coronastream: what’s in a name?

posted on june 23, 2021   by dr tim inglis

in this special blog series, medical microbiologists led by dr tim inglis summarise some of the research that will be essential to inform covid-19 countermeasures. find out more about the project in dr inglis' editorial 'logic in the time of coronavirus', published in the journal of medical microbiology.  

a rose by any other name, as the saying goes. not that it has stilled the debate over how to name sars-cov-2 variants, currently fought between the early adopters and classicists in the red corner, and the decimal pointers in the blue corner. we may yet see some benefits come out of removing geographic attribution from the name and blame game, but let’s not forget the weight disease control practitioners place on geographic localisation when defining covid-19 clusters. it is a little naïve to expect that removing all reference to place will help speed up the path to pandemic’s end. the choice of greek letters for sars-cov-2 variant designation opens another discussion point about how and when to call a new variant, and who has the authority to do so. oh, the perils of microbial taxonomy. whatever system is chosen for variants of concern and interest, microbiologists need to take care that the naming convention doesn’t perpetuate the exclusivity of the growing pile of acronyms non-specialists have to learn before they can understand covid-19 conversations. acronyms are a powerful means of locking the public out of professional business, and keeping the experts close. 

while much of australasia has stumbled from covid-19 suppression into elimination, melbourne has bucked the trend with a further small wave of cases, traced back to a leak in hotel quarantine. noting that the newly trending variant is more transmissible and may have a shorter incubation period, this is not the first leak from hotel quarantine in this region. there have been at least 20 in australia since the start of the pandemic. official reports recognise that hotels are not designed for quarantine purposes. the possibility that aerosol transmission is a means of indoor transmission has prompted renewed calls for dedicated quarantine facilities, similar in concept to the measures successfully used in the 1918–-19 influenza pandemic. droplet transmission dogma is remarkably tenacious and still has its advocates. unfortunately, sars-cov-2 appears not to have read the textbooks. 

in contrast to an evolving viral threat, the vaccine rollout here has been painfully slow; hampered by the adverse publicity given to the chadox-1 vaccine and its rare adverse effects. vaccine promotion has been best with mixed messages, missteps and antivaxx mischief. like the pandemic, local completion of the vaccination programme has no firm end date. international travel plans remain firmly on hold for the foreseeable future. 

congruence: saliva for sars-cov-2 detection

saliva as a gold-standard sample for sars-cov-2 detection

in this short article, tan and colleagues argue the case for using saliva as the preferred method of frequent sars-cov-2 screening tests. the foundation of their argument is that saliva is easier to obtain frequently, with less risk to samplers, less equipment and greater consistency for non-hospital subjects. as it becomes clear that mass screening is going to be with us for some time to come, these very practical considerations take on a greater importance, explored in some detail in this article. it notes the need for better standardisation of saliva collection, and techniques to improve sensitivity to make saliva testing compete with nasopharyngeal swab collection. a further useful attribute of saliva testing is its greater divergence with nasopharyngeal swab testing 21 days after symptom onset, making it less likely to detect long-term shedding. 

consistency: evolution of disease transmission

evolution of disease transmission during the covid-19 pandemic: patterns and determinants

in this elegant mathematical modelling study, zhu and gallego looked at the course of the pandemic in over a hundred countries in terms of public health policy, timing and gap. they found five distinct clusters of nations according to their public health policy interventions. disease transmission dynamics were couch in terms of a daily effective reproduction number or rt. they noted that “early adoption of social distancing measures and a shorter gap between interventions were associated with a reduction on the duration of outbreaks.” in their results from the first six months of the pandemic, the rt provided better prediction of future outbreaks and an early indication of the efficacy of containment. it will be fascinating to see how the rt fares during de-escalation as the pandemic wanes. 

cumulative dissonance: genotypes and disease severity 

association of hla class i genotypes with severity of covid-19

this paper from shkurnikov and colleagues found the hla-a *01:01 class i genotype was associated with higher risk, and homozygosity accompanied early deaths. when their risk score was used on an independent patient cohort, it also related to severity of disease. they note that hla class i antigens are important mediators of development of an immune response to covid-19.  peptides formed in response to cellular sars-cov-2 infection combine with the hla class i receptors and interact with the t cell receptor of the cd8+ t lymphocyte to produce a progeny of virus-specific cytotoxic lymphocytes. combinations of hla class i receptors affects the severity of various infectious diseases, and other hla genotypes have previously been reported to be connected with severe covid. the authors interpret their data cautiously, recognising the small size of subsets and preponderance of male patients. nevertheless, this study helps advance a mechanistic understanding of the complex relationship between the virus, the cellular immune response and disease outcomes. 

curtailment: vaccine interval impact

vaccine-escape and fast-growing mutations in the united kingdom, the united states, singapore, spain, india, and other covid-19-devastated countries

confidence in global and national covid vaccination programmes has been impacted recently by concerns about the arrival of variants of concern. in this paper wang and colleagues explore variations in the portion of the sars-cov-2 genome that determine the binding efficiency of viral spike protein to the ace2 receptor-binding domain (rbd). earlier work by this group suggested that these mutations could increase infectivity and reduce the efficacy of existing antibodies. this study extracts data from 31 countries with the highest number of snp profiles suggesting that s protein and ace2 binding will be stronger in these countries. wang et al argue that tracking the growth of ace2 binding-strengthening mutations in sars-cov-2 will guide vaccine development and antibody therapy. for the viral genome inclined, the average sars-cov-2 genome has 2.6 mutations on the s protein gene, and this figure is increasing. this underlines the importance of monitoring sars-cov-2 evolution through the course of the pandemic. 

resources: 

sars-cov-2 naming convention 
the australian covid-19 vaccine rollout