Coronavirus Research Tracking - 2 April
Vaccine effectiveness, T cells and variants, WHO report, superspreading, social science, and a Covid Misery Index
This Research Tracker includes reports on recent research and resources on vaccine effectiveness, the ability of T cells to recognise variants and how infections may cause long lasting changes in T cell populations. Also covered are how scientists are responding to the WHO report, the accuracy of rapid antigen tests, and opportunities for social science research. Added bonus: NZ ranks at #2 on a Covid Misery Index, but that’s good.
The Research Tracker is prepared by Dr Robert Hickson for the Science Media Centre.
Vaccine update resource
The University of Melbourne is producing weekly updates on Covid-19 vaccines. These summarise vaccine efficacy and effectiveness for a range of vaccines, including effectiveness against variants.
Pfizer and Moderna vaccines very effective at reducing infection risk
A study, published in the Morbidity and Mortality Weekly Report, of nearly 4,000 health care and essential frontline workers in the US found that the Pfizer/BioNTech and Moderna vaccines were very effective in reducing infection risk. Those who received both doses of the vaccines were 90% less likely to become infected, at least when assessed two weeks after receiving the second dose.
Effectiveness after receiving just the first dose was 80%. These results are consistent with other studies, although the number of infections overall in this study was relatively low, so levels of protection may vary in other populations.
Pfizer/BioNTech vaccine may also reduce transmission
A paper in Nature Medicine reports that people who became infected after receiving the first dose of the Pfizer/BioNTech vaccine had substantially reduced viral loads. At least if they became infected two to five weeks after the first dose. Lower viral load is probably associated with lower contagiousness, though further research is necessary to confirm this. However, the authors note that vaccination could result in more asymptomatic cases due to lower viral loads.
AstraZeneca vaccine effective against B.1.1.7
A paper published in The Lancet reports that while the AstraZeneca/Oxford vaccine has a slightly reduced neutralisation ability against the B.1.1.7 variant it does retain meaningful efficacy. Efficacy against an earlier variant was calculated to be 81.5%, while for B.1.1.7 efficacy was 70.4%.
T cells recognise variants
A study published in Open Forum Infectious Diseases reports that CD8+ T cells from 30 Covid-infected people were able to recognise the B.1.1.7, B.1.351 and P.1 variants. Only one mutation, found in B.1.351, was found to be at a site where the studied T cells bind. However, the extent to which they provide protective immunity, or are associated with reduced disease severity, was not assessed.
More severe Covid-19 can trigger longer lasting lymphocyte changes
A paper published in Med found hospitalised Covid-19 patients subsequently had high levels of cytotoxic T cells, and that these may persist for months after leaving hospital. This could have beneficial or adverse consequences for subsequent immune responses to other types of infection, and requires further study. This was a small study so the lymphocyte profiles of more convalescing Covid-19 patients is needed.
Pandemic origins - WHO report
A news item in Nature discusses some of the unanswered questions remaining after the release earlier this week of the WHO’s report on the pandemic. Some scientists are advocating a “follow the animals” approach to work back from the Wuhan market to identify which species passed the virus to people, and under what circumstances this may have occurred.
The news item notes the very difficult political conditions and constraints the WHO report team had to work under, so it isn’t surprising that definitive answers were not produced.
More emphasis needed on ventilation rather than disinfection
Another news item in Nature highlights that indoor spaces are the main place where infections occur, due to aerosol transmission. However, it also notes that guidance on how to reduce the risks is limited, and that more effort is spent on disinfecting surfaces than improving ventilation and indoor air quality.
Rapid, point‐of‐care antigen diagnostic tests
A review of 64 published studies, by the Cochrane Library, on rapid antigen and PCR diagnostic tests concluded that antigen tests vary in sensitivity. They work best when viral levels are high, within the first week of symptoms appearing. The accuracy of these tests for asymptomatic cases is uncertain. The review suggests that the more accurate antigen tests be used for symptomatic cases if PCR tests are not available or if quick patient care decisions are required.
SARS-CoV-2 has a limited mutational repertoire, so far
An article in Scientific American suggests that SARS-CoV-2 may be settling into a limited set of mutations. This can be viewed as encouraging, but the article notes that it doesn’t preclude further adaptation and evolution of the virus, particularly if infection levels remain high.
The mutations found in different variants and lineages are nicely shown on this website, where you can pick the viral regions of interest.
The importance of the type and location of particular mutations is highlighted by a paper published in Cell. This reports that although the P.1 and B.1.351 variants have similar mutations in their receptor binding domains the B.1.351 is more resistant to antibody neutralisation. The authors infer that the difference is due to mutations in the N-terminal domain of the spike protein.
Superspreading in NZ
A modelling paper by New Zealand researchers, published in Plos One, estimated that 20% of the cases among adults here were responsible for 65–85% of transmission events. Children under 10 were less likely to become infected and to infect others.
An interactive global map of all “superspreading” events has been created.
Mapping differences in vulnerability to Covid-19 in NZ
A paper describing regional differences in vulnerability to Covid-19 was published in the Journal of the Royal Society of New Zealand. Demographic, health and socio-economic data were used, and the results are applicable for other public health challenges.
An expert reaction to this paper was produced by the Science Media Centre.
A preprint about preprints
An analysis of Covid-19 (and other) preprint papers found that most of the ones that get peer reviewed and rapidly published don’t change too much. There were discrete changes to abstracts in 15% of the COVID-19-related papers, but the main message of the paper was not altered.
The analysis was of papers shared and published between January and April last year. While many thousand Covid-19 papers were made available on preprint servers during these months, the study only analysed 200 papers in detail. The authors recognise that papers that take longer to publish may undergo more substantial changes.
The proportion of preprints that eventually get published is unknown. The analyses also didn’t determine if the papers results were replicable. So caution is still required when reading preprints (and published papers).
How the pandemic provides opportunities for the social sciences
An opinion published in the Proceedings of the National Academy of Sciences notes that social science studies of one-off events, like the pandemic, provide great opportunities to better understand broader societal issues. However, this requires follow-up after the event has passed.
The challenge is in not knowing what will be the most important issues to follow-up, so detailed records need to be collected and kept now. The article suggests that this will need coordination between government agencies and research organisations to ethically curate the data being used to track cases and manage the pandemic.
Covid Misery Index
The Macdonald-Laurier Institute has developed a Covid Misery Index. This assesses government performance, measuring the extent to which the virus and responses to it have harmed human wellbeing.
New Zealand was ranked at number 2 (on 31 March) in terms of least miserable, behind Norway. Fifteen countries are currently included on the Index.