Demographics and Transmission Dynamics
We included 92 participants from 26 households, recruited between 1st March and 30th September 2020. The median family size was 3.5 (inter quartile range (IQR) 3.0 to 4.0). Overall, 47% (43/92) of participants were female, and 43% (40/92) children with a median age of 3.9 years (IQR 1.9 to 7.6). SARS-CoV-2 was detected in 54% (50/92) of participants (25 children, 25 adults) on NPS (Supplementary Figure 1). There were 26 index cases and 24 secondary cases, hence the secondary attack rate using NPS results alone was 36% (24/66). Genetic analysis was available from 15 samples which reflected the circulating community original Wuhan strain or ‘Alpha’ variants of SARS-CoV-2 at the time of recruitment, all of lineage D.2 except one which was B.1.338.
Twelve participants from 8 households also tested positive by PCR for SARS-CoV-2 in stool, with fifteen out of 92 participants testing positive in saliva (Supplementary Figure 1). Those who tested positive in saliva or stool were also positive on NPS PCR for SARS-CoV-2. NPS positivity rate decreased over time with 13% (6/46) positive 28 days following onset of infection. SARS-CoV-2 in stool was detected for the longest period of all virological samples, with 42% (5/12) positive at day 28.