key: cord-0280842-8nw79pv5
authors: Bukatko, A.; Lobato, M.; Mosites, E.; Stainken, C.; Reihl, K.; Deldari, M.; Bell, J.; Morris, M.; Wadford, D.; Harriman, K.; Mase, S.
title: Outbreak of COVID-19 among vaccinated and unvaccinated homeless shelter residents- Sonoma County, California, July 2021
date: 2021-12-08
journal: nan
DOI: 10.1101/2021.12.07.21267204
sha: ca952ce7f5e2b51de732c4d9483fdc3f6573af6c
doc_id: 280842
cord_uid: 8nw79pv5

On Saturday, July 3, 2021, the Sonoma County Health Department was alerted to three cases of COVID-19 among residents of a homeless shelter in Santa Rosa, California. Among 153 shelter residents, 83 (54%) were fully vaccinated; 71 (86%) vaccinated residents had received the Janssen COVID-19 vaccine and 12 (14%) received an mRNA (Pfizer BioNTech or Moderna) COVID-19 vaccine. Within 1 month, 116 shelter residents (76%) received positive SARS-CoV-2 test results, including 66 (80%) of 83 fully vaccinated residents and 50 (71%) of 70 residents who were not fully vaccinated. Nine (14%) of 66 fully vaccinated cases, compared with 1 of 50 (2%) of unvaccinated cases, were hospitalized with COVID-19. All hospitalized cases had at least one underlying medical condition. Two deaths occurred, one in a vaccinated resident and one in a resident who was not fully vaccinated. Specimens from 52 residents underwent whole genome sequencing; all were identified as SARS-CoV-2 (the virus that causes COVID-19) AY.13, a sublineage of the B.1.617.2 (Delta) variant. These findings suggest that comprehensive measures including routine testing, individual quarantine, mask wearing, and physical distancing are needed in addition to vaccination in homeless shelters and other similar congregate settings, particularly those with residents who are at high risk for severe COVID-19.

locations visited. Exposed staff members who were not fully vaccinated were sent home to quarantine.

On epidemiology week 28, 2021, Sonoma County Health Department initiated symptom checks and twice-weekly SARS-CoV-2 nucleic acid amplification tests (NAAT; reverse transcription-polymerase chain reaction) for residents and staff members in collaboration with a partner hospital. Cases were defined as receipt of a positive SARS-CoV-2 NAAT result. Fully vaccinated was defined as persons who were Four partially vaccinated residents (those who either did not complete the 2-dose series (for those receiving an mRNA vaccine) or for whom less than 2 weeks had elapsed since receipt of the final dose) were considered not fully vaccinated in the analysis. Reinfection was defined as a positive test result during this outbreak in a person who had a recorded positive test result >90 days earlier. Contacts were defined as any person within 6 feet of a COVID-19 patient for a cumulative total of residents who were vaccinated and those who were not fully vaccinated were performed using Fisher's exact test due to small sample size.

Specimens from 52 residents underwent whole genome sequencing at the California Department of Public Health Viral and Rickettsial Disease Laboratory and Sonoma County Public Health Laboratory. Sequencing was done with Clear-Labs automation platform using Oxford-nanopore technology for sequencing and Guppy algorithm for basecalling. The consensus genomes generated from whole genome sequences (n=51 sequenced in 2 groups) underwent phylogenic analysis using the Ultrafast Sample placement on Existing tRees (UShER) bioinformatics application (4). NC_045512.2 (SARS-Ncov-2 isolate Wuhan-Hu-1) was used as the reference genome sequence for phylogenic analysis. For the purpose of easier differentiation between sublineages of the basal strain (the most common ancestor between the detected sequences), sequences in the study were given alphanumeric designations corresponding to further divergence from the basal strain (Appendix Figure 1 , Appendix Table 1a ). Serum samples from eight of 10 hospitalized persons were tested for total anti-SARS-CoV-2 nucleocapsid (N) antibodies immunoglobulin (Ig)M, IgG, and IgA (BioRad Platelia, California, USA), and by SARS-CoV-2 enzyme-linked immunosorbent assay to detect anti-SARS-CoV-2

IgG to viral spike (S), matrix (M), and N proteins, and for neutralizing antibodies (United Biomedical, Inc, New York, USA).

In a month between Epi-weeks 27 and 32, 116 (76%) residents received positive SARS-CoV-2 test results ( Figure 1 ). The mean age of residents with positive test results was 52 years (standard deviation: 13 years), and 73 (63%) were male (Table 1) . Among those for whom information on ethnicity was available (n = 142), 118 (83%) were non-Hispanic and 24 (17%) for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. were Hispanic. Seventy-four residents (64%) had documented symptomatic disease. Data on existing medical conditions were available for 93 (80%) infected residents; 82 (88%) of whom had at least one condition associated with risk for severe COVID-19. Ten residents were hospitalized for COVID-19, including four who were admitted to an intensive care unit; two residents died. All 10 residents hospitalized for COVID-19 were >55 years old and had at least one underlying medical condition (seven had more than two conditions) including chronic obstructive pulmonary disease, diabetes, cardiovascular disease, and substance use disorders.

Cancers and rare conditions were also noted.

All sequenced specimens were identified as SARS-CoV-2 (the virus that causes COVID- Contact tracing at the shelter revealed additional epidemiologically linked NAATconfirmed cases, including 2 cases among health care providers who worked at the shelter, 10 cases at the primary workplace of the health care providers (five staff members, one visitor, and for use under a CC0 license.

This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; https://doi.org/10.1101/2021.12.07.21267204 doi: medRxiv preprint four staff family members), one case in a delivery person, and eight cases in three encampments where shelter residents spent time.

Among the 116 shelter residents with positive SARS-CoV-2 test results, 66 (57%) were fully vaccinated; 56 (85%) of those received the Janssen vaccine. The mean interval since achieving fully vaccinated status was 10 weeks, including among those with positive test results. Residents aged ≥ 55 years were more likely to be vaccinated (47/77; 61%) than were those aged <55 years (36/76; 47%), but the difference was not statistically significant (p = 0.11).

Residents with at least one underlying condition (55/82; 67%) were more likely to be vaccinated than were those without an underlying condition (3/11; 27%) (p = 0.02).

Infection occurred in 66 of 83 (80%) fully vaccinated residents and 50 of 70 (71%) residents who were not fully vaccinated (Table 1) This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; https://doi.org/10.1101/2021.12.07.21267204 doi: medRxiv preprint residents admitted to the ICU were fully vaccinated. Hospitalization was significantly associated with being fully vaccinated (p = 0.04). This association was not statistically significant after stratifying for age or having >2 underlying conditions. The type of vaccine received was not statistically significantly associated with infection or hospitalization. Neither stratifying by prior infection nor excluding persons who were partially vaccinated from the analysis meaningfully This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; https://doi.org/10.1101/2021.12.07.21267204 doi: medRxiv preprint vaccine effectiveness against hospitalization has remained high and vaccinated persons have accounted for the minority of hospitalizations (7, 8) . This outbreak in a unique setting with high risk of transmission showed results that differ from broader experience among vaccinated persons. This reinforces the importance of layered preventions strategies, including vaccination and non-pharmaceutical strategies (e.g. masking, physical distancing) to prevent SARS-CoV-2 transmission in settings at high risk for transmission such as homeless shelters. (3) The reason that persons who were vaccinated had severe outcomes after infection during this outbreak is not clear. The serology results for eight of 10 hospitalized patients were positive for SARS-CoV-2, suggesting that these patients did mount an immune response. However, many shelter residents had medical conditions associated with more severe outcomes after infection with SARS-CoV-2, which might have placed those who were fully vaccinated at higher risk.

Although we had limited ability to stratify data due to the size of the outbreak, confounding by age and underlying conditions likely led to the higher proportions of fully vaccinated persons who were hospitalized compared to those who were not fully vaccinated. Studies have also produced evidence that 1 dose and 2 dose regiments of currently available vaccines may yield insufficient protection in older age persons with no previous infection; additional vaccine doses may be beneficial for such persons to achieve adequate immune response to currently circulating variants (9,10).

The findings in this report are subject to at least four limitations. First the sample size was small, limiting the power to determine the statistical significance of some differences of interest. Second, almost all residents received the Janssen vaccine, so it was not possible to determine whether vaccine type contributed to the findings here. Third, vaccine status was confirmed through the California Immunization Registry; persons who might have been for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; https://doi.org/10.1101/2021.12.07.21267204 doi: medRxiv preprint immunized but not included in the registry could have been misclassified in this analysis.

Finally, data on underlying conditions were not available for uninfected residents.

In this population at higher risk for severe COVID-19 living in a homeless shelter, SARS-CoV-2 infection, symptomatic disease, hospitalization, and death occurred among residents who were fully vaccinated and those who were not fully vaccinated. These findings reinforce the importance of layered prevention strategies, including appropriate isolation and quarantine, screening testing, physical distancing, and masking in addition to providing vaccination, prevent COVID-19 outbreaks in homeless shelters and similar congregate settings.

for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. for use under a CC0 license.

This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; https://doi.org/10.1101/2021.12.07.21267204 doi: medRxiv preprint for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted December 8, 2021. ; https://doi.org/10.1101/2021.12.07.21267204 doi: medRxiv preprint

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