Coronastream: establishing cause and effect
Posted on May 4, 2020 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 Professor Inglis' Editorial 'Logic in the time of coronavirus', published in the Journal of Medical Microbiology.
Congruence: optimising coronavirus RT-PCR use
Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources
This study looked at how to conserve RT-PCR reagents by pooling specimens for SARS-CoV-2 group testing with the CDC assay. After using a web-based app to determine the best pool size, the study tested 25 experimental pools and an unselected group of 60 nasopharyngeal specimens with a saving of 38 reactions. The authors note an overall increase in test capability of 69% but note that the incidence of infection should be less than 10%.
Consistency: the role of comorbidities in COVID-19 outcomes
Though limited by incomplete data on clinical outcomes, this report on 5700 patients admitted to hospitals with COVID-19 in the New York area provides an insight into the relative importance of concurrent medical conditions. The median Charlson Index was four indicating significant comorbidity in this group. Hypertension, obesity and diabetes were the most common comorbidities. Interestingly, of those who died, those with diabetes were more likely to have had invasive mechanical ventilation or ICU care compared with those without diabetes; while those who died and who were hypertensive were less likely to have had mechanical ventilation or ICU care compared to those without. Only 2.1% had co-infection with another virus, most commonly entero/rhinovirus or respiratory syncytial virus.
Cumulative dissonance: tissue pathology of COVID-19
A pathological report of three COVID-19 cases by minimally invasive autopsies [Article in Chinese. One-click translation available]
This detailed account of minimally invasive post-mortems on three patients who died with COVID-19 describes the consequences of coronavirus infection at a molecular, tissue and organ level. The most significant findings were in the lungs where there was evidence of alveolar and interstitial inflammation, alveolar epithelial proliferation and hyaline membrane formation. Damage to the cardiovascular system, liver, kidneys and other organs is also described. This account is richly illustrated with tissue pathology images.
Curtailment: phased approach to COVID-19 containment and control
There has been a lot of variation in the approaches used by public health authorities to control the spread of COVID-19. In the USA where the disease has had a huge impact there have been substantial differences between US states. This morbidity and mortality weekly report compares the approaches taken in four states that all combined state and local community mitigation policies and declared a state of emergency. While this declaration appeared to have little sustained effect on population mobility, the combination of additional measures was associated with a significant reduction in mobility in all four locations. The timelines allow comparison of each state’s response.
Other resources:
- Picture of the week: a visual summary of SARS-CoV-2 vaccine candidates
- NIH treatment guidelines
