High Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission Rates Detected by Dense Saliva Sampling

Abstract

Background: Understanding the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission is important for adequate infection control measures in this ongoing pandemic.

Methods: Households were enrolled upon a polymerase chain reaction-confirmed index case between October and December 2020, prior to the coronavirus disease 2019 vaccination program. Saliva samples were obtained by self-sampling at days 1, 3, 5, 7, 10, 14, 21, 28, 35, and 42 from study inclusion. Nasopharyngeal swabs (NPS) and oropharyngeal swabs (OPS) were collected by the research team at day 7 and capillary blood samples at day 42. Household secondary attack rate (SAR) and per-person SAR were calculated based on at least 1 positive saliva, NPS, OPS, or serum sample. Whole genome sequencing was performed to investigate the possibility of multiple independent SARS-CoV-2 introductions within a household.

Results: Eighty-five households were included consisting of 326 (unvaccinated) individuals. Comparable numbers of secondary cases were identified by saliva (133/241 [55.2%]) and serum (127/213 [59.6%]). The household SAR was 88.2%. The per-person SAR was 64.3%. The majority of the secondary cases tested positive in saliva at day 1 (103/150 [68.7%]). Transmission from index case to household member was not affected by age or the nature of their relationship. Phylogenetic analyses suggested a single introduction for the investigated households.

Conclusions: Households have a pivotal role in SARS-CoV-2 transmission. By repeated saliva self-sampling combined with NPS, OPS, and serology, we found the highest SARS-CoV-2 household transmission rates reported to date. Salivary (self-) sampling of adults and children is suitable and attractive for near real-time monitoring of SARS-CoV-2 transmission in this setting.

Keywords: COVID-19; SARS-CoV-2; household transmission; saliva.

Figure 1.

Secondary transmission in household members (n = 241) defined with different sample type results. In this “upset plot,” each column is a pattern of co-occurrences of positivity (filled and connected dots indicate a positive test, gray dots indicate a negative or missing test result). The rows indicate the different tests, with the bar chart to the right showing the number of occurrences of positivity of each test. Below each column is a bar chart indicating the number of occurrences of the pattern. Data on saliva, nasopharyngeal swabs (NPS), oropharyngeal swabs (OPS), and serology were available for 241, 218, 220, and 213 household members, respectively; 155 household members were positive in either saliva, NPS, OPS, or serology (secondary cases); saliva positivity was defined as ≥1 reverse-transcription polymerase chain reaction–positive saliva sample at days 1–42; serology positivity was defined as immunoglobulin G antibody positivity for ≥1 antigen (severe acute respiratory syndrome coronavirus 2 spike trimer, S1, or N).

Figure 2.

Secondary transmission in household members (n = 241) defined with different sample type results and symptom status. In this “upset plot,” each column is a pattern of co-occurrences of positivity (filled and connected dots indicate a positive test, gray dots indicate a negative or missing test result). The rows indicate the different tests, with the bar chart to the right showing the number of occurrences of positivity of each test. Below each column is a bar chart indicating the number of occurrences of the pattern. One hundred twenty household members were symptomatic and 121 household members were asymptomatic; data on saliva, nasopharyngeal swabs (NPS), oropharyngeal swabs (OPS), and serology were available for 120, 109, 108, and 104 symptomatic household members, respectively; data on saliva, NPS, OPS and serology were available for 121, 109, 112, and 109 asymptomatic household members, respectively. Ninety-seven symptomatic and 58 asymptomatic household members were positive in either saliva, NPS, OPS, or serology (secondary cases); saliva positivity was defined as ≥1 reverse-transcription polymerase chain reaction–positive saliva sample at days 1–42; serology positivity was defined as immunoglobulin G antibody positivity for ≥1 antigen (severe acute respiratory syndrome coronavirus 2 spike trimer, S1, or N); asymptomatic household members were defined as not reporting symptoms on any of the examinations (day 1–42).

Figure 3.

Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 sequences within households (60 households, 103 individuals). Sequences were obtained from saliva samples with the highest viral load and are labeled per household. Households with 3 or more available sequences are indicated in color.