Characteristics and Timing of Initial Virus Shedding in Severe Acute Respiratory Syndrome Coronavirus 2, Utah, USA

Nathaniel M. Lewis; Lindsey M. Duca; Perrine Marcenac; Elizabeth A. Dietrich; Christopher J. Gregory; Victoria L. Fields; Michelle M. Banks; Jared R. Rispens; Aron Hall; Jennifer L. Harcourt; Azaibi Tamin; Sarah Willardson; Tair Kiphibane; Kimberly Christensen; Angela C. Dunn; Jacqueline E. Tate; Scott Nabity; Almea M. Matanock; Hannah L. Kirking


Emerging Infectious Diseases. 2021;27(2):352-359. 

In This Article


During April 19–25, 2020, a total of 5 households were enrolled, each consisting of an index case-patient and a median of 3 household members (range 2–4 persons). All index patients had the earliest symptom onset in their households. The day 0 visit occurred a median of 4 days (range 3–5 days) after symptom onset in the index patient. Secondary transmission was observed in 2 (40%) of the 5 households (HH-02 and HH-05), consisting of 7 (100%) of 7 contacts in these 2 households and 7 (47%) of 15 total household contacts in the study. The 8 contacts from the remaining 3 households did not become infected during the investigation (Figure 1). The median number of days between symptom onset in index patients and symptom onset in SARS-CoV-2–positive household contacts was 4 days (range 2–5 days). Eighty percent of index patients (4/5) were men and boys, and 80% of household contacts (12/15 [80%]) were women and girls (Table). The median age of index patients was 35 years (range 16–46 years). Of household contacts who tested positive, median age was 16 years (range 7–45 years); of household contacts who tested negative, median age was 45 years (range 14–67 years). Forty percent (2/5) of index patients, 43% (3/7) of SARS-CoV-2–positive household contacts, and 75% (6/8) of SARS-CoV-2–negative contacts reported ≥1 underlying medical condition.

Figure 1.

Results of rRT-PCR for SARS-CoV-2 and symptom onset among index case-patients, SARS-CoV-2–positive household contacts, and SARS-CoV-2–negative household contacts in study of initial virus shedding in SARS-CoV-2, Utah, USA, April–May 2020. The timelines of symptom onset and testing dates preceding and during the 15-day study period are ordered by individual households (HH-01–HH-05). Sex and age (in parentheses) are listed to the left. Symptom onset date is only included for household members who tested positive at any time during the study period or for whom onset of symptoms consistent with coronavirus disease prompted an interim visit from investigators. HH-05 opted out of day 14 nasopharyngeal specimen collection. Ct, cycle threshold; HH, household; rRT-PCR, real-time reverse transcription PCR; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Participants with a COVID-19 diagnosis had similar symptom profiles: headache was reported by 12/12 (100%); subjective fever, chills, fatigue, and nasal congestion were each reported by 10/12 (80%); myalgia was reported by 8/12 (67%); and partial loss of smell was reported by 7/12 (58%) (Appendix Figure, Classic symptoms were less common: dry cough was reported by 6/12 (50%); and productive cough, shortness of breath, and discomfort while breathing were each reported by <50% of those infected (Appendix Figure). Measured fever, sore throat, partial or full loss of taste, runny nose, chest pain, wheezing, nausea or vomiting, abdominal pain, and diarrhea were each reported by ≤33%. Nonclassic and asyndromic symptoms were also reported by SARS-CoV-2–negative household contacts (Appendix Figure). Median duration of illness was 7 days (range 2–14 days) among SARS-CoV-2–positive contacts and 11 days (range 4–19 days) among index case-patients. None of the 12 participants who tested positive for SARS-CoV-2 were hospitalized or experienced complications from pneumonia. Four (33%) of 12 tested positive on day 14, 3 (25%) were negative on day 14, and 5 (42%) refused swab tests on day 14. Among the 4 participants (02-00, 02-01, 02–03, and 03-00) with day 14 specimens positive for SARS-CoV-2 by rRT-PCR, 3 with Ct values <35 were cultured and viable virus was detected in 0/3 (0%). None of the 8 household members who tested negative by rRT-PCR tested positive by ELISA on day 0 or 14, suggesting no previous or undetected infections.

The 3 households (60%) that did not experience transmission (HH-01, HH-03, and HH-04) instituted household-level isolation practices. In HH-01, the index patient (01-00) moved out of the family home to a trailer on the property on the day of symptom onset (day –4), which coincided with the collection at a drive-through facility of the first specimen to test positive by rRT-PCR. He did report having had intimate contact (e.g., hugging or kissing) with 1 household member (01-01) after symptom onset but before diagnosis. The index patient wore gloves but no face mask on the few occasions he entered the family home. Household members also increased handwashing after diagnosis in the index patient. In HH-03, all household members had close contact (i.e., ≥10 minutes within 6 feet) with the index patient (03-00) between her symptom onset and the diagnosis; however, after diagnosis, the index patient used a separate bathroom (in addition to having her own bedroom) and ate meals separately from household contacts. Household contacts also increased disinfection of surfaces and handwashing after diagnosis in the index patient. In HH-04, between symptom onset and diagnosis in the index patient, 2 household contacts (04-02 and 04-03) had close contact with the index patient, and 1 contact (04-01) had intimate contact with the index patient. After diagnosis, the index patient stayed in a separate bedroom throughout the day (including for meals) but did not have access to a separate bathroom. He wore an N95 mask and gloves when leaving his room. Household members also disinfected surfaces regularly.

The 2 households (40%) where all contacts became infected (HH-02 and HH-05) did not institute household-level isolation practices, and all contacts had ongoing exposure to the index patient (Figure 2). During the investigation period, all members of both households were out of work and school because of school closures and stay-at-home recommendations in Salt Lake County. During the period from symptom onset in the index patient to enrollment in our study, all 7 (100%) contacts in these 2 households reported close contact with the index patient. During the same period, 6/7 (85%) household contacts who tested positive also reported intimate contact with the index patient after symptom onset, compared with 2/8 (25%) of household members who tested negative.

Figure 2.

Symptom timing, symptom type, cycle threshold values, and viral culture results among household contacts positive for SARS-CoV-2 by rRT-PCR in study of initial virus shedding in SARS-CoV-2, Utah, USA, April–May 2020. The symptom onset and progression of 7 SARS-CoV-2–positive household contacts in households 2 and 5 (HH-02 and HH-05), who tested positive by real-time reverse transcription PCR, are detailed from first symptom onset to the end of the daily swabbing period (days 0–4). Fading bars indicate symptoms persisting after day 5. CSTE, Council of State and Territorial Epidemiologists; Ct, cycle threshold; rRT-PCR, real-time reverse transcription PCR; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

In HH-02, which consisted of a male index patient, his wife, and their 2 children, all 3 household contacts tested positive within 5 days of symptom onset in the index patient. Two of the contacts (02-01 and 02–03) shed virus while presymptomatic, and their symptoms did not occur until after their first SARS-CoV-2–positive test by rRT-PCR. The 33-year-old wife (02-01), who had ongoing exposure to the index patient for the duration of his illness, had Ct values that progressed from high (i.e., lower viral load) on her first positive test (day 0) to low (i.e., higher viral load) on her third test (day 2), when she first reported a combination of classic and nonclassic symptoms and fatigue. She remained SARS-CoV-2–positive by rRT-PCR at day 14, with a medium Ct value but no viable virus detected from culture. The second household member with presymptomatic virus shedding was a 7-year-old girl (02–03) whose daily Ct values were consistently medium during days 0–4. After testing positive for 2 days (days 0–1), she first reported nonclassic symptoms on day 2 and was symptomatic for only 2 days. She also remained positive at day 14, with a high Ct value and no viable virus detected from culture. The third household member, an 11-year-old girl (02–02), converted to rRT-PCR–positive (day 2) after testing negative for 2 days (days 0–1). She reported classic and nonclassic symptoms (dry cough and headache) on day 1. On day 2, she tested positive with a high Ct value and reported onset of a sore throat. On day 3, she tested positive with a medium Ct value, reported onset of chills and fatigue, and had a positive viral culture, before testing negative again on day 4.

Household 5 (HH-05) consisted of a male index patient, his wife, an adult child, and 2 adolescent children. All 4 household contacts tested positive for SARS-CoV-2 by rRT-PCR within 6 days of symptom onset in the index patient. Although all household contacts sought drive-through testing the day before the investigation began (day −1), only the 18-year-old woman (05-02) and the 16-year-old girl (05-03) met symptom criteria for testing; consequently, both had 1 positive test result before the investigation. The 16-year-old girl (05-03) reported nonclassic and asyndromic symptoms (day −2) starting the day before her first positive test by rRT-PCR (day −1) administered at the drive-through facility. Her next 2 positive tests, administered by the investigation team on day 0 and day 1, had low Ct values and coincided with the onset of fatigue (day 0) and cough (day 1). The 18-year-old woman (05-02) and 11-year-old girl (05-04) each reported symptoms starting the same day as their first rRT-PCR–positive tests, with 1 (05-02) administered at a drive-through facility (day −1) and the other (05-04) by the investigation team (day 0). Although they had a range of nonclassic and asyndromic symptoms during illness, the 18-year-old female (05-02) had a cough at onset (day –1) and low Ct values for her first 2 team-administered tests (days 0–1), whereas the 11-year-old girl had generally milder illness and high Ct values (i.e., lower viral load) for 4 of 5 tests. The 45-year-old woman (05-01) tested negative for 2 days (days 0–1) and had nonclassic and asyndromic symptoms for 3 days (days –1 to 1) before her first positive test on day 2; on that day, she tested positive with a high Ct value and reported onset of a cough. Her next 2 positive tests (days 3–4) had low Ct values, coinciding with onset of additional symptoms (chest pain, myalgia, and loss of taste and smell) and positive viral cultures on both days. All HH-05 members refused testing by nasopharyngeal swab on day 14 because of concerns about the potential need to self-isolate beyond 14 days after an initial positive test, which was the required isolation period at the time in Salt Lake County.