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

Factors influencing long-term care facility performance during the COVID-19 pandemic: a scoping review

BACKGROUND

The COVID-19 pandemic wreaked havoc on long-term care facilities (LTCFs). Some LTCFs performed better than others at slowing COVID-19 transmission. Emerging literature has mostly described infection prevention and control strategies implemented by LTCFs during the pandemic. However, there is a need for a comprehensive review of factors that influenced the performance of LTCFs in containing COVID-19 spread to inform public health policy.

OBJECTIVE

To build on the existing literature, we conducted a scoping review of factors that influenced LTCF performance during the COVID-19 pandemic using a multidimensional conceptual framework of performance.

METHODS

We followed the Joanna Briggs Institute's methodology for scoping reviews. We queried CINAHL, MEDLINE (Ovid), CAIRN, Science Direct, Scopus, and Web of Science for peer-reviewed literature in English or French published between January 1st, 2020 and December 31st, 2021. Retrieved records were screened for context (COVID-19 pandemic), population (LTCFs), interest (internal and external factors that influenced LTCF performance), and outcomes (dimensions of performance: equity, accessibility, reactivity, safety, continuity, efficacy, viability, efficiency). Descriptive characteristics of included articles were summarized. Dimensions of performance as well as internal (e.g., facility characteristics) and external (e.g., visitors) factors identified to have influenced LTCF performance were presented.

RESULTS

We retained 140 articles of which 68% were classified as research articles, 47% originated in North America, and most covered a period between March and July 2020. The most frequent dimensions of performance were "efficacy" (75.7%) and "safety" (75.7%). The most common internal factors were "organizational context" (72.9%) and "human resources" (62.1%), and the most common external factors were "visitors" (27.1%) and "public health guidelines" (25.7%).

CONCLUSIONS

Our review contributes to a global interest in understanding the impact of the COVID-19 pandemic on vulnerable populations residing and working in LTCFs. Though a myriad of factors were reported, a lack of randomized controlled trials makes it impossible to establish causality between the identified factors and LTCF performance. The use of a multidimensional framework can be recommended to evaluate healthcare system performance not merely in terms of efficacy and safety, but alongside other critical dimensions such as efficiency and equity.

TRIAL REGISTRATION

Research Registry ID: researchregistry7026.

Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance

Introduction

The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings.

Methods

California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements.

Results

Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state.

Discussion

Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.

Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital

Background

Identifying the source of healthcare personnel (HCP) coronavirus disease 2019 (COVID-19) is important to guide occupational safety efforts. We used a combined whole genome sequencing (WGS) and epidemiologic approach to investigate the source of HCP COVID-19 at a tertiary-care center early in the COVID-19 pandemic.

Methods

Remnant nasopharyngeal swab samples from HCP and patients with polymerase chain reaction-proven COVID-19 from a period with complete sample retention (14 March 2020 to 10 April 2020) at Rush University Medical Center in Chicago, Illinois, underwent viral RNA extraction and WGS. Genomes with >90% coverage underwent cluster detection using a 2 single-nucleotide variant genetic distance cutoff. Genomic clusters were evaluated for epidemiologic linkages, with strong linkages defined by evidence of time/location overlap.

Results

We analyzed 1031 sequences, identifying 49 clusters that included ≥1 HCP (265 patients, 115 HCP). Most HCP infections were not healthcare associated (88/115 [76.5%]). We did not identify any strong epidemiologic linkages for patient-to-HCP transmission. Thirteen HCP cases (11.3%) were attributed to a potential patient source (weak evidence involving nonclinical staff that lacked location data to prove or disprove contact with patients in same cluster). Fourteen HCP cases (12.2%) were attributed to HCP source (11 with strong evidence).

Conclusions

Using genomic and epidemiologic data, we found that most HCP severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were not healthcare associated. We did not find strong evidence of patient-to-HCP transmission of SARS-CoV-2.

Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium

Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual’s risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.

Occupational and community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study

BACKGROUND

We investigated the contribution of both occupational and community exposure for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among employees of a university-affiliated long-term care facility (LTCF), during the 1st pandemic wave in Switzerland (March-June 2020).

METHODS

We performed a nested analysis of a seroprevalence study among all volunteering LTCF staff to determine community and nosocomial risk factors for SARS-CoV-2 seropositivity using modified Poison regression. We also combined epidemiological and genetic sequencing data from a coronavirus disease 2019 (COVID-19) outbreak investigation in a LTCF ward to infer transmission dynamics and acquisition routes of SARS-CoV-2, and evaluated strain relatedness using a maximum likelihood phylogenetic tree.

RESULTS

Among 285 LTCF employees, 176 participated in the seroprevalence study, of whom 30 (17%) were seropositive for SARS-CoV-2. Most (141/176, 80%) were healthcare workers (HCWs). Risk factors for seropositivity included exposure to a COVID-19 inpatient (adjusted prevalence ratio [aPR] 2.6; 95% CI 0.9-8.1) and community contact with a COVID-19 case (aPR 1.7; 95% CI 0.8-3.5). Among 18 employees included in the outbreak investigation, the outbreak reconstruction suggests 4 likely importation events by HCWs with secondary transmissions to other HCWs and patients.

CONCLUSIONS

These two complementary epidemiologic and molecular approaches suggest a substantial contribution of both occupational and community exposures to COVID-19 risk among HCWs in LTCFs. These data may help to better assess the importance of occupational health hazards and related legal implications during the COVID-19 pandemic.

A qualitative assessment of factors affecting nursing home caregiving staff experiences during the COVID-19 pandemic

Background

A large portion of COVID-19 cases and deaths in the United States have occurred in nursing homes; however, current literature including the frontline perspective of staff working in nursing homes is limited. The objective of this qualitative assessment was to better understand what individual and facility level factors may have contributed to the impact of COVID-19 on Certified Nursing Assistants (CNAs) and Environmental Services (EVS) staff working in nursing homes.

Methods

Based on a simple random sample from the National Healthcare Safety Network (NHSN), 7,520 facilities were emailed invitations requesting one CNA and/or one EVS staff member for participation in a voluntary focus group over Zoom. Facility characteristics were obtained via NHSN and publicly available sources; participant demographics were collected via SurveyMonkey during registration and polling during focus groups. Qualitative information was coded using NVIVO and Excel.

Results

Throughout April 2021, 23 focus groups including 110 participants from 84 facilities were conducted homogenous by participant role. Staffing problems were a recurring theme reported. Participants often cited the toll the pandemic took on their emotional well-being, describing increased stress, responsibilities, and time needed to complete their jobs. The lack of consistent and systematic guidance resulting in frequently changing infection prevention protocols was also reported across focus groups.

Conclusions

Addressing concerns of low wages and lack of financial incentives may have the potential to attract and retain employees to help alleviate nursing home staff shortages. Additionally, access to mental health resources could help nursing home staff cope with the emotional burden of the COVID-19 pandemic. These frontline staff members provided invaluable insight and should be included in improvement efforts to support nursing homes recovering from the impact of COVID-19 as well as future pandemic planning.