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


Index patients with laboratory-confirmed SARS-CoV-2 infection were reported to 2 health departments in the Salt Lake City, Utah, USA, metropolitan area during April 19–25, 2020. Households were recruited through convenience sampling with assistance from health department staff and were considered eligible if the index patient was not hospitalized, lived with ≥2 additional persons, and tested positive for SARS-CoV-2 by rRT-PCR in a respiratory tract specimen collected ≤5 days before enrollment. A sample size of 5 households was chosen because of time constraints and workload capacity; we also took into consideration the likelihood of observing secondary transmission within households, on the basis of the estimated secondary attack rate in a larger household transmission investigation conducted by the Centers for Disease Control and Prevention (CDC).[11] CDC investigation staff visited all enrolled households (day 0) within 2–4 days of diagnosis (within 3–5 days of symptom onset) and conducted daily visits on 4 subsequent days (days 1–4) and a final visit on day 14.

Before the day 0 visit, questionnaires were administered to all index patients and household contacts by telephone to request demographic information and data on symptoms, exposure to the index patient and others outside the household, and any previous SARS-CoV-2 testing. A household-level questionnaire, completed by the index patient or self-declared head of household, documented the home's square footage; the number of persons per bedroom and bathroom; isolation measures undertaken by the index patient; and extent of household use of gloves, masks, or cloth face coverings after symptom onset in the index patient. A household-level closeout questionnaire reassessing isolation measures and glove and face mask use during the observation period was completed on the day 14 visit. In addition, during the day 0 and day 14 visits, nasopharyngeal swab specimens and blood samples were collected from all index patients and household contacts. During day 1–4 follow-up visits, nasopharyngeal swab specimens were collected daily from non–index patient household members, including those with SARS-CoV-2 test results pending or confirmed from specimens collected at other facilities before the investigation. If symptoms occurred in a household contact during days 1–14 that were not reported on day 0, investigation staff conducted an interim household visit, during which nasopharyngeal swab specimens were collected from all household members, including the index patient.

During days 1–4, if a household contact had an inconclusive result (1 of 2 target gene regions positive for SARS-CoV-2 by rRT-PCR assay) or positive result (both target gene regions positive) after an rRT-PCR–negative test (i.e., first detection of viral shedding), the associated specimen and all subsequent daily specimens from the person were submitted for viral culture to evaluate infectiousness. Results that were inconclusive by rRT-PCR were categorized as negative unless a positive viral culture was obtained from the same specimen. Specimens positive by rRT-PCR that were collected on day 14 with Ct values <35 were also cultured. For household contacts, the date of first positive test was defined as the day on which the first SARS-CoV-2–positive specimen was collected. The Utah Public Health Laboratory (UPHL) tested specimens by using the CDC 2019 novel coronavirus (2019-nCoV) real-time RT-PCR assay;[12] viral cultures were performed at CDC.[13] Nasopharyngeal specimens were transported at 4°C in viral transport media, first from households to UPHL and then (if applicable) onward to CDC for viral culture. Blood samples were processed by UPHL; serum samples were subsequently shipped to CDC and tested by using a CDC-developed SARS-CoV-2 ELISA kit (B. Freeman, unpub. data,

During days 0–14, all index patients and household members completed a daily symptom diary. Symptoms were grouped according to Council of State and Territorial Epidemiologists (CSTE) categories of classic (cough, shortness of breath, or discomfort while breathing), nonclassic (≥2 of measured or subjective fever, chills, headache, myalgia, sore throat, loss of taste, or loss of smell), and asyndromic (symptoms other than CSTE classic or nonclassic).[14] Symptom onset was defined as the first day of any reported symptom. Onset of viral shedding was defined as the date of first detection of SARS-CoV-2 by rRT-PCR in the nasopharynx. Presymptomatic shedding was defined as symptom onset ≥1 day after the first positive SARS-CoV-2 result by rRT-PCR. Ct values were categorized as low (<20), medium (20–30), and high (>30). Lower Ct values indicated that more viral RNA was detected in the specimen.

This protocol was reviewed by CDC human subjects research officials, and the activity was deemed nonresearch as part of the COVID-19 public health response. Verbal assent to participate was initially obtained by telephone during questionnaire administration, and written consent was collected during the first visit.