coronastream: down on the delta

posted on august 12, 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 common experience among pandemic responders worldwide is frustration with covid’s tenacity. sars-cov-2 appears to have a prodigious ability to keep on going. and going. even in this relatively covid-19 unencumbered corner of the world, the prospect of sustainment beyond some distant, undefined finishing point is no closer now than at the beginning of the year. add to the mix the delta variant, and we have an urgent need to review all the plans, procedures and protocols we drew up in 2020. as noted previously, sars-cov-2 has an unrivalled ability to run rings around public sector administration. agile decision-making and risk adept actions are attributes the current wave of delta variant infection demands. it has the makings of a pandemic within the pandemic. this month’s blog homes in on what makes the delta variant that bit more successful than its predecessors and how we might respond to a redoubled covid-19 challenge. 

congruence: testing times  

diagnostic accuracy of rapid antigen tests in asymptomatic and presymptomatic close contacts of individuals with confirmed sars-cov-2 infection: cross sectional study 

the importance of widely available tests for sars-cov-2 has been highlighted in previous coronastream postings. the relentless global progress of the delta variant raises the need for high volume, fast turnaround tests to support public health decisions on outbreak control, strengthen quarantine measures and, where relevant, border controls.  a recent cochrane review drew attention to the lack of data on rapid antigen test evaluation in asymptomatic persons. this is a key deficiency in the battle against the highly transmissible delta variant, which is unforgiving of delays in contact tracing and testing. a study into the use of rapid antigen tests for detection of asymptomatic infection in close contacts in a high prevalence european setting found a relatively low sensitivity, but higher specificity; the opposite of the ideal presumptive screening test. 

scent dog identification of sars-cov-2 infections in different body fluids  

there is growing interest in the use of the high sensitivity of odour recognition by detection dogs, to sniff out covid before its clinical features are evident. this study demonstrates that detection dogs can be trained to detect persons with sars-cov-2 infection with comparable sensitivity to rapid antigen tests when saliva, urine or sweat are inactivated and sensitivity comparable with rt-pcr when not inactivated. 

consistency: the delta pandemic

rapid spread of the sars-cov-2 delta variant in some french regions, june 2021 

in this eurosurveillance study, the delta variant expanded rapidly in three french metropolitan regions during may and june, with an estimated 79% advantage over the alpha variant. 

sars-cov-2 delta voc in scotland: demographics, risk of hospital admission, and vaccine effectiveness 

in this study from scotland, the delta variant was detected in younger affluent groups, with a risk of hospital admission about twice that of infection with the alpha variant. both the oxford and biontech vaccines reduced the risk of viral infection and hospitalisation attributable to the delta variant, but with apparently reduced effect compared to the alpha variant. 

cumulative dissonance: enhanced molecular mechanism 

how the coronavirus infects cells – and why delta is so dangerous

in a recent commentary in nature, possible explanations for the increased transmission efficiency of the delta variant are considered, with the finger of blame pointing to higher replication rate, higher viral load and a shorter time to detection. scudellari’s paper nicely illustrates the structure of the sars-cov-2 spike and explains how mutations in the receptor binding domain contribute to its improved cellular infection efficiency. the animation of viral penetration of a cell is particularly helpful. 

countermeasures

effectiveness of covid-19 vaccines against the b.1.617.2 (delta) variant 

n this case-control study of vaccine efficacy against the alpha and delta sars-cov-2 variants, bernal and colleagues estimated effectiveness over a period of delta variant circulation in england. they found that efficacy of pfizer and astrazeneca vaccines against the delta variant was reduced after a single dose compared to alpha. after two doses of the pfizer vaccine, it was 88% and after astrazeneca it was 67% respectively against the delta voc. taking into account confidence limits, these differences were modest after second vaccine doses, adding evidence for continued vaccine efficacy and highlighting the importance of completing the full vaccination course.  

weekly population testing could stop this pandemic and prevent the next 

thus, coronastream comes full circle, in identifying a sars-cov-2 investigation as an intervention in its own right. in wuhan, where new clusters of infection have occurred, there has been mass testing of the city’s population of 12 million. peto makes a call for systematic testing of the population in post-lockdown britain, noting the somewhat gloomy prediction that covid will continue to spread in the uk despite widespread vaccine coverage. while many dismiss saliva testing as a low sensitivity option, peto argues that the combination of saliva testing with locally delivered rt-lamp could be used to suppress the current pandemic and prepare for the next. it is a provocative stance, but in current circumstances bold ideas need to be canvassed and actively considered.   

resources: a comprehensive update on sars-cov-2 and covid-19

features, evaluation, and treatment of coronavirus (covid-19). 2021 jul 17.
a visual guide to the sars-cov-2 coronavirus.