Rapid Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in Detention Facility, Louisiana, USA, May–June, 2020

Megan Wallace; Allison E. James; Rachel Silver; Mitsuki Koh; Farrell A. Tobolowsky; Sean Simonson; Jeremy A. W. Gold; Rena Fukunaga; Henry Njuguna; Keith Bordelon; Jonathan Wortham; Melissa Coughlin; Jennifer L. Harcourt; Azaibi Tamin; Brett Whitaker; Natalie J. Thornburg; Ying Tao; Krista Queen; Anna Uehara; Clinton R. Paden; Jing Zhang; Suxiang Tong; Danielle Haydel; Ha Tran; Kaylee Kim; Kiva A. Fisher; Mariel Marlow; Jacqueline E. Tate; Reena H. Doshi; Theresa Sokol; Kathryn G. Curran

Disclosures

Emerging Infectious Diseases. 2021;27(2):421-429. 

In This Article

Results

Dormitory and Detained Persons Characteristics

All 143 detained persons from 6 dormitories were invited for testing, and 143 (100%) participated in the day 0 testing and survey (Figure 1). Median age was 33 (interquartile range 28–42) years, and most (136, 95%) were male (Table 1). Most (102, 71%) were Black non-Hispanic persons, and 36 (25%) were White non-Hispanic persons. One third (49, 34%) of the 143 detained persons had an underlying medical condition. Dormitory E was the only female dormitory. Dormitory C had the highest median age (45 years; interquartile range 35–52 years) and the highest proportion (7/11; 64%) of persons with underlying medical conditions. Dormitory E had the lowest percent occupancy (7/22; 32%), whereas dormitory F was near full capacity (45/50; 90%). All dormitories had 3–4 shared toilets and sinks and 2–3 shared showers.

Serial Testing

In dormitories A–E, 53 (54%) persons tested positive on day 0 (Table 2). Among persons with negative test results from day 0 testing in dormitories A–E (n = 45), 16 (36%) had SARS-CoV-2 detected on day 4 testing. Two additional persons tested positive for SARS-CoV-2 on day 14, both of whom originally resided in dormitory B. No SARS-CoV-2 infections (0/45) were detected during the day 0 testing in dormitory F. However 40 (89%) of 45 persons tested positive for SARS-CoV-2 on day 18. No detained persons testing positive for SARS-CoV-2 from any dormitory required hospitalization during their illness.

The overall cumulative incidence during May 7–June 3 of SARS-CoV-2 infection for all dormitories was 78% (111/143). Dormitory E had the lowest cumulative incidence (57%; 4/7), and dormitory F had the highest cumulative incidence (89%; 40/45). Day 0 testing in dormitory E was initiated 14 days after the diagnosis of the first known COVID-19 case in the dormitory, and dormitories A–D had reported cases 20–30 days before the investigation.

Of 111 detained persons with SARS-CoV-2-positive test results, 66 persons received a second test (day 14) and 50 people received a third test (during days 19–27) during the investigation (Figure 1). Nineteen (29%) of 66 persons had positive test results 14 days after the first positive test result, and 4 (8%) of 50 persons had positive test results ≈3 weeks after first testing positive, 3 of whom had negative results on day 14.

Symptom and Behavioral Risk Assessment

Among 111 detained persons who tested positive for SARS-CoV-2, 21 (19%) were symptomatic at the time of their first positive test result, and 27 (24%) reported symptoms that had resolved before their first positive test result (Table 3). The most commonly reported symptoms among persons with SARS-CoV-2 infection were headache (32%), loss of taste or smell (31%), and nasal congestion (26%); measured fever (5%) and dyspnea (8%) were less commonly reported (Appendix Table 1, https://wwwnc.cdc.gov/EID/article/27/2/20-4158-App1.pdf). Forty-nine (44%) detained persons who tested positive for SARS-CoV-2 were asymptomatic and 3 (3%) were presymptomatic. Symptom onset among presymptomatic persons was 0–7 days from the day of first positive specimen collection. Among 32 detained persons with negative test results, 8 (25%) were symptomatic and 9 (28%) were postsymptomatic. No enrolled detained persons were hospitalized or died. No major differences in handwashing practices, mask use, and movement within the facility were reported by those who tested positive compared with those who tested negative (Appendix Table 2).

Ct Values and Viral Culture

Median Ct values were lowest among presymptomatic persons (30.6, range 20.0–31.1) and highest among postsymptomatic persons (33.2, range 25.2–37.5) (p = 0.03). The overall ranges for Ct values were similar for symptomatic (19.7–36.3) and asymptomatic persons (19.8–36.9). Among the 51 symptomatic SARS-CoV-2–positive persons, positive rRT-PCR results occurred 7 days before symptom onset to 48 days after symptom onset (Figure 2, panel A).

Figure 2.

Rapid transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in detention facility, Louisiana, USA, May–June 2020. A) Ct values and viral culture results by days from symptom onset of any symptom in SARS-CoV-2–positive detained persons. Nucleocapsid protein 1 target Ct values and viral culture results of 66 specimens from 51 persons who were positive for SARS-CoV-2 by days from reported symptom onset. Ct values and viral culture results are also shown for 14 of the 51 specimens from persons who were positive a second time, and for 1 specimen that remained positive for a third test. Vertical dashed line indicates day 14 to depict the recommended medical isolation timeframe from symptom onset for persons in congregate settings. Shapes indicate culture results, and colors indicate day of positive test result. One positive test result is not included because Ct values were not reported. B) Ct values and viral culture results for SARS-CoV-2–positive detained persons at the time of first sample collection according to dormitory residence and day of first positive result. Nucleocapsid protein 1 target Ct values and viral culture results of the first SARS-CoV-2–positive test result for 110 detained persons is shown by dormitory of residence at the time of first sample collection. Horizontal lines indicate median Ct values for first positive samples from residents in each dormitory. One positive test result from a dormitory F resident is not included because Ct value was not reported. Ct, cycle threshold.

Among 111 specimens that resulted in the first positive results for detained persons, 110 were submitted for viral culture and 25 (23%) had replication-competent virus isolated (Table 3). Replication-competent virus isolates were obtained from 25% (12/48) of nasopharyngeal swab specimens from asymptomatic persons, 67% (2/3) from presymptomatic persons, 29% (6/21) from symptomatic persons, and 11% (3/27) from postsymptomatic persons. Among persons reporting symptoms, specimens with replication-competent virus were collected during 6 days before to 4 days after symptom onset. Two postsymptomatic persons reported symptom resolution the day of testing; for the third person, date of symptom resolution was unknown.

The Ct values at the first positive test result and the proportion of specimens with positive viral culture for SARS-CoV-2 varied by dormitory (Figure 2, panel B). The median Ct value for 53 specimens collected from detained persons in dormitories A–E was 33.6 (range 20.0–37.5); 2 (4%) samples from persons in dormitories D and E were replication competent. The median Ct value for 39 samples from detained persons in dormitory F was 29.3 (range 19.7–34.3). Of these samples, 23 (59%) were replication competent.

Of 22 persons that had positive test results ≥14 days after the first positive test, 4 remained rRT-PCR positive for SARS-CoV-2 ≈3 weeks after first testing positive. Virus isolation was attempted but was not successful for any of the specimens from repeat-positive persons.

Phylogenetic Analysis

We compared sequencing results for 41 specimens collected from persons in dormitories A (n = 2), D (n = 5), E (n = 2), and F (n = 32) at facility X during May 7–29 with each other and representative sequences from GISAID. All sequences clustered together within clade 20C and among other sequences reported from Louisiana (Appendix Figure). A phylogenetic tree illustrated 3 groups: 1 with sequences from persons in dormitories D and E, a second with sequences from persons in dormitories A and D, and a third with sequences from persons in dormitory F. Two identical SARS-CoV-2 sequences were identified from a person in dormitory D and a person from dormitory E. The third group differed from the first cluster by ≥6 nt and from the second cluster by 2 nt mutations.

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