coronastream: margins, machine learning and mechanisms

posted on november 10, 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 dr inglis' editorial 'logic in the time of coronavirus', published in the journal of medical microbiology. 

it may well have been, in wellington's words, a near-run thing, but i'm sure readers of this blog will all be relieved to welcome the return of science. yes, it's good to hear president-elect biden insist from the outset that the pandemic must be fought with science, and it is even better to hear vice president-elect harris set the tone for her precedent-setting inauguration by including science in her agenda. it is notable how many leading voices for biomedical science went on record during the election campaign to decry the politicisation of science, and a shoot-the-messenger approach to inconvenient scientific truth. from the outset, this blog has stood for a balanced, non-partisan, evidence-based reflection on the current state of knowledge. if the incoming biden administration needs a plan and a process, we have done some of the groundwork here:  

pandemic planning: plotting a course through the coronawars 

preparation for this month's blog preceded the us election results, and as previously, highlights the incremental progress in our understanding of the covid-19 pandemic.  

congruence: clinico-pathological features

clinical impact of monocyte distribution width and neutrophil-to-lymphocyte ratio for distinguishing covid-19 and influenza from other upper respiratory tract infections: a pilot study 

there have been numerous claims for use of machine learning techniques in covid-19 diagnosis and a few have drawn attention to potential diagnostic applications of haematological data analysis. in this report, lin and colleagues show how measurements of monocyte distribution width (mdw) and neutrophil to lymphocyte ratio (nlr) can be used to both distinguish covid-19 and influenza from minor respiratory infections, and also to distinguish them apart. monocyte distribution width is already known to change in sepsis and can be generated in routine full blood count analysis by current haemocytometer models.  lin et al. note that the ease and speed of generation of mdw and nlr measurements makes them an attractive approach to rapid identification of patients for subsequent, definitive covid-19 tests such as sars-cov-2 rt-pcr. 

consistency: epidemiology

implementation of environmental surveillance for sars-cov-2 virus to support public health decisions: opportunities and challenges 

there has been a lot of interest in using wastewater samples for sars-cov-2 surveillance testing, but opinions differ on how best to overcome the challenges to inform decision-making. this group provides a critical review of published sewage surveillance studies, including preprints. advocates of sars-cov-2 wastewater testing should note that there are important unresolved issues, including agreed controls for molecular methods, optimal sample collection methods, use of replicate samples, and temporo-spatial resolution. of particular interest to public health microbiologists, is this paper's discussion of methods to establish a connection between the concentration of sars-cov-2 in sewage and the prevalence of virus shedders, which needs seroprevalence data and epidemiological modelling. 

cumulative dissonance: pathophysiology 

pathophysiology of covid-19: mechanisms underlying disease severity and progression

as understanding of the pathogenesis of covid-19 increases, insight reviews pick off more specialist areas of the field. it is getting difficult to keep the whole picture in view. this review is a welcome departure from the segregation into microbiology, immunology, tissue pathology and so on. in this article, bohn and colleagues offer a balanced perspective, and take us on a tour through the respective specialist fields. 

curtailment: countermeasures 

stringent containment measures without complete city lockdown to achieve low incidence and mortality across two waves of covid-19 in hong kong

with many parts of the world struggling to handle the revolving door of public health-driven lockdowns, curfews and quarantines, the issue of border controls has been particularly contentious. in australia, interstate borders have been the subject of courtroom battles, and disputes between members of the national cabinet. this paper by wong and colleagues takes a critical look at the range of public health measures introduced in hong kong and highlights the value of controlling movement at the international border. as our leaders consider the relaxation of border controls, publication of the hong kong experience comes at a good time to inform their decisions. 

resources

• rapid tests for covid-19.  fast coronavirus tests: what they can and can’t do.  

• figure of the month: global spread of sars-cov-2 traced by viral genomes.