The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.
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ABSTRACT:
SUBMITTER: Aggarwal D
PROVIDER: S-EPMC8480962 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Diagnostic difficulties may have led to underestimation of rhinovirus infections in long-term care facilities. Using surveillance data, we found that rhinovirus caused 59% (174/297) of respiratory outbreaks in these facilities during 6 months in 2009. Disease was sometimes severe. Molecular diagnostic testing can differentiate these outbreaks from other infections such as influenza.
| S-EPMC3294989 | biostudies-literature
Project description:BackgroundThe COVID-19 pandemic has devastatingly affected Long-Term Care Facilities (LTCF), exposing aging people, staff members, and visitors. The world has learned through the pandemic and lessons can be taken to adopt effective measures to deal with COVID-19 outbreaks in LTCF. We aimed to systematically review the available evidence on the effect of measures to minimize the risk of transmission of COVID-19 in LTCs during outbreaks since 2021.MethodsThe search method was guided by the preferred reporting items for systematic reviews (PRISMA) and the reporting guideline synthesis without meta-analysis (SWiM) in systematic reviews. The search was performed in April 2023. Observational and interventional studies from the databases of PubMed, Web of Science, Scopus, Cochrane Systematic Reviews, CINAHL, and Academic Search were systematically reviewed. We included studies conducted in the LTCF with outbreaks that quantitatively assess the effect of non-pharmacological measures on cases of COVID-19. Two review authors independently reviewed titles for inclusion, extracted data, and undertook the risk of bias according to pre-specified criteria. The quality of studies was analyzed using the Joanna Briggs Institute Critical Appraisal.ResultsThirteen studies were included, with 8442 LTCF experiencing COVID-19 outbreaks and 598 thousand participants (residents and staff members). Prevention and control of COVID-19 infection interventions were grouped into three themes: strategic, tactical, and operational measures. The strategic measures reveal the importance of COVID-19 prevention and control as LTCF structural characteristics, namely the LTCF size, new admissions, infection control surveillance, and architectural structure. At the tactical level, the lack of personal and long staff shifts is related to COVID-19's spread. Operational measures with a favorable effect on preventing COVID-19 transmission are sufficient. Personal protective equipment stock, correct mask use, signaling, social distancing, and resident cohorting.ConclusionsOperational, tactical, and strategic approaches may have a favorable effect on preventing the spread of COVID-19 in LTCFs experiencing outbreaks. Given the heterogeneous nature of the measures, performing a meta-analysis was not possible. Future research should use more robust study designs to explore similar infection control measures in LTCFs during endemic situations with comparable outbreaks.Trial registrationThe protocol of this systematic review was registered in PROSPERO (CRD42020214566).
| S-EPMC10546730 | biostudies-literature
Project description:Outbreaks of influenza-like illness (ILI) are common in long-term care facilities (LTCFs) and result in significant morbidity and mortality among residents.We describe patterns of reported ILI outbreaks in LTCFs in Winnipeg, Canada, and examine LTCF and outbreak characteristics that influence the clinical outcomes of these outbreaks.We analyzed the electronic records of all ILI outbreaks reported by LTCFs in Winnipeg from 2003 to 2011. Outbreak duration, ILI attack rates among staff and residents, and residents' death rates were calculated by presumed viral etiology, staff vaccination rates, type of influenza chemoprophylaxis used, and time to notification to public health.Of a total of 154 reported outbreaks, most (N=80) were attributed to influenza, and these outbreaks tended to have higher attack and death rates among LTCF residents compared with outbreaks caused by other respiratory viruses (12) or those of unknown etiology (62). About 92% of residents and 38% of staff of the average LTCFs were vaccinated. Chemoprophylaxis was used in 57·5% of influenza outbreaks. Regardless of presumed viral etiology, outbreaks reported within 3 days of onset ended sooner and had lower attack and mortality rates among residents.Influenza-like illness outbreaks still occur among highly immunized LTCF residents, so in addition to vaccination of staff and residents, it is important to maintain competent infection control practices. Early identification and notification to public health authorities and possibly early initiation of control measures could improve clinical outcomes of ILI outbreaks.
| S-EPMC4634272 | biostudies-other
Project description:The novel coronavirus disease 2019 (COVID-19) has caused severe outbreaks in Canadian long-term care facilities (LTCFs). In Canada, over 80% of COVID-19 deaths during the first pandemic wave occurred in LTCFs. We sought to evaluate the effect of mitigation measures in LTCFs including frequent testing of staff, and vaccination of staff and residents. We developed an agent-based transmission model and parameterized it with disease-specific estimates, temporal sensitivity of nasopharyngeal and saliva testing, results of vaccine efficacy trials, and data from initial COVID-19 outbreaks in LTCFs in Ontario, Canada. Characteristics of staff and residents, including contact patterns, were integrated into the model with age-dependent risk of hospitalization and death. Estimates of infection and outcomes were obtained and 95% credible intervals were generated using a bias-corrected and accelerated bootstrap method. Weekly routine testing of staff with 2-day turnaround time reduced infections among residents by at least 25.9% (95% CrI: 23.3%-28.3%), compared to baseline measures of mask-wearing, symptom screening, and staff cohorting alone. A similar reduction of hospitalizations and deaths was achieved in residents. Vaccination averted 2-4 times more infections in both staff and residents as compared to routine testing, and markedly reduced hospitalizations and deaths among residents by 95.9% (95% CrI: 95.4%-96.3%) and 95.8% (95% CrI: 95.5%-96.1%), respectively, over 200 days from the start of vaccination. Vaccination could have a substantial impact on mitigating disease burden among residents, but may not eliminate the need for other measures before population-level control of COVID-19 is achieved.
| S-EPMC8053216 | biostudies-literature
Project description:The novel coronavirus disease 2019 (COVID-19) has caused severe outbreaks in Canadian long-term care facilities (LTCFs). In Canada, over 80% of COVID-19 deaths during the first pandemic wave occurred in LTCFs. We sought to evaluate the effect of mitigation measures in LTCFs including frequent testing of staff, and vaccination of staff and residents. We developed an agent-based transmission model and parameterized it with disease-specific estimates, temporal sensitivity of nasopharyngeal and saliva testing, results of vaccine efficacy trials, and data from initial COVID-19 outbreaks in LTCFs in Ontario, Canada. Characteristics of staff and residents, including contact patterns, were integrated into the model with age-dependent risk of hospitalization and death. Estimates of infection and outcomes were obtained and 95% credible intervals were generated using a bias-corrected and accelerated bootstrap method. Weekly routine testing of staff with 2-day turnaround time reduced infections among residents by at least 25.9% (95% CrI: 23.3% - 28.3%), compared to baseline measures of mask-wearing, symptom screening, and staff cohorting alone. A similar reduction of hospitalizations and deaths was achieved in residents. Vaccination averted 2-4 times more infections in both staff and residents as compared to routine testing, and markedly reduced hospitalizations and deaths among residents by 95.9% (95% CrI: 95.4% - 96.3%) and 95.8% (95% CrI: 95.5% - 96.1%), respectively, over 200 days from the start of vaccination. Vaccination could have a substantial impact on mitigating disease burden among residents, but may not eliminate the need for other measures before population-level control of COVID-19 is achieved.
| S-EPMC7743093 | biostudies-literature
Project description:We tested fecal samples from 93 norovirus-negative gastroenteritis outbreaks; 21 outbreaks were caused by sapovirus. Of these, 71% were caused by sapovirus genogroup IV and 66% occurred in long-term care facilities. Future investigation of gastroenteritis outbreaks should include multi-organism testing.
| S-EPMC3358050 | biostudies-literature
Project description:We report 5 clustered acute gastroenteritis outbreaks in long-term care facilities in Utah, USA, that were linked to healthcare employees working at multiple facilities. Four outbreaks were caused by norovirus genotype GIX. We recommend continued norovirus surveillance and genotyping to determine contributions of this genotype to norovirus outbreaks.
| S-EPMC9622255 | biostudies-literature
Project description:BackgroundIn the Unites States, long-term care facilities (LTCFs) are the most common setting for norovirus outbreaks. These outbreaks provide a unique opportunity to better characterize the viral and host characteristics of norovirus disease.MethodsWe enrolled 43 LTCFs prospectively to study the epidemiology, virology, and genetic host factors of naturally occurring norovirus outbreaks. Acute and convalescent stool, serum, and saliva samples from cases, exposed and nonexposed controls were collected. Norovirus infection was confirmed using quantitative polymerase chain reaction testing of stool samples or 4-fold increase in serum antibody titers. The presence of histo-blood group antigens (secretor, ABO, and Lewis type) was determined in saliva.ResultsSixty-two cases, 34 exposed controls, and 18 nonexposed controls from 10 norovirus outbreaks were enrolled. Forty-six percent of acute, 27% of convalescent case, and 11% of control stool samples tested norovirus positive. Outbreak genotypes were GII.4 (Den Haag, n = 3; New Orleans, n = 4; and Sydney, n = 2) and GI.1 (n = 1). Viral load in GII.4 Sydney outbreaks was significantly higher than in outbreaks caused by other genotypes; cases and controls shed similar amounts of virus. Forty-seven percent of cases shed virus for ≥ 21 days. Symptomatic infections with GII.4 Den Haag and GII.4 New Orleans were detected among nonsecretor individuals.ConclusionsAlmost half of all symptomatic individuals shed virus for at least 21 days. Viral load was highest in GII.4 viruses that most recently emerged; these viruses also infect the nonsecretor population. These findings will help to guide development of targeted prevention and control measures in the elderly.
| S-EPMC5921905 | biostudies-literature
Project description:BackgroundAged-care facilities (ACF's) provide unique challenges when implementing infection control methods for respiratory outbreaks such as COVID-19. Research on this highly vulnerable setting is lacking and there was no national reporting data of COVID-19 cases in ACFs in Australia early in the pandemic. We aimed to estimate the burden of aged-care worker (ACW) infections and outbreaks of COVID-19 in Australian aged-care.MethodsA line list of publicly available aged-care related COVID-19 reported cases from January 25 to June 10, 2020 was created and was enhanced by matching data extracted from media reports of aged-care related COVID-19 relevant outbreaks and reports. Rate ratios (RR) were used to predict risk of infection in ACW and aged-care residents, and were calculated independently, by comparing overall cases to ACW and aged-care residents' cases.ResultsA total of 14 ACFs with COVID-19 cases were recorded by June 2020 nationwide, with a high case fatality rate (CFR) of 50% (n = 34) and 100% (n = 3) seen in two ACFs. Analysis on the resident risk found that the COVID-19 risk is 1.27 times higher (unadjusted RR 1.27 95% confidence interval [CI] 1.00 to1.61; P = 0.047) as compared with the risk of infection in the general population. In over 60% of cases identified in ACFs, the source of infection in the index case was unknown. A total of 28 deaths associated within ACFs were reported, accounting for 54.9% of total deaths in New South Wales and 26.9% of total deaths in Australia.ConclusionsThis high-risk population requires additional prevention and control measures, such as routine testing of all staff and patients regardless of symptoms. Prompt isolation and quarantine as soon as a case is confirmed within a facility is essential.
| S-EPMC8983895 | biostudies-literature
Project description:BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread rapidly in nursing homes and long-term care (LTC) facilities. Symptoms-based screening and manual contact tracing have limitations that render them ineffective for containing the viral spread in LTC facilities. Symptoms-based screening alone cannot identify asymptomatic people who are infected, and the viral spread is too fast in confined living quarters to be contained by slow manual contact tracing processes.ObjectiveWe describe the development of a digital contact tracing system that LTC facilities can use to rapidly identify and contain asymptomatic and symptomatic SARS-CoV-2 infected contacts. A compartmental model was also developed to simulate disease transmission dynamics and to assess system performance versus conventional methods.MethodsWe developed a compartmental model parameterized specifically to assess the coronavirus disease (COVID-19) transmission in LTC facilities. The model was used to quantify the impact of asymptomatic transmission and to assess the performance of several intervention groups to control outbreaks: no intervention, symptom mapping, polymerase chain reaction testing, and manual and digital contact tracing.ResultsOur digital contact tracing system allows users to rapidly identify and then isolate close contacts, store and track infection data in a respiratory line listing tool, and identify contaminated rooms. Our simulation results indicate that the speed and efficiency of digital contact tracing contributed to superior control performance, yielding up to 52% fewer cases than conventional methods.ConclusionsDigital contact tracing systems show promise as an effective tool to control COVID-19 outbreaks in LTC facilities. As facilities prepare to relax restrictions and reopen to outside visitors, such tools will allow them to do so in a surgical, cost-effective manner that controls outbreaks while safely giving residents back the life they once had before this pandemic hit.
| S-EPMC7451111 | biostudies-literature