Optimal symptom combinations to aid COVID-19 case identification: Analysis from a community-based, prospective, observational cohort

Objectives

Diagnostic work-up following any COVID-19 associated symptom will lead to extensive testing, potentially overwhelming laboratory capacity whilst primarily yielding negative results. We aimed to identify optimal symptom combinations to capture most cases using fewer tests with implications for COVID-19 vaccine developers across different resource settings and public health.

Methods

UK and US users of the COVID-19 Symptom Study app who reported new-onset symptoms and an RT-PCR test within seven days of symptom onset were included. Sensitivity, specificity, and number of RT-PCR tests needed to identify one case (test per case [TPC]) were calculated for different symptom combinations. A multi-objective evolutionary algorithm was applied to generate combinations with optimal trade-offs between sensitivity and specificity.

Findings

UK and US cohorts included 122,305 (1,202 positives) and 3,162 (79 positive) individuals. Within three days of symptom onset, the COVID-19 specific symptom combination (cough, dyspnoea, fever, anosmia/ageusia) identified 69% of cases requiring 47 TPC. The combination with highest sensitivity (fatigue, anosmia/ageusia, cough, diarrhoea, headache, sore throat) identified 96% cases requiring 96 TPC.

Interpretation

We confirmed the significance of COVID-19 specific symptoms for triggering RT-PCR and identified additional symptom combinations with optimal trade-offs between sensitivity and specificity that maximize case capture given different resource settings.

Optimal symptom combinations to aid COVID-19 case identification: analysis from a community-based, prospective, observational cohort

OBJECTIVES

Diagnostic work-up following any COVID-19 associated symptom will lead to extensive testing, potentially overwhelming laboratory capacity whilst primarily yielding negative results. We aimed to identify optimal symptom combinations to capture most cases using fewer tests with implications for COVID-19 vaccine developers across different resource settings and public health.

METHODS

UK and US users of the COVID-19 Symptom Study app who reported new-onset symptoms and an RT-PCR test within seven days of symptom onset were included. Sensitivity, specificity, and number of RT-PCR tests needed to identify one case (test per case [TPC]) were calculated for different symptom combinations. A multi-objective evolutionary algorithm was applied to generate combinations with optimal trade-offs between sensitivity and specificity.

FINDINGS

UK and US cohorts included 122,305 (1,202 positives) and 3,162 (79 positive) individuals. Within three days of symptom onset, the COVID-19 specific symptom combination (cough, dyspnoea, fever, anosmia/ageusia) identified 69% of cases requiring 47 TPC. The combination with highest sensitivity (fatigue, anosmia/ageusia, cough, diarrhoea, headache, sore throat) identified 96% cases requiring 96 TPC.

INTERPRETATION

We confirmed the significance of COVID-19 specific symptoms for triggering RT-PCR and identified additional symptom combinations with optimal trade-offs between sensitivity and specificity that maximize case capture given different resource settings.

A mathematical model for prokaryotic protein synthesis

A kinetic model for the synthesis of proteins in prokaryotes is presented and analysed. This model is based on a Markov model for the state of the DNA strand encoding the protein. The states that the DNA strand can occupy are: ready, repressed, or having a mRNA chain of length i in the process of being completed. The case i = 0 corresponds to the RNA polymerase attached, but no nucleotides attached to the chain. The Markov model consists of differential equations for the rates of change of the probabilities. The rate of production of the mRNA molecules is equal to the probability that the chain is assembled to the penultimate nucleotide, times the rate at which that nucleotide is attached. Similarly, the mRNA molecules can also be in different states, including: ready and having an amino acid chain of length j attached. The rate of protein synthesis is the rate at which the chain is completed. A Michaelis-Menten type of analysis is done, assuming that the rate of protein degradation determines the 'slow' time, and that all the other kinetic rates are 'fast'. In the self-regulated case, this results in a single ordinary differential equation for the protein concentration.