Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) outbreak investigation in a hospital emergency department-California, December 2020-January 2021

We describe a large outbreak of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) involving an acute-care hospital emergency department during December 2020 and January 2021, in which 27 healthcare personnel worked while infectious, resulting in multiple opportunities for SARS-CoV-2 transmission to patients and other healthcare personnel. We provide recommendations for improving infection prevention and control.

Integrating social services with disease investigation: A randomized trial of COVID-19 high-touch contact tracing

COVID-19 exposed and exacerbated health disparities, and a core challenge has been how to adapt pandemic response and public health in light of these disproportionate health burdens. Responding to this challenge, the County of Santa Clara Public Health Department designed a model of "high-touch" contact tracing that integrated social services with disease investigation, providing continued support and resource linkage for clients from structurally vulnerable communities. We report results from a cluster randomized trial of 5,430 cases from February to May 2021 to assess the ability of high-touch contact tracing to aid with isolation and quarantine. Using individual-level data on resource referral and uptake outcomes, we find that the intervention, randomized assignment to the high-touch program, increased the referral rate to social services by 8.4% (95% confidence interval, 0.8%-15.9%) and the uptake rate by 4.9% (-0.2%-10.0%), with the most pronounced increases in referrals and uptake of food assistance. These findings demonstrate that social services can be effectively combined with contact tracing to better promote health equity, demonstrating a novel path for the future of public health.

Automated vs. manual case investigation and contact tracing for pandemic surveillance: Evidence from a stepped wedge cluster randomized trial

BACKGROUND

Case investigation and contact tracing (CICT) is an important tool for communicable disease control, both to proactively interrupt chains of transmission and to collect information for situational awareness. We run the first randomized trial of COVID-19 CICT to investigate the utility of manual (i.e., call-based) vs. automated (i.e., survey-based) CICT for pandemic surveillance.

METHODS

Between December 15, 2021 and February 5, 2022, a stepped wedge cluster randomized trial was run in which Santa Clara County ZIP Codes progressively transitioned from manual to automated CICT. Eleven individual-level data fields on demographics and disease dynamics were observed for non-response. The data contains 106,522 positive cases across 29 ZIP Codes.

FINDINGS

Automated CICT reduced overall collected information by 29 percentage points (SE = 0.08, p < 0.01), as well as the response rate for individual fields. However, we find no evidence of differences in information loss by race or ethnicity.

INTERPRETATIONS

Automated CICT can serve as a useful alternative to manual CICT, with no substantial evidence of skewing data along racial or ethnic lines, but manual CICT improves completeness of key data for monitoring epidemiologic patterns.

FUNDING

This research was supported in part by the Stanford Office of Community Engagement and the Stanford Institute for Human-Centered Artificial Intelligence.

Designing Accountable Health Care Algorithms: Lessons from Covid-19 Contact Tracing

An academic team at Stanford University worked with the County of Santa Clara Public Health Department to develop a machine-learning system for language matching in Covid-19 contact tracing through a collaborative design process. Although developed for a specific public health activity, the setting is representative of a wide range of health care delivery contexts, and the experience lays out how health care organizations can develop accountable algorithms that improve care, mitigate risk, and enable evaluation by stakeholders. Key elements of the design process involved: (1) a partnership and stakeholder consultation to develop a common understanding of and iteration around algorithmic design; (2) the use of a model understandable to all stakeholders, which exhibited only modest performance degradation relative to more complex models; and (3) a randomized controlled trial and qualitative survey of how the algorithm impacted real-world contact tracing, providing an evaluation that goes beyond narrow technical measures of algorithmic performance.

Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California

BACKGROUND

Outbreaks of SARS-CoV-2 in long-term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within and between facilities by combining genomic sequencing with epidemiologic investigations enables targeting infection-control interventions.

METHODS

We conducted weekly surveillance of residents and staff in LTCFs in Santa Clara County, California, with ≥1 confirmed COVID-19 case between March and July 2020. Positive samples were referred for whole-genome sequencing. Epidemiological investigations and phylogenetic analyses of the largest outbreaks (>30 cases) were carried out in 6 LTCFs (Facilities A through F).

RESULTS

Among the 61 LTCFs in the county, 41 had ≥1 confirmed case during the study period, triggering weekly SARS-CoV-2 testing. The 6 largest outbreaks accounted for 60% of cases and 90% of deaths in LTCFs, although the bed capacity of these facilities represents only 11% of the LTCF beds in the county. Phylogenetic analysis of 196 whole-genome sequences recovered from those facilities showed that each outbreak was monophyletic, with staff and residents sharing a common viral lineage. Outbreak investigations revealed that infected staff members often worked at multiple facilities, and in 1 instance, a staff member infected while working in 1 facility was the likely index case in another.

CONCLUSIONS

We detected a pattern of rapid and sustained transmission after a single introduction of SARS-CoV-2 in 6 large LTCF outbreaks, with staff playing a key role in transmission within and between facilities. Infection control, testing, and occupational policies to reduce exposure and transmission risk for staff are essential components to keeping facility residents safe.

Evaluation of Allocation Schemes of COVID-19 Testing Resources in a Community-Based Door-to-Door Testing Program

Question

What are effective mechanisms to identify and reach vulnerable populations and equalize access to COVID-19 testing resources in the presence of substantial demographic disparities?

Findings

In this cohort study of 756 participants, a door-to-door program with community-based health workers was associated with a substantial increase in the proportion of Latinx and elderly individuals undergoing testing, relative to neighborhood testing sites. The protocol associated with the greatest increase in testing at-risk individuals was uncertainty sampling, followed by local knowledge, and then targeting households in areas with a high number of index cases.

Meaning

These findings suggest that community-based testing programs that allocate resources using uncertainty sampling might effectively reduce COVID-19 testing disparities.

Importance

Overcoming social barriers to COVID-19 testing is an important issue, especially given the demographic disparities in case incidence rates and testing. Delivering culturally appropriate testing resources using data-driven approaches in partnership with community-based health workers is promising, but little data are available on the design and effect of such interventions.

Objectives

To assess and evaluate a door-to-door COVID-19 testing initiative that allocates visits by community health workers by selecting households in areas with a high number of index cases, by using uncertainty sampling for areas where the positivity rate may be highest, and by relying on local knowledge of the health workers.

Design, Setting, and Participants

This cohort study was performed from December 18, 2020, to February 18, 2021. Community health workers visited households in neighborhoods in East San Jose, California, based on index cases or uncertainty sampling while retaining discretion to use local knowledge to administer tests. The health workers, also known as promotores de salud (hereinafter referred to as promotores) spent a mean of 4 days a week conducting door-to-door COVID-19 testing during the 2-month study period. All residents of East San Jose were eligible for COVID-19 testing. The promotores were selected from the META cooperative (Mujeres Empresarias Tomando Acción [Entrepreneurial Women Taking Action]).

Interventions

The promotores observed self-collection of anterior nasal swab samples for SARS-CoV-2 reverse transcriptase–polymerase chain reaction tests.

Main Outcomes and Measures

A determination of whether door-to-door COVID-19 testing was associated with an increase in the overall number of tests conducted, the demographic distribution of the door-to-door tests vs local testing sites, and the difference in positivity rates among the 3 door-to-door allocation strategies.

Results

A total of 785 residents underwent door-to-door testing, and 756 were included in the analysis. Among the 756 individuals undergoing testing (61.1% female; 28.2% aged 45-64 years), door-to-door COVID-19 testing reached different populations than standard public health surveillance, with 87.6% (95% CI, 85.0%-89.8%) being Latinx individuals. The closest available testing site only reached 49.0% (95% CI, 48.3%-49.8%) Latinx individuals. Uncertainty sampling provided the most effective allocation, with a 10.8% (95% CI, 6.8%-16.0%) positivity rate, followed by 6.4% (95% CI, 4.1%-9.4%) for local knowledge, and 2.6% (95% CI, 0.7%-6.6%) for index area selection. The intervention was also associated with increased overall testing capacity by 60% to 90%, depending on the testing protocol.

Conclusions and Relevance

In this cohort study of 785 participants, uncertainty sampling, which has not been used conventionally in public health, showed promising results for allocating testing resources. Community-based door-to-door interventions and leveraging of community knowledge were associated with reduced demographic disparities in testing.

Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California

We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January to 21 March 2020. From 558 persons with coronavirus disease 2019, 101 genomes from 143 available clinical samples comprised 17 lineages, including SCC1 (n = 41), WA1 (n = 9; including the first 2 reported deaths in the United States, with postmortem diagnosis), D614G (n = 4), ancestral Wuhan Hu-1 (n = 21), and 13 others (n = 26). Public health intervention may have curtailed the persistence of lineages that appeared transiently during February and March. By August, only D614G lineages introduced after 21 March were circulating in Santa Clara County.

Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States

Coronavirus disease 2019 (COVID-19), the respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. In response to the first cases identified in the United States, close contacts of confirmed COVID-19 cases were investigated to enable early identification and isolation of additional cases and to learn more about risk factors for transmission. Close contacts of nine early travel-related cases in the United States were identified and monitored daily for development of symptoms (active monitoring). Selected close contacts (including those with exposures categorized as higher risk) were targeted for collection of additional exposure information and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction at the Centers for Disease Control and Prevention. Four hundred four close contacts were actively monitored in the jurisdictions that managed the travel-related cases. Three hundred thirty-eight of the 404 close contacts provided at least basic exposure information, of whom 159 close contacts had ≥1 set of respiratory samples collected and tested. Across all actively monitored close contacts, two additional symptomatic COVID-19 cases (i.e., secondary cases) were identified; both secondary cases were in spouses of travel-associated case patients. When considering only household members, all of whom had ≥1 respiratory sample tested for SARS-CoV-2, the secondary attack rate (i.e., the number of secondary cases as a proportion of total close contacts) was 13% (95% CI: 4-38%). The results from these contact tracing investigations suggest that household members, especially significant others, of COVID-19 cases are at highest risk of becoming infected. The importance of personal protective equipment for healthcare workers is also underlined. Isolation of persons with COVID-19, in combination with quarantine of exposed close contacts and practice of everyday preventive behaviors, is important to mitigate spread of COVID-19.

Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States

Coronavirus disease 2019 (COVID-19), the respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. In response to the first cases identified in the United States, close contacts of confirmed COVID-19 cases were investigated to enable early identification and isolation of additional cases and to learn more about risk factors for transmission. Close contacts of nine early travel-related cases in the United States were identified and monitored daily for development of symptoms (active monitoring). Selected close contacts (including those with exposures categorized as higher risk) were targeted for collection of additional exposure information and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction at the Centers for Disease Control and Prevention. Four hundred four close contacts were actively monitored in the jurisdictions that managed the travel-related cases. Three hundred thirty-eight of the 404 close contacts provided at least basic exposure information, of whom 159 close contacts had ≥1 set of respiratory samples collected and tested. Across all actively monitored close contacts, two additional symptomatic COVID-19 cases (i.e., secondary cases) were identified; both secondary cases were in spouses of travel-associated case patients. When considering only household members, all of whom had ≥1 respiratory sample tested for SARS-CoV-2, the secondary attack rate (i.e., the number of secondary cases as a proportion of total close contacts) was 13% (95% CI: 4-38%). The results from these contact tracing investigations suggest that household members, especially significant others, of COVID-19 cases are at highest risk of becoming infected. The importance of personal protective equipment for healthcare workers is also underlined. Isolation of persons with COVID-19, in combination with quarantine of exposed close contacts and practice of everyday preventive behaviors, is important to mitigate spread of COVID-19.

Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States

Data on the detailed clinical progression of COVID-19 in conjunction with epidemiological and virological characteristics are limited. In this case series, we describe the first 12 US patients confirmed to have COVID-19 from 20 January to 5 February 2020, including 4 patients described previously^1-3. Respiratory, stool, serum and urine specimens were submitted for SARS-CoV-2 real-time reverse-transcription polymerase chain reaction (rRT-PCR) testing, viral culture and whole genome sequencing. Median age was 53 years (range: 21-68); 8 patients were male. Common symptoms at illness onset were cough (n = 8) and fever (n = 7). Patients had mild to moderately severe illness; seven were hospitalized and demonstrated clinical or laboratory signs of worsening during the second week of illness. No patients required mechanical ventilation and all recovered. All had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2-3 weeks after illness onset. Lowest real-time PCR with reverse transcription cycle threshold values in the upper respiratory tract were often detected in the first week and SARS-CoV-2 was cultured from early respiratory specimens. These data provide insight into the natural history of SARS-CoV-2. Although infectiousness is unclear, highest viral RNA levels were identified in the first week of illness. Clinicians should anticipate that some patients may worsen in the second week of illness.