SARS-CoV-2 infection dynamics in household case-contact study: Biological sample analysis from India

This study aimed to determine RNA positivity in nasopharyngeal samples, urine and stool, period to seropositivity, viral clearance and associated factors. A cohort study was conducted multicentrically in Kerala, India, among 147 SARS-CoV-2 patients and 347 household contacts. Serial nasopharyngeal swabs, feces, urine, and serum samples were collected on days 1, 7, 14, and 28. Multivariable logistic regression was used to determine factors associated with RNA positivity, viral clearance and seropositivity. Among the index cases, median duration for respiratory samples to test negative was 10.5, 7 days in <18 and > 18 years respectively. The median period of RNA detection in feces was longer at 14 days (IQR 7, 28). The independent determinants of RT-PCR negativity of nasopharyngeal samples at >7 days was fever a OR 3.3 (95 % CI 1.1, 10.5). In the multivariable analysis for antibody response, those with less than or equal to 12 years of schooling had five times higher risk of being seronegative [aOR 5.2 (95 % CI 1.6, 16.7)]. Shedding of the virus in stool was more common among those aged <40 years (a OR 2.8, 95 % CI 1.2, 6.4) and among those who had fever (a OR 3.4, 95 % CI 1.1, 10.8). Among the contacts the seropositivity was determined by being illiterate 1.8 (95 % CI 1.1, 3.2), and reporting any symptom from day 1–14 aOR 3.2 (95 % CI 1.9, 5.2). The shorter duration of RNA positivity in respiratory samples and viral shedding in stool has implications for managing infection control and monitoring in diverse populations. • 147 COVID-19 index patients and their 347 household contacts were followed up with serial collection of biological samples. RNA samples from nasopharynx, urine and stool of index cases and serum for total antibody. Among household contacts serial collection of nasopharyngeal samples for RTPCR, serum antibody was done. • The median duration for RT-PCR negativity in respiratory samples was 7 days. • The mean period of RNA detection in feces was longer at 14 (10.21,17.78) days. • At 14 days of follow up sero-positivity among the newly infected cases and contacts were 97.5 % and 80.5 % respectively. • Fever appears to be a predictive feature of prolonged shedding.