper. Although in the current cases, close scrutiny of the data sets was required.

Wastewater sludge as a surveillance target

Several recent pre-print papers have reported testing wastewater facilities for SARS-CoV-2.

  • Spanish and American studies (both pre-prints) found that the virus is detectable in wastewater sludge during large outbreaks

  • The US study also found that viral levels in sludge were a good indicator of Covid-19 hospitalisations three days later, and community cases one week later. The method may, therefore, help health services prepare for rising demands.

These studies need to be validated by further testing elsewhere. NZ’s Crown Research Institute ESR tested wastewater samples in April and detected the virus, but recently noted that the methodology needs to be improved.  

Wastewater-based epidemiology is an emerging method for monitoring infectious diseases. Current detection methods require relatively high levels of infection, so they can be useful for monitoring epidemic progress, rather than being an early warning system.

Temperature appears to have little effect on rates of transmission

A retrospective study of Covid-19 outbreaks in many regions of the world looked at the influence temperature and humidity may have in spreading the infection. While differences in testing and reporting schemes in different places make comparisons difficult, the researchers concluded that there is little evidence that temperature influences spread.

Low humidity may help viral transmission to a small degree. However, the researchers found that public health initiatives (prohibiting mass gatherings, closing schools, and adopting physical distancing), rather than environmental conditions, were the factors that had the greatest impact on reducing spread.

An Australian study also found that low humidity may lead to small increases in infection risk.

A 2019 investigation of influenza spread in mice found that low humidity affected the body’s ability to clear, fight and repair infection. 

The origin of SARS-CoV-2 is complex, both ecologically and genetically

While scientific consensus is that SARS-CoV-2 is derived from a bat coronavirus, there is still uncertainty about the precise source and timing of its transmission to people.

A study of over 1,000 coronaviruses collected from many species of bats in China may have narrowed down the group of bats from which Covid-19 emerged. While only a small part of the coronavirus genome was analysed, and the paper has not yet been peer-reviewed, the researchers suggest horseshoe bats of the genus Rhinolophus may be the ultimate source. 

The study also infers high levels of coronavirus transfers between some bat species, increasing opportunities for the emergence of new viral strains. The researchers identified two regional hotspots in the southern and south western regions of China where such transfers appear more common. The authors note that research in other South East Asian countries is still needed.

Analysis of complete coronavirus genomes from humans, horseshoe bats and pangolins by a different research team (pre-print paper) provides some support for this hypothesis. They propose that the SARS-CoV-2 virus may be derived from a “generalist” bat coronavirus that is able to infect several non-bat species without requiring an intermediate host. 

However, other research notes that strong similarity between parts of the SARS-CoV-2 and pangolin coronavirus spike protein. This leads some to propose that an intermediate host may have been involved in the spread to humans. 

The patterns of selection and recombination being identified through comparisons of coronavirus genomes means that reconstructing SARS-CoV-2’s origin is not simple. Further genetic and ecological research is required. But it is clear that coronaviruses from bats pose potential risks to humans.

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