Clinical features and natural history of the first 2073 suspected COVID-19 cases in the Corona São Caetano primary care programme: a prospective cohort study

Abstract

Background: Despite most cases not requiring hospital care, there are limited community-based clinical data on COVID-19.

Methods: The Corona São Caetano programme is a primary care initiative providing care to all residents with COVID-19 in São Caetano do Sul, Brazil. It was designed to capture standardised clinical data on community COVID-19 cases. After triage of potentially severe cases, consecutive patients presenting to a multimedia screening platform between 13 April and 13 May 2020 were tested at home with SARS-CoV-2 reverse transcriptase (RT) PCR; positive patients were followed up for 14 days with phone calls every 2 days. RT-PCR-negative patients were offered additional SARS-CoV-2 serology testing to establish their infection status. We describe the clinical, virological and natural history features of this prospective population-based cohort.

Findings: Of 2073 suspected COVID-19 cases, 1583 (76.4%) were tested by RT-PCR, of whom 444 (28.0%, 95% CI 25.9 to 30.3) were positive; 604/1136 (53%) RT-PCR-negative patients underwent serology, of whom 52 (8.6%) tested SARS-CoV-2 seropositive. The most common symptoms of confirmed COVID-19 were cough, fatigue, myalgia and headache; whereas self-reported fever (OR 3.0, 95% CI 2.4 to 3.9), anosmia (OR 3.3, 95% CI 2.6 to 4.4) and ageusia (OR 2.9, 95% CI 2.3 to 3.8) were most strongly associated with a positive COVID-19 diagnosis by RT-PCR or serology. RT-PCR cycle thresholds were lower in men, older patients, those with fever and arthralgia and closer to symptom onset. The rates of hospitalisation and death among 444 RT-PCR-positive cases were 6.7% and 0.7%, respectively, with older age and obesity more frequent in the hospitalised group.

Conclusion: COVID-19 presents in a similar way to other mild community-acquired respiratory diseases, but the presence of fever, anosmia and ageusia can assist the specific diagnosis. Most patients recovered without requiring hospitalisation with a low fatality rate compared with other hospital-based studies.

Keywords: epidemiology; infectious diseases; primary care; public health.

Figure 1

Patient flow chart for the Corona São Caetano platform between 13 April and 13 May 2020. In the upper section (white background), the numbers correspond to individual presentations to the system; among 2073 suspected cases, 60 had two presentations and 1 had three. In the lower section (grey background), numbers correspond to individual patients making up the final analytic groups.

Figure 2

Panel A presents prevalence (point) and exact binomial 95% CIs (vertical lines) of symptoms at presentation among patients with suspected COVID-19 according to reverse transcriptase (RT)-PCR result and serostatus (A). Panels B and C present the prevalence of presenting symptoms among patients with COVID-19 (RT-PCR and serology positive) stratified by age (B) and sex (C).

Figure 3

ORs (black dot) and 95% CIs (lines) for testing positive for COVID-19 (reverse transcriptase (RT)-PCR positive or serology positive) associated with the presence of each presenting symptom. Horizontal axis is on log scale. Point estimates of ORs are shown inline with their corresponding symptom.

Figure 4

Relationship between mean reverse transcriptase (RT)-PCR cycle threshold (Ct) and day of illness course when the nasopharyngeal swab was collected (A), patient age (B), patient sex (C) and different symptoms at presentation (D). Panels A and B show the best-fit linear regression lines, panels C and D are violin plots (rotated kernel density plots showing the full distribution of data) of the Ct values with median (black dot) and IQR (black line).