Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks - Minnesota, April-June 2020

SARS-CoV-2 rapid antigen testing positive rate in community testing stations as an indicator for COVID-19 epidemic trend, Taipei, Taiwan, May to August 2021

BACKGROUND

Real-time surveillance of COVID-19 in large-scale community outbreaks presents challenges. Simple counts of the daily confirmed cases can be misleading due to constraints from bottlenecks in access to care or laboratory testing. This study aimed to investigate the role of the SARS-CoV-2 antigen rapid diagnostic test (Ag-RDT) in addressing these challenges for real-time COVID-19 surveillance.

METHODS

This study included the results of 86,933 SARS-CoV-2 Ag-RDT and real-time reverse transcription polymerase chain reaction (RT-PCR) tests. These were conducted at four community testing stations within the Taipei metropolitan area during a community COVID-19 outbreak spanning from May 17, 2021, to August 9, 2021. We examined the correlation between the positive rates of Ag-RDT tests and the epidemic curve of laboratory-confirmed COVID-19 cases by onset date to examine its role in real-time surveillance.

RESULTS

During the 85-day study period, the trend of Ag-RDT test positive rates paralleled that of the epidemic curve. The correlation between the Ag-RDT positive rate and the number of cases (Pearson correlation coefficient: 0.968) is comparable to that of the RT-PCR positive rate (Pearson correlation coefficient: 0.964). The Ag-RDT positive rate exhibited a more advanced leading trend, with Ag-RDT leading by 3 days in comparison to the 2-day lead for RT-PCR.

CONCLUSION

The positive rate of SARS-CoV-2 Ag-RDT tests at community testing stations serves as a good surrogate for assessing virus activity within the community and a useful tool for real-time COVID-19 surveillance. It is a robust indicator of the outbreak trend and near-term numbers of cases. This finding may facilitate the management of subsequent outbreaks of emerging infectious diseases.

Surveillance for Unexplained Deaths of Possible Infectious Etiologies During the COVID-19 Pandemic-Minnesota, 2020-2021

OBJECTIVES

Surveillance systems for unexplained deaths that might have an infectious etiology are rare. We examined the Minnesota Department of Health Unexplained Deaths and Critical Illnesses of Possible Infectious Etiology and Medical Examiner Infectious Deaths (UNEX/MED-X) surveillance system,-a system that expanded postmortem surveillance for infectious diseases during the COVID-19 pandemic by leveraging standard (medical examiner [ME]) and expanded (mortuary) surveillance to identify COVID-19-related deaths.

METHODS

MEs, coroners, or morticians collected postmortem swabs from decedents with an infectious prodrome or with SARS-CoV-2 exposure before death but with no known recent infectious disease testing. The Minnesota Department of Health Public Health Laboratory used nucleic acid amplification, viral culture, and standard algorithms to test specimens collected postmortem for SARS-CoV-2, influenza virus, and other infectious pathogens. We reviewed UNEX/MED-X data from March 2, 2020, through December 31, 2021, and characterized decedents by location of swab collection (ie, ME or mortuary).

RESULTS

From March 2, 2020, through December 31, 2021, the UNEX/MED-X surveillance system received samples from 182 decedents from mortuaries and 955 decedents from MEs. Mortuary decedents were older than ME decedents (median age, 78 vs 46 y). Seventy-three mortuary decedents (40.1%) and 197 ME decedents (20.6%) had SARS-CoV-2 detections. The UNEX/MED-X system identified 212 COVID-19-related deaths, representing 2.0% of total COVID-19-related deaths in Minnesota. Eighty-nine decedents (42.0%) were from racial and ethnic minority populations, representing 6.1% more COVID-19-related deaths among people from racial and ethnic minority populations than would have been detected without this surveillance system.

PRACTICE IMPLICATIONS

Expanded and standard UNEX/MED-X surveillance builds capacity and flexibility for responding to emerging public health threats. Similar programs should be considered elsewhere as resources allow.

COVID-19 outbreak and genomic investigation in an inpatient behavioral health unit

Background

Inpatient behavioral health units (BHUs) had unique challenges in implementing interventions to mitigate coronavirus disease 2019 (COVID-19) transmission, in part due to socialization in BHU settings. The objective of this study was to identify the transmission routes and the efficacy of the mitigation strategies employed during a COVID-19 outbreak in an inpatient BHU during the Omicron surge from December 2021 to January 2022.

Methods

An outbreak investigation was performed after identifying 2 COVID-19-positive BHU inpatients on December 16 and 20, 2021. Mitigation measures involved weekly point prevalence testing for all inpatients, healthcare workers (HCWs), and staff, followed by infection prevention mitigation measures and molecular surveillance. Whole-genome sequencing on a subset of COVID-19-positive individuals was performed to identify the outbreak source. Finally, an outbreak control sustainability plan was formulated for future BHU outbreak resurgences.

Results

We identified 35 HCWs and 8 inpatients who tested positive in the BHU between December 16, 2021, and January 17, 2022. We generated severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomes from 15 HCWs and all inpatients. Phylogenetic analyses revealed 3 distinct but genetically related clusters: (1) an HCW and inpatient outbreak likely initiated by staff, (2) an HCW and inpatient outbreak likely initiated by an inpatient visitor, and (3) an HCW-only cluster initiated by staff.

Conclusions

Distinct transmission clusters are consistent with multiple, independent SARS-CoV-2 introductions with further inpatient transmission occurring in communal settings. The implemented outbreak control plan comprised of enhanced personal protective equipment requirements, limited socialization, and molecular surveillance likely minimized disruptions to patient care as a model for future pandemics.

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study

Background

Understanding routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in long-term care facilities is essential for the development of effective control measures.

Methods

Between March 1, 2020, and August 31, 2023, we identified coronavirus disease 2019 (COVID-19) cases among residents and employees in a Veterans Affairs community living center that conducted routine screening for asymptomatic COVID-19. Contact tracing was conducted to identify suspected transmission events, and whole genome sequencing was performed to determine the relatedness of SARS-CoV-2 samples.

Results

During the 42-month study period, 269 cases of COVID-19 were diagnosed, including 199 employees and 70 residents. A total of 48 (24.1%) employees and 30 (42.9%) residents were asymptomatic. Sequencing analysis provided support for multiple events in which employees transmitted SARS-CoV-2 to co-workers and residents. There was 1 episode of likely transmission of SARS-CoV-2 from one resident to another resident, but no documented transmissions from residents to employees.

Conclusions

Transmission of SARS-CoV-2 in the community living center predominantly involved transmission from employees to co-workers and residents. There is a need for improved measures to prevent transmission of SARS-CoV-2 by healthcare personnel.

Coronavirus disease 2019 (COVID-19) vaccination rates and staffing shortages among healthcare personnel in nursing homes before, during, and after implementation of mandates for COVID-19 vaccination among 15 US jurisdictions, National Healthcare Safety Network, June 2021-January 2022

OBJECTIVE

To examine temporal changes in coverage with a complete primary series of coronavirus disease 2019 (COVID-19) vaccination and staffing shortages among healthcare personnel (HCP) working in nursing homes in the United States before, during, and after the implementation of jurisdiction-based COVID-19 vaccination mandates for HCP.

SAMPLE AND SETTING

HCP in nursing homes from 15 US jurisdictions.

DESIGN

We analyzed weekly COVID-19 vaccination data reported to the Centers for Disease Control and Prevention's National Healthcare Safety Network from June 7, 2021, through January 2, 2022. We assessed 3 periods (preintervention, intervention, and postintervention) based on the announcement of vaccination mandates for HCP in 15 jurisdictions. We used interrupted time-series models to estimate the weekly percentage change in vaccination with complete primary series and the odds of reporting a staffing shortage for each period.

RESULTS

Complete primary series vaccination among HCP increased from 66.7% at baseline to 94.3% at the end of the study period and increased at the fastest rate during the intervention period for 12 of 15 jurisdictions. The odds of reporting a staffing shortage were lowest after the intervention.

CONCLUSIONS

These findings demonstrate that COVID-19 vaccination mandates may be an effective strategy for improving HCP vaccination coverage in nursing homes without exacerbating staffing shortages. These data suggest that mandates can be considered to improve COVID-19 coverage among HCP in nursing homes to protect both HCP and vulnerable nursing home residents.

Positive COVID-19 Diagnosis Following Primary Elective Total Joint Arthroplasty: Increased Complication and Mortality Rates

BACKGROUND

This study analyzed complication rates following primary elective total joint arthroplasty (TJA) in patients who subsequently contracted COVID-19.

METHODS

A large national database was queried for adult patients who underwent primary elective TJA in 2020. Patients who contracted COVID-19 after total knee arthroplasty (TKA) or total hip arthroplasty (THA) underwent 1:6 matching (age [±6 years], sex, month of surgery, COVID-19-related comorbidities) to patients who did not. Differences between groups were assessed using univariate and multivariate analyses. Overall, 712 COVID-19 patients were matched to 4,272 controls (average time to diagnosis: 128-117 days [range, 0-351]).

RESULTS

Of patients diagnosed <90 days postoperatively, 32.5%-33.6% required COVID-19-driven readmission. Discharge to a skilled nursing facility (adjusted odds ratio [aOR] 1.72, P = .003) or acute rehabilitation unit (aOR 4.93, P < .001) and Black race (aOR 2.28, P < .001) were associated with readmission after TKA. Similar results were associated with THA. COVID-19 patients were at increased risk of pulmonary embolism (aOR 4.09, P = .001) after TKA and also periprosthetic joint infection (aOR 4.65, P < .001) and sepsis (aOR 11.11, P < .001) after THA. The mortality rate was 3.51% in COVID-19 patients and 7.94% in readmitted COVID-19 patients compared to 0.09% in controls, representing a 38.7 OR and 91.8 OR of death, respectively. Similar results were observed for TKA and THA separately.

CONCLUSION

Patients who contracted COVID-19 following TJA were at greater risk of numerous complications, including death. These patients represent a high-risk cohort who may require more aggressive medical interventions. Given the potential limitations presently, prospectively collected data may be warranted to validate these findings.

SARS-CoV-2 Outbreak Investigation Using Contact Tracing and Whole-Genome Sequencing in an Ontario Tertiary Care Hospital

Genomic epidemiology can facilitate an understanding of evolutionary history and transmission dynamics of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak. We used next-generation sequencing techniques to study SARS-CoV-2 genomes isolated from patients and health care workers (HCWs) across five wards of a Canadian hospital with an ongoing SARS-CoV-2 outbreak. Using traditional contact tracing methods, we show transmission events between patients and HCWs, which were also supported by the SARS-CoV-2 lineage assignments. The outbreak predominantly involved SARS-CoV-2 B.1.564.1 across all five wards, but we also show evidence of community introductions of lineages B.1, B.1.1.32, and B.1.231, falsely assumed to be outbreak related. Altogether, our study exemplifies the value of using contact tracing in combination with genomic epidemiology to understand the transmission dynamics and genetic underpinnings of a SARS-CoV-2 outbreak. IMPORTANCE Our manuscript describes a SARS-CoV-2 outbreak investigation in an Ontario tertiary care hospital. We use traditional contract tracing paired with whole-genome sequencing to facilitate an understanding of the evolutionary history and transmission dynamics of this SARS-CoV-2 outbreak in a clinical setting. These advancements have enabled the incorporation of phylogenetics and genomic epidemiology into the understanding of clinical outbreaks. We show that genomic epidemiology can help to explore the genetic evolution of a pathogen in real time, enabling the identification of the index case and helping understand its transmission dynamics to develop better strategies to prevent future spread of SARS-CoV-2 in congregate, clinical settings such as hospitals.

Excess risk of SARS-CoV-2 infection among in-person nonhealthcare workers in six states, September 2020-June 2021

BACKGROUND

While the occupational risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection for healthcare personnel in the United States has been relatively well characterized, less information is available on the occupational risk for workers employed in other settings. Even fewer studies have attempted to compare risks across occupations and industries. Using differential proportionate distribution as an approximation, we evaluated excess risk of SARS-CoV-2 infection by occupation and industry among non-healthcare workers in six states.

METHODS

We analyzed data on occupation and industry of employment from a six-state callback survey of adult non-healthcare workers with confirmed SARS-CoV-2 infection and population-based reference data on employment patterns, adjusted for the effect of telework, from the U.S. Bureau of Labor Statistics. We estimated the differential proportionate distribution of SARS-CoV-2 infection by occupation and industry using the proportionate morbidity ratio (PMR).

RESULTS

Among a sample of 1111 workers with confirmed SARS-CoV-2 infection, significantly higher-than-expected proportions of workers were employed in service occupations (PMR 1.3, 99% confidence interval [CI] 1.1-1.5) and in the transportation and utilities (PMR 1.4, 99% CI 1.1-1.8) and leisure and hospitality industries (PMR 1.5, 99% CI 1.2-1.9).

CONCLUSIONS

We found evidence of significant differences in the proportionate distribution of SARS-CoV-2 infection by occupation and industry among respondents in a multistate, population-based survey, highlighting the excess risk of SARS-CoV-2 infection borne by some worker populations, particularly those whose jobs require frequent or prolonged close contact with other people.

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

BACKGROUND

The first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over a third of care homes reported an outbreak while there was limited testing of hospital patients discharged to care homes.

AIM

Investigate hospital discharges as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave.

METHODS

A clinical review was performed for all discharges from hospitals to care homes starting 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease (COVID-19) test history, clinical assessment at discharge, whole genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis by cluster investigation and virus epidemiological tool (CIVET). Patient timelines were obtained using electronic hospital records.

FINDINGS

In total 787 hospital discharges to care homes were identified. Out of these 776 (99%) were ruled out for hospital discharge introduction. However, for 10 episodes the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission leading to 10 further positive cases in the care home.

CONCLUSION

Majority of hospital discharges were ruled out for introduction into Lothian care homes highlighting the importance of screening all new admissions when faced with a novel emerging virus and no vaccine available.

Use of serial testing to interrupt a severe acute respiratory coronavirus virus 2 (SARS-CoV-2) outbreak on a hospital medical floor-Minnesota, October-December 2020

OBJECTIVE

Describe a severe acute respiratory coronavirus virus 2 (SARS-CoV-2) hospital outbreak and the role of serial testing of patients and healthcare personnel (HCP) in interrupting SARS-CoV-2 transmission.

DESIGN

Outbreak investigation.

SETTING

Medical floor of a tertiary-care center in Minnesota.

METHODS

Serial testing for SARS-CoV-2 and whole-genome sequencing (WGS) of positive specimens from HCP and patients were used. An outbreak-associated case was defined as a positive SARS-CoV-2 molecular test in an HCP who worked on the floor prior to testing positive or in a patient who was hospitalized on the medical floor bewteen October 27 and December 1, 2020. WGS was used to determine potential routes of transmission.

RESULTS

The outbreak was detected after a patient hospitalized for 12 days tested positive for SARS-CoV-2. Serial testing of patients and HCP was conducted in response. Overall, 247 HCP and 41 patients participated in serial SARS-CoV-2 testing; 52 HCP (21%) and 19 hospitalized patients (46%) tested positive. One additional HCP tested positive outside serial testing. The WGS of specimens from 27 (51%) HCP and 15 (79%) patients identified 3 distinct transmission clusters. WGS and epidemiologic evidence suggested intrafacility transmission. The proportions of asymptomatic and presymptomatic patients who tested positive (63%) and HCP who worked during their infectious period (75%) highlight the need for serial testing of asymptomatic patients and HCP during outbreaks.

CONCLUSIONS

Coupled with preventive measures such as personal protective equipment use and physical distancing, serial testing of HCP and patients could help detect and prevent transmission within healthcare facilities during outbreaks and when nosocomial transmission is suspected.

Impact of the COVID-19 pandemic and corresponding control measures on long-term care facilities: a systematic review and meta-analysis

BACKGROUND

Long-term care facilities (LTCFs) were high-risk settings for COVID-19 outbreaks.

OBJECTIVE

To assess the impacts of the COVID-19 pandemic on LTCFs, including rates of infection, hospitalisation, case fatality, and mortality, and to determine the association between control measures and SARS-CoV-2 infection rates in residents and staff.

METHOD

We conducted a systematic search of six databases for articles published between December 2019 and 5 November 2021, and performed meta-analyses and subgroup analyses to identify the impact of COVID-19 on LTCFs and the association between control measures and infection rate.

RESULTS

We included 108 studies from 19 countries. These studies included 1,902,044 residents and 255,498 staff from 81,572 LTCFs, among whom 296,024 residents and 36,807 staff were confirmed SARS-CoV-2 positive. The pooled infection rate was 32.63% (95%CI: 30.29 ~ 34.96%) for residents, whereas it was 10.33% (95%CI: 9.46 ~ 11.21%) for staff. In LTCFs that cancelled visits, new patient admissions, communal dining and group activities, and vaccinations, infection rates in residents and staff were lower than the global rate. We reported the residents' hospitalisation rate to be 29.09% (95%CI: 25.73 ~ 32.46%), with a case-fatality rate of 22.71% (95%CI: 21.31 ~ 24.11%) and mortality rate of 15.81% (95%CI: 14.32 ~ 17.30%). Significant publication biases were observed in the residents' case-fatality rate and the staff infection rate, but not in the infection, hospitalisation, or mortality rate of residents.

CONCLUSION

SARS-CoV-2 infection rates would be very high among LTCF residents and staff without appropriate control measures. Cancelling visits, communal dining and group activities, restricting new admissions, and increasing vaccination would significantly reduce the infection rates.

On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study

Objectives

We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings.

Design and setting

This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures.

Results

Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases.

Conclusion

SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available.

Trial registration

clinicaltrials.gov identifier: NCT05411562.

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.

Missing science: A scoping study of COVID-19 epidemiological data in the United States

Systematic approaches to epidemiologic data collection are critical for informing pandemic responses, providing information for the targeting and timing of mitigations, for judging the efficacy and efficiency of alternative response strategies, and for conducting real-world impact assessments. Here, we report on a scoping study to assess the completeness of epidemiological data available for COVID-19 pandemic management in the United States, enumerating authoritative US government estimates of parameters of infectious transmission, infection severity, and disease burden and characterizing the extent and scope of US public health affiliated epidemiological investigations published through November 2021. While we found authoritative estimates for most expected transmission and disease severity parameters, some were lacking, and others had significant uncertainties. Moreover, most transmission parameters were not validated domestically or re-assessed over the course of the pandemic. Publicly available disease surveillance measures did grow appreciably in scope and resolution over time; however, their resolution with regards to specific populations and exposure settings remained limited. We identified 283 published epidemiological reports authored by investigators affiliated with U.S. governmental public health entities. Most reported on descriptive studies. Published analytic studies did not appear to fully respond to knowledge gaps or to provide systematic evidence to support, evaluate or tailor community mitigation strategies. The existence of epidemiological data gaps 18 months after the declaration of the COVID-19 pandemic underscores the need for more timely standardization of data collection practices and for anticipatory research priorities and protocols for emerging infectious disease epidemics.

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.

The implications of the COVID-19 pandemic for long term care facilities

PURPOSE OF REVIEW

Despite advances in infection prevention and control and breakthroughs in vaccination development, challenges remain for long-term care facilities (LTCFs) as they face a likely future of emerging infectious diseases. To ensure the safety of LTCF residents from the current and future pandemics, we identify lessons learned from the coronavirus disease 2019 (COVID-19) experience for improving future prevention and response efforts.

RECENT FINDINGS

In addition to high disease susceptibility among LTCF residents, LTCF vulnerabilities include a lack of pandemic preparedness, a lack of surge capacity in human, material and testing resources, and poorly designed buildings. External sources of vulnerability include staff working in multiple LTCFs and high COVID-19 rates in surrounding communities. Other challenges include poor cooperation between LTCFs and the other components of health systems, inadequately enforced regulations, and the sometimes contradictory interests for-profit LTCFs face between protecting their residents and turning a profit.

SUMMARY

These challenges can be addressed in the post-COVID-19 period through systemic reforms. Governments should establish comprehensive health networks that normalize mechanisms for prediction/preparedness and response/recovery from disruptive events including pandemics. In addition, governments should facilitate cooperation among public and private sector health systems and institutions while utilizing advanced digital communication technologies. These steps will greatly reduce the threat to LTCFs posed by emerging infectious diseases in future.

Estimating COVID-19 Vaccine Effectiveness for Skilled Nursing Facility Healthcare Personnel, California, USA

We estimated real-world vaccine effectiveness among skilled nursing facility healthcare personnel who were regularly tested for SARS-CoV-2 infection in California, USA, during January‒March 2021. Vaccine effectiveness for fully vaccinated healthcare personnel was 73.3% (95% CI 57.5%-83.3%). We observed high real-world vaccine effectiveness in this population.

Analysis of the Transmission of SARS-CoV-2 Delta VOC in Yantai, China, August 2021

Objective

Starting 31 July 2021, a SARS-CoV-2 outbreak occurred in Yantai, Shandong Province. The investigation showed that this outbreak was closely related to the epidemic at Nanjing Lukou Airport. In view of the fact that there were many people involved in this outbreak and these people had a complex activity area, the transmission route cannot be analyzed by simple epidemiological investigation. Here we combined the SARS-COV-2 whole-genome sequencing with epidemiology to determine the epidemic transmission route of Yantai.

Methods

Thirteen samples of SARS-CoV-2 outbreak cases from 31 July to 4 August 2021 were collected and identified by fluorescence quantitative PCR, then whole-genome deep sequencing based on NGS was performed, and the data were analyzed and processed by biological software.

Results

All sequences were over 29,000 bases in length and all belonged to B.1.617.2, which was the Delta strain. All sequences shared two amino acid deletions and 9 amino acid mutations in Spike protein compared with reference sequence NC_045512.2 (Wuhan virus strain). Compared with the sequence of Lukou Airport Delta strain, the homology was 99.99%. In order to confirm the transmission relationship between patients, we performed a phylogenetic tree analysis. The results showed that patient 1, patient 2, and patient 9 belong to an independent branch, and other patients have a close relationship. Combined with the epidemiological investigation, we speculated that the epidemic of Yantai was transmitted by two routes at the same time. Based on this information, our prevention and control work was carried out in two ways and effectively prevented the further spread of this epidemic.

Further observations on hydrogen peroxide antisepsis and COVID-19 cases among healthcare workers and inpatients

Background

The use of prophylactic antisepsis to protect against coronavirus disease 2019 (COVID-19) has been suggested. This study investigated hydrogen peroxide antisepsis (HPA) at two hospitals in Ghana.

Methods

Cases of COVID-19 among healthcare workers (HCWs) using hydrogen peroxide (HP-HCWs) or not using hydrogen peroxide (NHP-HCWs), vaccinated or unvaccinated, were recorded at Shai-Osudoku Hospital (SODH), Dodowa, and Mount Olives Hospital (MOH), Techiman, between May 2020 and December 2021. The effect of HPA in all inpatients at MOH was also observed. Permutation tests were used to determine P values.

Findings

At SODH, there were 62 (13.5%) cases of COVID-19 among 458 NHP-HCWs but no cases among eight HP-HCWs (P=0.622) from May to December 2020. Between January and March 2021, 10 (2.7%) of 372 NHP-HCWs had COVID-19, but there were no cases among 94 HP-HCWs (P=0.206). At MOH, prior to HPA, 17 (20.2%) of 84 HCWs and five (1.4%) of 370 inpatients had COVID-19 in July 2020. From August 2020 to March 2021, two of 54 (3.7%) HCWs who stopped HPA had COVID-19; none of 32 NHP-HCWs contracted COVID-19. At SODH, none of 23 unvaccinated HP-HCWs and 35 (64%) of 55 unvaccinated NHP-HCWs had COVID-19 from April to December 2021 (P<0.0001). None of 34 vaccinated HP-HCWs and 53 (13.6%) of 390 vaccinated NHP-HCWs had COVID-19 (P=0.015). No inpatients on prophylactic HPA (total 7736) contracted COVID-19.

Conclusion

Regular, daily HPA protects HCWs from COVID-19, and curtails nosocomial spread of SARS-CoV-2.

Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis

BACKGROUND

Debate about the level of asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection continues. The amount of evidence is increasing and study designs have changed over time. We updated a living systematic review to address 3 questions: (1) Among people who become infected with SARS-CoV-2, what proportion does not experience symptoms at all during their infection? (2) What is the infectiousness of asymptomatic and presymptomatic, compared with symptomatic, SARS-CoV-2 infection? (3) What proportion of SARS-CoV-2 transmission in a population is accounted for by people who are asymptomatic or presymptomatic?

METHODS AND FINDINGS

The protocol was first published on 1 April 2020 and last updated on 18 June 2021. We searched PubMed, Embase, bioRxiv, and medRxiv, aggregated in a database of SARS-CoV-2 literature, most recently on 6 July 2021. Studies of people with PCR-diagnosed SARS-CoV-2, which documented symptom status at the beginning and end of follow-up, or mathematical modelling studies were included. Studies restricted to people already diagnosed, of single individuals or families, or without sufficient follow-up were excluded. One reviewer extracted data and a second verified the extraction, with disagreement resolved by discussion or a third reviewer. Risk of bias in empirical studies was assessed with a bespoke checklist and modelling studies with a published checklist. All data syntheses were done using random effects models. Review question (1): We included 130 studies. Heterogeneity was high so we did not estimate a mean proportion of asymptomatic infections overall (interquartile range (IQR) 14% to 50%, prediction interval 2% to 90%), or in 84 studies based on screening of defined populations (IQR 20% to 65%, prediction interval 4% to 94%). In 46 studies based on contact or outbreak investigations, the summary proportion asymptomatic was 19% (95% confidence interval (CI) 15% to 25%, prediction interval 2% to 70%). (2) The secondary attack rate in contacts of people with asymptomatic infection compared with symptomatic infection was 0.32 (95% CI 0.16 to 0.64, prediction interval 0.11 to 0.95, 8 studies). (3) In 13 modelling studies fit to data, the proportion of all SARS-CoV-2 transmission from presymptomatic individuals was higher than from asymptomatic individuals. Limitations of the evidence include high heterogeneity and high risks of selection and information bias in studies that were not designed to measure persistently asymptomatic infection, and limited information about variants of concern or in people who have been vaccinated.

CONCLUSIONS

Based on studies published up to July 2021, most SARS-CoV-2 infections were not persistently asymptomatic, and asymptomatic infections were less infectious than symptomatic infections. Summary estimates from meta-analysis may be misleading when variability between studies is extreme and prediction intervals should be presented. Future studies should determine the asymptomatic proportion of SARS-CoV-2 infections caused by variants of concern and in people with immunity following vaccination or previous infection. Without prospective longitudinal studies with methods that minimise selection and measurement biases, further updates with the study types included in this living systematic review are unlikely to be able to provide a reliable summary estimate of the proportion of asymptomatic infections caused by SARS-CoV-2.

REVIEW PROTOCOL

Open Science Framework (https://osf.io/9ewys/).

Systematic on-site testing for SARS-CoV-2 infection among asymptomatic essential workers in Montréal, Canada: a prospective observational and cost-assessment study

BACKGROUND

Essential workers are at increased risk for SARS-CoV-2 infection. We aimed to estimate the yield, acceptability and cost of systematic workplace-based testing of asymptomatic essential workers for SARS-CoV-2 infection.

METHODS

From Jan. 27 to Mar. 12, 2021, we prospectively recruited non-health care essential businesses in Montréal, Canada, through email or telephone contact. Two trained mobile teams, each composed of 2 non-health care professionals, visited businesses. Consenting asymptomatic employees provided saline gargle samples under supervision. Samples were analyzed by means of reverse transcription polymerase chain reaction (RT-PCR). At businesses with outbreaks (≥ 2 participants with a positive result), we retested all participants with a negative result on initial testing. Our primary outcomes were yield (proportion of test results that were positive), acceptability (proportion of participants estimated to be present at the business who agreed to participate) and costs (including training, sample collection and analysis, and communicating results). Our secondary outcome was identification of factors associated with a positive test result on multivariable logistic regression.

RESULTS

Of the 366 businesses contacted, 69 (18.8%) agreed to participate. Nineteen businesses (28%) were manufacturers or suppliers, 12 (17%) were in auto sales or repair, and 11 (16%) were in childcare; the corresponding number of employees was 1225, 242 and 113. The median number of participants per business was 13 (interquartile range [IQR] 8-22). Of an estimated 2348 employees on site, 2128 (90.6%) participated (808 [38.0%] female, median age 48 [IQR 37-57] yr). Of the 2626 tests performed, 53 (2.0%) gave a positive result. Self-reported nonwhite ethnicity (adjusted odds ratio [OR] 3.7, 95% confidence interval [CI] 1.4-9.9) and a negative SARS-CoV-2 test result before the study (adjusted OR 0.4, 95% CI 0.2-0.8) were associated with a positive test result. Five businesses were experiencing an outbreak; at these businesses, 40/917 participants (4.4%) had a positive result on the initial test. We repeated testing for employees with initially negative results at 3 of these businesses over 2-3 weeks: 8/350 participants (2.3%) had a positive result on the second test, and none had a positive result on the third and fourth tests; no employer reported new positive results after our final visit (up to Mar. 26, 2021). At the remaining 64 businesses, 1211 participants were tested once, of whom 5 (0.4%) had a positive result. The per-person RT-PCR cost was $34, and all other costs, $8.67.

INTERPRETATION

On-site saline gargle sampling of essential workers for SARS-CoV-2 testing was acceptable and of modest cost, and appears most useful in the context of outbreaks. This sampling strategy should be evaluated further as a component of efforts to prevent SARS-CoV-2 transmission. PREPRINT: medRxiv - doi:10.1101/2021.05.12.21256956.

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.

Cross-sectional study of SARS-CoV-2 seropositivity among health-care workers and residents of long-term facilities in Italy, January 2021

Long‐term care facilities (LTCFs) are high‐risk settings for SARS‐CoV‐2 infection. This study aimed to describe SARS‐CoV‐2 seropositivity among residents of LTCFs and health‐care workers (HCWs). Subjects were recruited in January 2021 among unvaccinated HCWs of LTCFs and hospitals and residents of LTCFs in Northern Italy. Information concerning previous SARS‐CoV‐2 infections and a sample of peripheral blood were collected. Anti‐S SARS‐CoV‐2 IgG antibodies were measured using the EUROIMMUN Anti‐SARS‐CoV‐2 QuantiVac ELISA kit (EUROIMMUN Medizinische Labordiagnostika AG). For subjects with previous COVID‐19 infection, gender, age, type of subject (HCW or resident), and time between last positive swab and blood draw were considered as possible determinants of two outcomes: the probability to obtain a positive serological result and antibody titer. Six hundred and fifty‐eight subjects were enrolled. 56.1% of all subjects and 65% of residents presented positive results (overall median antibody titer: 31.0 RU/ml). Multivariable models identified a statistically significant 4% decrease in the estimated antibody level for each 30‐day increase from the last positive swab. HCWs were associated with significant odds for seroreversion over time (OR: 0.926 for every 30 days, 95% CI: 0.860–0.998), contrary to residents (OR: 1.059, 95% CI: 0.919–1.22). Age and gender were not factors predicting seropositivity over time. Residents could have a higher probability of maintaining a seropositive status over time compared to HCWs.

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Background

The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard.

Results

As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories.

Conclusions

Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.

Phylogenomics of SARS-CoV-2 in Emergency Shelters for People Experiencing Homelessness

Residents and staff of emergency shelters for people experiencing homelessness (PEH) are at high risk of infection with SARS-CoV-2. The importance of shelter-related transmission of SARS-CoV-2 in this population remains unclear. It is also unknown whether there is significant spread of shelter-related viruses into surrounding communities. We analyzed genome sequence data for 28 SARS-CoV-2-positive specimens collected from 8 shelters in King County, Washington between March and October, 2020. We identified at least 12 separate SARS-CoV-2 introduction events into these 8 shelters and estimated that 57% (16 out of 28) of the examined cases of SARS-CoV-2 infection were the result of intra-shelter transmission. However, we identified just a few SARS-CoV-2 specimens from Washington that were possible descendants of shelter viruses. Our data suggest that SARS-CoV-2 spread in shelters is common, but we did not observe evidence of wide-spread transmission of shelter-related viruses into the general population.

Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study

Background

There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings.

Methods

We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, to determine who infected whom. We evaluated general transmission patterns according to case type (HCWs working in dedicated Covid-19 cohorting wards: HCW_covid; HCWs working in non-Covid-19 wards where outbreaks occurred: HCW_outbreak; patients with nosocomial Covid-19: patient_noso) by deriving the proportion of infections attributed to each case type across all posterior trees and comparing them to random expectations.

Results

During the study period (1 March to 7 May 2020), we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCW_covid, 36 HCW_outbreak) and 53 patients. The attack rates ranged from 10% to 19% for patients, and 21% for HCWs. We estimated that 16 importation events occurred with high confidence (4 patients, 12 HCWs) that jointly led to up to 41 secondary cases; in six additional cases (5 HCWs, 1 patient), importation was possible with a posterior probability between 10% and 50%. Most patient-to-patient transmission events involved patients having shared a ward (95.2%, 95% credible interval [CrI] 84.2%-100%), in contrast to those having shared a room (19.7%, 95% CrI 6.7%-33.3%). Transmission events tended to cluster by case type: patient_noso were almost twice as likely to be infected by other patient_noso than expected (observed:expected ratio 2.16, 95% CrI 1.17-4.20, p=0.006); similarly, HCW_outbreak were more than twice as likely to be infected by other HCW_outbreak than expected (2.72, 95% CrI 0.87-9.00, p=0.06). The proportion of infectors being HCW_covid was as expected as random. We found a trend towards a greater proportion of high transmitters (≥2 secondary cases) among HCW_outbreak than patient_noso in the late phases (28.6% vs. 11.8%) of the outbreak, although this was not statistically significant.

Conclusions

Most importation events were linked to HCW. Unexpectedly, transmission between HCW_covid was more limited than transmission between patients and HCW_outbreak. This finding highlights gaps in infection control and suggests the possible areas of improvements to limit the extent of nosocomial transmission.

Funding

This study was supported by a grant from the Swiss National Science Foundation under the NRP78 funding scheme (Grant no. 4078P0_198363).

Case-control study evaluating risk factors for SARS-CoV-2 outbreak amongst healthcare personnel at a tertiary care center

BACKGROUND

Despite several outbreaks of SARS-CoV-2 amongst healthcare personnel (HCP) exposed to COVID-19 patients globally, risk factors for transmission remain poorly understood.

METHODS

We conducted an outbreak investigation and case-control study to evaluate SARS-CoV-2 transmission risk in an outbreak among HCP at an academic medical center in California that was confirmed by whole genome sequencing.

RESULTS

A total of 7/9 cases and 93/182 controls completed a voluntary survey about risk factors. Compared to controls, cases reported significantly more patient contact time. Cases were also significantly more likely to have performed airway procedures on the index patient, particularly placing the patient on high flow nasal cannula, continuous positive airway pressure (CPAP), or bilevel positive airway pressure (BiPAP) (OR = 11.6; 95% CI = 1.7 -132.1).

DISCUSSION

This study highlights the risk of nosocomial infection of SARS-CoV-2 from patients who become infectious midway into their hospitalization. Our findings also reinforce the importance of patient contact time and aerosol-generating procedures as key risk factors for HCP infection with SARS-CoV-2.

CONCLUSIONS

Re-testing patients for SARS-CoV-2 after admission in suspicious cases and using N95 masks for all aerosol-generating procedures regardless of initial patient SARS-CoV-2 test results can help reduce the risk of SARS-COV-2 transmission to HCP.

Early Adoption of Longitudinal Surveillance for SARS-CoV-2 among Staff in Long-Term Care Facilities: Prevalence, Virologic and Sequence Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 has been notable due to its impacts on residents in long-term care facilities (LTCFs). LTCF residents tend to possess several risk factors for severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of comorbidities. Indeed, residents of LTCFs represent approximately 40% of SARS-CoV-2 deaths in the United States. Few studies have focused on the prevalence and transmission dynamics of SARS-CoV-2 among LTCF staff during the early months of the pandemic, prior to mandated surveillance testing. To assess the prevalence and incidence of SARS-CoV-2 among LTCF staff, characterize the extent of asymptomatic infections, and investigate the genomic epidemiology of the virus within these settings, we sampled staff for 8 to 11 weeks at six LTCFs with nasopharyngeal swabs from March through June of 2020. We determined the presence and levels of viral RNA and infectious virus and sequenced 54 nearly complete genomes. Our data revealed that over 50% of infections were asymptomatic/mildly symptomatic and that there was a strongly significant relationship between viral RNA (vRNA) and infectious virus, prolonged infections, and persistent vRNA (4+ weeks) in a subset of individuals, and declining incidence over time. Our data suggest that asymptomatic SARS-CoV-2-infected LTCF staff contributed to virus persistence and transmission within the workplace during the early pandemic period. Genetic epidemiology data generated from samples collected during this period support that SARS-CoV-2 was commonly spread between staff within an LTCF and that multiple-introduction events were less common.

IMPORTANCE Our work comprises unique data on the characteristics of SARS-CoV-2 dynamics among staff working at LTCFs in the early months of the SARS-CoV-2 pandemic prior to mandated staff surveillance testing. During this time period, LTCF residents were largely sheltering-in-place. Given that staff were able to leave and return daily and could therefore be a continued source of imported or exported infection, we performed weekly SARS-CoV-2 PCR on nasal swab samples collected from this population. There are limited data from the early months of the pandemic comprising longitudinal surveillance of staff at LTCFs. Our data reveal the surprisingly high level of asymptomatic/presymptomatic infections within this cohort during the early months of the pandemic and show genetic epidemiological analyses that add novel insights into both the origin and transmission of SARS-CoV-2 within LTCFs.

Temperature and oxygen saturation in skilled nursing facility residents positive for SARS-CoV-2 prior to symptom onset

BACKGROUND

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spreads rapidly amongst residents of skilled nursing facilities (SNFs). The rapid transmission dynamics and high morbidity and mortality that occur in SNFs emphasize the need for early detection of cases. We hypothesized that residents of SNFs infected with SARS-CoV-2 would demonstrate an acute change in either temperature or oxygen saturation (SpO₂ ) prior to symptom onset. The Minnesota Department of Health (MDH) conducted a retrospective analysis of both temperature and SpO₂ at two separate SNFs to assess the utility of these quantitative markers to identify SARS-CoV-2 infection prior to the development of symptoms.

METHODS

A retrospective analysis was conducted of 165 individuals positive for SARS-CoV-2 who were residents of SNFs that experienced coronavirus disease 2019 (COVID-19) outbreaks during April-June 2020 in a metropolitan area of Minnesota. Age, sex, symptomology, temperature and SpO₂ values, date of symptom onset, and date of positive SARS-CoV-2 test were analyzed. Temperature and SpO₂ values for the period 14 days before and after the date of initial positive test were included. Descriptive analyses evaluated changes in temperature and SpO₂ , defined as either exceeding a set threshold or demonstrating an acute change between consecutive measurements.

RESULTS

Two (1%) residents had a temperature value ≥100°F, and 30 (18%) had at least one value ≥99°F within 14 days before symptom development. One hundred and sixteen residents (70%) had at least one SpO₂ value ≤94%, while 131 (80%) had an acute decrease in SpO₂ of ≥3% between consecutive values in the 14 days prior to symptom onset.

CONCLUSIONS

Our results suggest that acute change in SpO₂ might be useful in the identification of SARS-CoV-2 infection prior to the development of symptoms among residents living in SNFs. Facilities may consider adding SpO₂ to daily temperature and symptom screening checklists to improve early detection of residents of SNFs infected with SARS-CoV-2.

Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction

BACKGROUND

Nosocomial outbreaks of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are frequent despite implementation of conventional infection control measures. An outbreak investigation was undertaken using advanced genomic and statistical techniques to reconstruct likely transmission chains and assess the role of healthcare workers (HCWs) in SARS-CoV-2 transmission.

METHODS

A nosocomial SARS-CoV-2 outbreak in a university-affiliated rehabilitation clinic was investigated, involving patients and HCWs, with high coverage of pathogen whole-genome sequences (WGS). The time-varying reproduction number from epidemiological data (R_t) was estimated, and maximum likelihood phylogeny was used to assess genetic diversity of the pathogen. Genomic and epidemiological data were combined into a Bayesian framework to model the directionality of transmission, and a case-control study was performed to investigate risk factors for nosocomial SARS-CoV-2 acquisition in patients.

FINDINGS

The outbreak lasted from 14^th March to 12^th April 2020, and involved 37 patients (31 with WGS) and 39 employees (31 with WGS), 37 of whom were HCWs. Peak R_t was estimated to be between 2.2 and 3.6. The phylogenetic tree showed very limited genetic diversity, with 60 of 62 (96.7%) isolates forming one large cluster of identical genomes. Despite the resulting uncertainty in reconstructed transmission events, the analyses suggest that HCWs (one of whom was the index case) played an essential role in cross-transmission, with a significantly greater fraction of infections (P<2.2e-16) attributable to HCWs (70.7%) than expected given the number of HCW cases (46.7%). The excess of transmission from HCWs was higher when considering infection of patients [79.0%; 95% confidence interval (CI) 78.5-79.5%] and frail patients (Clinical Frailty Scale score >5; 82.3%; 95% CI 81.8-83.4%). Furthermore, frail patients were found to be at greater risk for nosocomial COVID-19 than other patients (adjusted odds ratio 6.94, 95% CI 2.13-22.57).

INTERPRETATION

This outbreak report highlights the essential role of HCWs in SARS-CoV-2 transmission dynamics in healthcare settings. Limited genetic diversity in pathogen genomes hampered the reconstruction of individual transmission events, resulting in substantial uncertainty in who infected whom. However, this study shows that despite such uncertainty, significant transmission patterns can be observed.

Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component, and there is accumulating evidence that whole-genome sequencing of the virus may provide more objective insight.

METHODS

We report a large nosocomial outbreak in 1 of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that 1 of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole-genome sequencing of the virus of 14 infected individuals involved in the outbreak.

RESULTS

Surprisingly, the results of whole-genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, 1 of which led to a cluster of 10 of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the 1 that arose from our initial investigation.

CONCLUSIONS

These results underscore the important added value of using whole-genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.

Non-pharmacological measures implemented in the setting of long-term care facilities to prevent SARS-CoV-2 infections and their consequences: a rapid review

BACKGROUND

Starting in late 2019, COVID-19, caused by the novel coronavirus SARS-CoV-2, spread around the world. Long-term care facilities are at particularly high risk of outbreaks, and the burden of morbidity and mortality is very high among residents living in these facilities.

OBJECTIVES

To assess the effects of non-pharmacological measures implemented in long-term care facilities to prevent or reduce the transmission of SARS-CoV-2 infection among residents, staff, and visitors.

SEARCH METHODS

On 22 January 2021, we searched the Cochrane COVID-19 Study Register, WHO COVID-19 Global literature on coronavirus disease, Web of Science, and CINAHL. We also conducted backward citation searches of existing reviews.

SELECTION CRITERIA

We considered experimental, quasi-experimental, observational and modelling studies that assessed the effects of the measures implemented in long-term care facilities to protect residents and staff against SARS-CoV-2 infection. Primary outcomes were infections, hospitalisations and deaths due to COVID-19, contaminations of and outbreaks in long-term care facilities, and adverse health effects.

DATA COLLECTION AND ANALYSIS

Two review authors independently screened titles, abstracts and full texts. One review author performed data extractions, risk of bias assessments and quality appraisals, and at least one other author checked their accuracy. Risk of bias and quality assessments were conducted using the ROBINS-I tool for cohort and interrupted-time-series studies, the Joanna Briggs Institute (JBI) checklist for case-control studies, and a bespoke tool for modelling studies. We synthesised findings narratively, focusing on the direction of effect. One review author assessed certainty of evidence with GRADE, with the author team critically discussing the ratings.

MAIN RESULTS

We included 11 observational studies and 11 modelling studies in the analysis. All studies were conducted in high-income countries. Most studies compared outcomes in long-term care facilities that implemented the measures with predicted or observed control scenarios without the measure (but often with baseline infection control measures also in place). Several modelling studies assessed additional comparator scenarios, such as comparing higher with lower rates of testing. There were serious concerns regarding risk of bias in almost all observational studies and major or critical concerns regarding the quality of many modelling studies. Most observational studies did not adequately control for confounding. Many modelling studies used inappropriate assumptions about the structure and input parameters of the models, and failed to adequately assess uncertainty. Overall, we identified five intervention domains, each including a number of specific measures. Entry regulation measures (4 observational studies; 4 modelling studies) Self-confinement of staff with residents may reduce the number of infections, probability of facility contamination, and number of deaths. Quarantine for new admissions may reduce the number of infections. Testing of new admissions and intensified testing of residents and of staff after holidays may reduce the number of infections, but the evidence is very uncertain. The evidence is very uncertain regarding whether restricting admissions of new residents reduces the number of infections, but the measure may reduce the probability of facility contamination. Visiting restrictions may reduce the number of infections and deaths. Furthermore, it may increase the probability of facility contamination, but the evidence is very uncertain. It is very uncertain how visiting restrictions may adversely affect the mental health of residents. Contact-regulating and transmission-reducing measures (6 observational studies; 2 modelling studies) Barrier nursing may increase the number of infections and the probability of outbreaks, but the evidence is very uncertain. Multicomponent cleaning and environmental hygiene measures may reduce the number of infections, but the evidence is very uncertain. It is unclear how contact reduction measures affect the probability of outbreaks. These measures may reduce the number of infections, but the evidence is very uncertain. Personal hygiene measures may reduce the probability of outbreaks, but the evidence is very uncertain.  Mask and personal protective equipment usage may reduce the number of infections, the probability of outbreaks, and the number of deaths, but the evidence is very uncertain. Cohorting residents and staff may reduce the number of infections, although evidence is very uncertain. Multicomponent contact -regulating and transmission -reducing measures may reduce the probability of outbreaks, but the evidence is very uncertain. Surveillance measures (2 observational studies; 6 modelling studies) Routine testing of residents and staff independent of symptoms may reduce the number of infections. It may reduce the probability of outbreaks, but the evidence is very uncertain. Evidence from one observational study suggests that the measure may reduce, while the evidence from one modelling study suggests that it probably reduces hospitalisations. The measure may reduce the number of deaths among residents, but the evidence on deaths among staff is unclear.  Symptom-based surveillance testing may reduce the number of infections and the probability of outbreaks, but the evidence is very uncertain. Outbreak control measures (4 observational studies; 3 modelling studies) Separating infected and non-infected residents or staff caring for them may reduce the number of infections. The measure may reduce the probability of outbreaks and may reduce the number of deaths, but the evidence for the latter is very uncertain. Isolation of cases may reduce the number of infections and the probability of outbreaks, but the evidence is very uncertain. Multicomponent measures (2 observational studies; 1 modelling study) A combination of multiple infection-control measures, including various combinations of the above categories, may reduce the number of infections and may reduce the number of deaths, but the evidence for the latter is very uncertain.

AUTHORS' CONCLUSIONS

This review provides a comprehensive framework and synthesis of a range of non-pharmacological measures implemented in long-term care facilities. These may prevent SARS-CoV-2 infections and their consequences. However, the certainty of evidence is predominantly low to very low, due to the limited availability of evidence and the design and quality of available studies. Therefore, true effects may be substantially different from those reported here. Overall, more studies producing stronger evidence on the effects of non-pharmacological measures are needed, especially in low- and middle-income countries and on possible unintended consequences of these measures. Future research should explore the reasons behind the paucity of evidence to guide pandemic research priority setting in the future.

Durable Antibody Responses in Staff at Two Long-Term Care Facilities, during and Post SARS-CoV-2 Outbreaks

SARS-CoV-2 has had a disproportionate impact on nonhospital health care settings, such as long-term-care facilities (LTCFs). The communal nature of these facilities, paired with the high-risk profile of residents, has resulted in thousands of infections and deaths and a high case fatality rate. To detect presymptomatic infections and identify infected workers, we performed weekly surveillance testing of staff at two LTCFs, which revealed a large outbreak at one of the sites. We collected serum from staff members throughout the study and evaluated it for binding and neutralization to measure seroprevalence, seroconversion, and type and functionality of antibodies. At the site with very few incident infections, we detected that over 40% of the staff had preexisting SARS-CoV-2 neutralizing antibodies, suggesting prior exposure. At the outbreak site, we saw rapid seroconversion following infection. Neutralizing antibody levels were stable for many weeks following infection, suggesting a durable, long-lived response. Receptor-binding domain antibodies and neutralizing antibodies were strongly correlated. The site with high seroprevalence among staff had two unique introductions of SARS-CoV-2 into the facility through seronegative infected staff during the period of study, but these did not result in workplace spread or outbreaks. Together, our results suggest that a high seroprevalence rate among staff can contribute to immunity within a workplace and protect against subsequent infection and spread within a facility. IMPORTANCE Long-term care facilities (LTCFs) have been disproportionately impacted by COVID-19 due to their communal nature and high-risk profile of residents. LTCF staff have the ability to introduce SARS-CoV-2 into the facility, where it can spread, causing outbreaks. We tested staff weekly at two LTCFs and collected blood throughout the study to measure SARS-CoV-2 antibodies. One site had a large outbreak and infected individuals rapidly generated antibodies after infection. At the other site, almost half the staff already had antibodies, suggesting prior infection. The majority of these antibodies bind to the receptor-binding domain of the SARS-CoV-2 spike protein and are potently neutralizing and stable for many months. The non-outbreak site had two unique introductions of SARS-CoV-2 into the facility, but these did not result in workplace spread or outbreaks. Our results reveal that high seroprevalence among staff can contribute to immunity and protect against subsequent infection and spread within a facility.

Asymptomatic SARS-CoV-2 infection: A systematic review and meta-analysis

Quantification of asymptomatic infections is fundamental for effective public health responses to the COVID-19 pandemic. Discrepancies regarding the extent of asymptomaticity have arisen from inconsistent terminology as well as conflation of index and secondary cases which biases toward lower asymptomaticity. We searched PubMed, Embase, Web of Science, and World Health Organization Global Research Database on COVID-19 between January 1, 2020 and April 2, 2021 to identify studies that reported silent infections at the time of testing, whether presymptomatic or asymptomatic. Index cases were removed to minimize representational bias that would result in overestimation of symptomaticity. By analyzing over 350 studies, we estimate that the percentage of infections that never developed clinical symptoms, and thus were truly asymptomatic, was 35.1% (95% CI: 30.7 to 39.9%). At the time of testing, 42.8% (95% prediction interval: 5.2 to 91.1%) of cases exhibited no symptoms, a group comprising both asymptomatic and presymptomatic infections. Asymptomaticity was significantly lower among the elderly, at 19.7% (95% CI: 12.7 to 29.4%) compared with children at 46.7% (95% CI: 32.0 to 62.0%). We also found that cases with comorbidities had significantly lower asymptomaticity compared to cases with no underlying medical conditions. Without proactive policies to detect asymptomatic infections, such as rapid contact tracing, prolonged efforts for pandemic control may be needed even in the presence of vaccination.

Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2)

OBJECTIVE

Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data.

DESIGN

Retrospective cohort study.

SETTING

Tertiary-care hospital.

PARTICIPANTS

Patients and healthcare workers (HCWs) from the ward with a nasopharyngeal sample (NPS) positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA during the outbreak period.

METHODS

Patient data regarding clinical characteristics, exposure and outcome were collected retrospectively from medical records. Stored NPSs from 32 patients and 15 HCWs were selected for WGS and phylogenetic analysis.

RESULTS

The median patient age was 84 years and 17 (53%) of 32 were male. Also, 14 patients (44%) died within 30 days of sampling. Viral loads were significantly higher among the deceased. WGS was successful in 28 (88%) of 32 patient samples and 14 (93%) of 15 HCW samples. Moreover, 3 separate viral clades were identified: 1 clade and 2 subclades among both patient and HCW samples. Integrated epidemiological and genetic analyses revealed 6 probable transmission events between patients and supported hospital-acquired COVID-19 among 25 of 32 patients.

CONCLUSIONS

WGS provided an insight into the outbreak dynamics and true extent of nosocomial COVID-19. The extensive transmission between patients and HCWs indicated that current IPC measures were insufficient. We recommend increased use of WGS in outbreak investigations to identify otherwise unknown transmission links and to evaluate IPC measures.

Modeling Effectiveness of Testing Strategies to Prevent Coronavirus Disease 2019 (COVID-19) in Nursing Homes-United States, 2020

Background

SARS-CoV-2 outbreaks in nursing homes can be large with high case fatality. Identifying asymptomatic individuals early through serial testing is recommended to control COVID-19 in nursing homes, both in response to an outbreak (“outbreak testing” of residents and healthcare personnel) and in facilities without outbreaks (“non-outbreak testing” of healthcare personnel). The effectiveness of outbreak testing and isolation with or without non-outbreak testing was evaluated.

Methods

Using published SARS-CoV-2 transmission parameters, the fraction of SARS-CoV-2 transmissions prevented through serial testing (weekly, every three days, or daily) and isolation of asymptomatic persons compared to symptom-based testing and isolation was evaluated through mathematical modeling using a Reed-Frost model to estimate the percentage of cases prevented (i.e., “effectiveness”) through either outbreak testing alone or outbreak plus non-outbreak testing. The potential effect of simultaneous decreases (by 10%) in the effectiveness of isolating infected individuals when instituting testing strategies was also evaluated.

Results

Modeling suggests that outbreak testing could prevent 54% (weekly testing with 48-hour test turnaround) to 92% (daily testing with immediate results and 50% relative sensitivity) of SARS-CoV-2 infections. Adding non-outbreak testing could prevent up to an additional 8% of SARS-CoV-2 infections (depending on test frequency and turnaround time). However, added benefits of non-outbreak testing were mostly negated if accompanied by decreases in infection control practice.

Conclusions

When combined with high-quality infection control practices, outbreak testing could be an effective approach to preventing COVID-19 in nursing homes, particularly if optimized through increased test frequency and use of tests with rapid turnaround.

Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March-June 2020

Coronavirus disease has disproportionately affected persons in congregate settings and high-density workplaces. To determine more about the transmission patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings, we performed whole-genome sequencing and phylogenetic analysis on 319 (14.4%) samples from 2,222 SARS-CoV-2-positive persons associated with 8 outbreaks in Minnesota, USA, during March-June 2020. Sequencing indicated that virus spread in 3 long-term care facilities and 2 correctional facilities was associated with a single genetic sequence and that in a fourth long-term care facility, outbreak cases were associated with 2 distinct sequences. In contrast, cases associated with outbreaks in 2 meat-processing plants were associated with multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak. Early identification and cohorting (segregating) of virus-positive persons in these settings, along with continued vigilance with infection prevention and control measures, is imperative.

COVID-19 Outbreak Associated with a Fitness Center - Minnesota, September-November 2020

The Minnesota Department of Health investigated a COVID-19 outbreak at a fitness center in Olmsted County, Minnesota. Twenty-three SARS-CoV-2 infections (five employees and 18 members) were identified. An epidemiological investigation supported by whole genome sequencing demonstrated that transmission of SARS-CoV-2 occurred at the fitness center despite following recommended prevention strategies.

Use of Immunochromatographic SARS-CoV-2 Antigen Testing in Eight Long-Term Care Facilities for the Elderly

The clinical validation of the NADAL COVID-19 antigen test (Nal von Minden, Moers, Germany) started in eight Slovenian long-term health care facilities in October 2020. The purpose of clinical validation is to implement the test into the everyday working process in long-term care (LTC) facilities and demonstrate how it can be used to mitigate the spread of the virus in these environments. The facilities compared the results of antigen tests to the results obtained using Cobas 6800 SARS-CoV-2 real-time reverse transcription polymerase chain reaction (RT-PCR) (Roche, USA). Sensitivity (86.96%, 95% CI: 66.41-97.23%) and specificity (88.24%, 95% CI: 80.35-93.77%) of the NADAL COVID-19 antigen test were good. Rapid antigen testing served well for early detection of infection and helped to prevent and control spread of the SARS Cov2 in six out of eight LTCs. Moreover, mini-outbreaks were quickly resolved in all six LTCs. Locally validated immunochromatographic SARS-CoV-2 antigen testing can be used to contain the spread of the virus in LTCs. Antigen tests also deliver accurate information very quickly if used early with a low threshold. The NADAL COVID-19 antigen test proved to be a good screening tool to detect SARS-COV-2 in LTCs.

Performance Evaluation of Serial SARS-CoV-2 Rapid Antigen Testing During a Nursing Home Outbreak

BACKGROUND

To address high COVID-19 burden in U.S. nursing homes, rapid SARS-CoV-2 antigen tests have been widely distributed in those facilities. However, performance data are lacking, especially in asymptomatic people.

OBJECTIVE

To evaluate the performance of SARS-CoV-2 antigen testing when used for facility-wide testing during a nursing home outbreak.

DESIGN

A prospective evaluation involving 3 facility-wide rounds of testing where paired respiratory specimens were collected to evaluate the performance of the BinaxNOW antigen test compared with virus culture and real-time reverse transcription polymerase chain reaction (RT-PCR). Early and late infection were defined using changes in RT-PCR cycle threshold values and prior test results.

SETTING

A nursing home with an ongoing SARS-CoV-2 outbreak.

PARTICIPANTS

532 paired specimens collected from 234 available residents and staff.

MEASUREMENTS

Percentage of positive agreement (PPA) and percentage of negative agreement (PNA) for BinaxNOW compared with RT-PCR and virus culture.

RESULTS

BinaxNOW PPA with virus culture, used for detection of replication-competent virus, was 95%. However, the overall PPA of antigen testing with RT-PCR was 69%, and PNA was 98%. When only the first positive test result was analyzed for each participant, PPA of antigen testing with RT-PCR was 82% among 45 symptomatic people and 52% among 343 asymptomatic people. Compared with RT-PCR and virus culture, the BinaxNOW test performed well in early infection (86% and 95%, respectively) and poorly in late infection (51% and no recovered virus, respectively).

LIMITATION

Accurate symptom ascertainment was challenging in nursing home residents; test performance may not be representative of testing done by nonlaboratory staff.

CONCLUSION

Despite lower positive agreement compared with RT-PCR, antigen test positivity had higher agreement with shedding of replication-competent virus. These results suggest that antigen testing could be a useful tool to rapidly identify contagious people at risk for transmitting SARS-CoV-2 during nascent outbreaks and help reduce COVID-19 burden in nursing homes.

PRIMARY FUNDING SOURCE

None.

Prevalence of SARS-CoV-2 among Belgian workers in long-term care facilities

Background

Healthcare workers (HCWs) can be a source of SARS-CoV-2 within long-term care facilities (LTCFs); therefore, we analysed the data from a testing programme among LTCF employees.

Aims

The aim of this study was to investigate the prevalence of SARS-CoV-2 and its determinants among employees of LTCFs and the risk for fellow workers and residents.

Methods

Testing started at week 15, the first wave’s peak, using nasopharyngeal swabs for PCR up to week 23. At the start of the second wave (week 32), testing resumed.

Results

A total of 32 457 test results were available from 446 LTCFs: 2% were positive: 1% in men, 2% in women, 2% in HCWs (=having patient contact), 1% in non-HCWs, higher in younger age groups. In total, 30 729 employees were tested once, 823 twice, 66 thrice and 4 four times. Prevalence was 13% during the first week of testing (week 15) and declined to 7% (week 16) to stay at around 1% (from week 17 until week 23). At the start of the second wave (week 31–33), the prevalence was around 3%. In 70% of positive tests, the employee was asymptomatic.

Conclusions

Our study confirms the presence of HCWs with SARS-CoV-2 as a possible source of infection in LTCFs even when the incidence in the general population was low; 70% were asymptomatic. To control the spread of SARS-CoV-2 in LTCFs vaccination, infection prevention and control measures are necessary as well as testing of all LTCF HCWs during possible outbreaks, even if asymptomatic.

Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster

Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission.

Incidence of Reported Flu-Like Syndrome Cases in Brazilian Health Care Workers in 2020 (March to June)

Health care workers (HCWs) are at an increased risk of being exposed to COVID-19. This study aimed to characterize flu-like syndrome cases (FS) in HCWs notified in Brazil and compare them with FS cases in the general community (GC). In the Brazilian protocol, FS corresponds to a suspected case of COVID-19. The manuscript analyzed cases of FS in five Brazilian states, estimating the incidence rates of cases of FS and clinical and epidemiological characteristics. Registered cases (March to June 2020) totaled about 1,100,000 cases of FS. HCWs represented 17% of the registers, whose incidence was 20.41/100 vs. 2.15/100 in the GC. FS cases in HCWs concentrated the highest percentages in the age group of 30 to 49 years (65.15%) and among the nursing staff (46.86%). This study was the first interstate evaluation in Brazil to estimate suspected cases of FS by COVID-19 in HCWs. In order to control the spread of viral respiratory infections in HCWs, including COVID-19, it is necessary to review the management of health information to identify who they are, how many they are, and to what situations these workers are most frequently exposed, as well as in what professions they have. This information can guide specific, practical, and far-reaching actions.

Management and outcomes of a COVID-19 outbreak in a nursing home with predominantly Black residents

BACKGROUND/OBJECTIVES

Few studies present clinical management approaches and outcomes of coronavirus disease 2019 (COVID-19) outbreaks in skilled nursing facilities (SNFs). We describe outcomes of a clinical management pathway for a large COVID-19 outbreak in an urban SNF with predominantly racial minority (>90% black), medically complex, older residents.

DESIGN

Single-center, retrospective, and observational cohort study (March 1, 2020-May 31, 2020).

SETTING AND PARTICIPANTS

All subacute and long-term care residents at an urban SNF between March 1, 2020 and May 31, 2020 (Chicago, IL).

INTERVENTION

A multicomponent management pathway was developed to manage a large COVID-19 outbreak in an SNF.

MEASUREMENTS

Chart review was used to extract demographics, comorbidities, symptoms, lab results, and clinical outcomes over 12 weeks, which were summarized and compared between residents with and without COVID-19.

RESULTS

A multicomponent clinical management pathway was used to care for residents with COVID-19, which included frequent scheduled clinical and laboratory evaluation, use of intravenous fluids, supplemental oxygen, antibiotics when indicated, and goals-of-care discussions. Of the 204 residents, 172 (84.3%) tested positive for SARS-CoV-2 during the 3-month period, with 50.5% symptomatic, 9.3% presymptomatic, and 24.5% asymptomatic, with a 30-day mortality rate of 15.7%. Predominant symptoms were low-grade fever >99 °F, anorexia, delirium, and fatigue. While in the facility, approximately one-quarter of residents experienced hypernatremia [Na > 145 mEq/L] (24.5%), acute kidney injury [Cr > 0.03 mg/dL or 1.5× baseline] (29.7%), or leukopenia [WBC < 4.8 1000/mm3 ] (39.4%).

CONCLUSION

We present the first available clinical strategy guiding the medical management of a COVID-19 syndrome in an urban SNF, caring for largely black residents, which may lead to improved mortality.

SARS-CoV-2 in Nursing Homes after 3 Months of Serial, Facilitywide Point Prevalence Testing, Connecticut, USA

Nursing homes house populations that are highly vulnerable to coronavirus disease. Point prevalence surveys (PPSs) provide information on the severe acute respiratory syndrome coronavirus 2 infection status of staff and residents in nursing homes and enable isolation of infectious persons to halt disease spread. We collected 16 weeks of public health surveillance data on a subset of nursing homes (34/212) in Connecticut, USA. We fit a Poisson regression model to evaluate the association between incidence and time since serial PPS onset, adjusting for decreasing community incidence and other factors. Nursing homes conducted a combined total of 205 PPSs in staff and 232 PPSs in residents. PPS was associated with 41%-80% reduction in incidence rate in nursing homes. Our findings provide support for the use of repeated PPSs in nursing home staff and residents, combined with strong infection prevention measures such as cohorting, in contributing to outbreak control.

Severe Acute Respiratory Syndrome Coronavirus 2 Seropositivity among Healthcare Personnel in Hospitals and Nursing Homes, Rhode Island, USA, July-August 2020

Healthcare personnel are recognized to be at higher risk for infection with severe acute respiratory syndrome coronavirus 2. We conducted a serologic survey in 15 hospitals and 56 nursing homes across Rhode Island, USA, during July 17–August 28, 2020. Overall seropositivity among 9,863 healthcare personnel was 4.6% (95% CI 4.2%–5.0%) but varied 4-fold between hospital personnel (3.1%, 95% CI 2.7%–3.5%) and nursing home personnel (13.1%, 95% CI 11.5%–14.9%). Within nursing homes, prevalence was highest among personnel working in coronavirus disease units (24.1%; 95% CI 20.6%–27.8%). Adjusted analysis showed that in hospitals, nurses and receptionists/medical assistants had a higher likelihood of seropositivity than physicians. In nursing homes, nursing assistants and social workers/case managers had higher likelihoods of seropositivity than occupational/physical/speech therapists. Nursing home personnel in all occupations had elevated seropositivity compared with hospital counterparts. Additional mitigation strategies are needed to protect nursing home personnel from infection, regardless of occupation.

High impact of COVID-19 outbreak in a nursing home in the Nouvelle-Aquitaine region, France, March to April 2020

Background

Elderly people in nursing homes are particularly vulnerable to COVID-19 due to their age, the presence of comorbidities, and community living. On March 14, 2020, at the beginning of the first epidemic wave of COVID-19 in France, a cluster was reported in a nursing home in the Nouvelle-Aquitaine region. We monitored the outbreak as well as the infection prevention and control (IPC) measures implemented.

Methods

A confirmed case was defined as laboratory-confirmed COVID-19 in a resident or staff member present in the nursing home between March 7 and May 1, 2020; and a probable case as a person presenting an acute respiratory illness after contact with a confirmed case. Symptomatic inpatient residents and symptomatic staff members were systematically tested for SARS-CoV-2. In addition, two screening sessions were held on site.

Results

We identified 109 cases (98 confirmed, 11 probable). The attack rate was 66% among residents and 45% among staff. Half of all cases were identified during the screening sessions. One-quarter of cases had minor symptoms or were asymptomatic. The case fatality rate among residents was 29%. IPC measures were rapidly implemented such as the quarantine of residents, the reinforcement of staff personal protective equipment, and home quarantine of staff testing positive, which were supplemented in April by systematic controls at the entrance of the nursing home and the creation of additional staff break rooms.

Conclusions

This outbreak confirmed the considerable health impact of SARS-CoV-2 transmission in a nursing home. In addition to the implementation of IPC measures, the early detection of cases through the screening of residents and staff is essential to identify asymptomatic and pre-symptomatic cases and limit the spread of the virus.