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1.
J Am Geriatr Soc ; 70(3): 701-708, 2022 03.
Article in English | MEDLINE | ID: covidwho-1723290

ABSTRACT

An effective clinical research effort in nursing homes to address prevention and treatment of COVID-19 faced overwhelming challenges. Under the Health Care Systems Research Network-Older Americans Independence Centers AGING Initiative, a multidisciplinary Stakeholder Advisory Panel was convened to develop recommendations to improve the capability of the clinical research enterprise in US nursing homes. The Panel considered the nursing home as a setting for clinical trials, reviewed the current state of clinical trials in nursing homes, and ultimately developed recommendations for the establishment of a nursing home clinical trials research network that would be centrally supported and administered. This report summarizes the Panel's recommendations, which were developed in alignment with the following core principles: build on available research infrastructure where appropriate; leverage existing productive partnerships of researchers with groups of nursing homes and nursing home corporations; encompass both efficacy and effectiveness clinical trials; be responsive to a broad range of stakeholders including nursing home residents and their care partners; be relevant to an expansive range of clinical and health care delivery research questions; be able to pivot as necessary to changing research priorities and circumstances; create a pathway for industry-sponsored research as appropriate; invest in strategies to increase diversity in study populations and the research workforce; and foster the development of the next generation of nursing home researchers.


Subject(s)
Clinical Trials as Topic/organization & administration , Nursing Homes/organization & administration , Aged , COVID-19/epidemiology , Female , Humans , Male , Pandemics , SARS-CoV-2 , United States/epidemiology
2.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329278

ABSTRACT

T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by Major Histocompatibility Complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. This approach identifies binders missed by computational prediction and serves as a framework for diverse objectives, including examining relationships between viral conservation and MHC binding.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315587

ABSTRACT

We introduce the maximum $n$-times coverage problem that selects $k$ overlays to maximize the summed coverage of weighted elements, where each element must be covered at least $n$ times. We also define the min-cost $n$-times coverage problem where the objective is to select the minimum set of overlays such that the sum of the weights of elements that are covered at least $n$ times is at least $τ$. Maximum $n$-times coverage is a generalization of the multi-set multi-cover problem, is NP-complete, and is not submodular. We introduce two new practical solutions for $n$-times coverage based on integer linear programming and sequential greedy optimization. We show that maximum $n$-times coverage is a natural way to frame peptide vaccine design, and find that it produces a pan-strain COVID-19 vaccine design that is superior to 29 other published designs in predicted population coverage and the expected number of peptides displayed by each individual's HLA molecules.

4.
J Am Geriatr Soc ; 70(4): 1198-1207, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1673190

ABSTRACT

BACKGROUND: Federal minimum nurse staffing levels for skilled nursing facilities (SNFs) were proposed in 2019 U.S. Congressional bills. We estimated costs and personnel needed to meet the proposed staffing levels, and examined characteristics of SNFs not meeting these thresholds. METHODS: This was a cross-sectional analysis of 2019Q4 payroll data, the Hospital Wage Index, and other administrative data for 14,964 Medicare and Medicaid-certified SNFs. We examined characteristics of SNFs not meeting proposed minimum thresholds: 4.1 total nursing hours per resident day (HPRD); 0.75 registered nurse (RN) HPRD; 0.54 licensed practical nurse (LPN) HPRD; and 2.81 certified nursing assistant (CNA) HPRD. For SNFs falling below the thresholds, we calculated the additional HPRD needed, along with the associated full-time equivalent (FTE) personnel and salary costs. RESULTS: In 2019, 25.0% of SNFs met the minimum 4.1 total nursing HPRD, while 31.0%, 84.5%, and 10.7% met the RN, LPN, and CNA thresholds, respectively. Only 5.0% met all four categories. In adjusted analyses, factors most strongly associated with SNFs not meeting the proposed minimums were: higher Medicaid census, larger bed size, for-profit ownership, higher county SNF competition; and, for RNs specifically, higher community poverty and lower Medicare census. Rural SNFs were less likely to meet all categories and this was explained primarily by county SNF competition. We estimate that achieving the proposed federal minimums across SNFs nationwide would require an estimated additional 35,804 RN, 3509 LPN, and 116,929 CNA FTEs at $7.25 billion annually in salary costs based on current wage rates and prepandemic resident census levels. CONCLUSIONS: Achieving proposed minimum nurse staffing levels in SNFs will require substantial financial investment in the workforce and targeted support of low-resource facilities. Extensive recruitment and retention efforts are needed to overcome supply constraints, particularly in the aftermath of the COVID-19 pandemic.


Subject(s)
COVID-19 , Skilled Nursing Facilities , Aged , Cross-Sectional Studies , Humans , Medicare , Pandemics , United States , Workforce
5.
JAMA Intern Med ; 182(3): 324-331, 2022 03 01.
Article in English | MEDLINE | ID: covidwho-1661562

ABSTRACT

Importance: Identifying successful strategies to increase COVID-19 vaccination among skilled nursing facility (SNF) residents and staff is integral to preventing future outbreaks in a continually overwhelmed system. Objective: To determine whether a multicomponent vaccine campaign would increase vaccine rates among SNF residents and staff. Design, Setting, and Participants: This was a cluster randomized trial with a rapid timeline (December 2020-March 2021) coinciding with the Pharmacy Partnership Program (PPP). It included 133 SNFs in 4 health care systems across 16 states: 63 and 70 facilities in the intervention and control arms, respectively, and participants included 7496 long-stay residents (>100 days) and 17 963 staff. Interventions: Multicomponent interventions were introduced at the facility level that included: (1) educational material and electronic messaging for staff; (2) town hall meetings with frontline staff (nurses, nurse aides, dietary, housekeeping); (3) messaging from community leaders; (4) gifts (eg, T-shirts) with socially concerned messaging; (5) use of a specialist to facilitate consent with residents' proxies; and (6) funds for additional COVID-19 testing of staff/residents. Main Outcomes and Measures: The primary outcomes of this study were the proportion of residents (from electronic medical records) and staff (from facility logs) who received a COVID-19 vaccine (any), examined as 2 separate outcomes. Mixed-effects generalized linear models with a binomial distribution were used to compare outcomes between arms, using intent-to-treat approach. Race was examined as an effect modifier in the resident outcome model. Results: Most facilities were for-profit (95; 71.4%), and 1973 (26.3%) of residents were Black. Among residents, 82.5% (95% CI, 81.2%-83.7%) were vaccinated in the intervention arm, compared with 79.8% (95% CI, 78.5%-81.0%) in the usual care arm (marginal difference 0.8%; 95% CI, -1.9% to 3.7%). Among staff, 49.5% (95% CI, 48.4%-50.6%) were vaccinated in the intervention arm, compared with 47.9% (95% CI, 46.9%-48.9%) in usual care arm (marginal difference: -0.4%; 95% CI, -4.2% to 3.1%). There was no association of race with the outcome among residents. Conclusions and Relevance: A multicomponent vaccine campaign did not have a significant effect on vaccination rates among SNF residents or staff. Among residents, vaccination rates were high. However, half the staff remained unvaccinated despite these efforts. Vaccination campaigns to target SNF staff will likely need to use additional approaches. Trial Registration: ClinicalTrials.gov Identifier: NCT04732819.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Health Promotion/organization & administration , Skilled Nursing Facilities , Adult , Aged , Female , Humans , Male , Middle Aged , Pandemics , SARS-CoV-2 , United States
6.
J Am Geriatr Soc ; 70(1): 19-28, 2022 01.
Article in English | MEDLINE | ID: covidwho-1526377

ABSTRACT

BACKGROUND: After the first of three COVID-19 vaccination clinics in U.S. nursing homes (NHs), the median vaccination coverage of staff was 37.5%, indicating the need to identify strategies to increase staff coverage. We aimed at comparing the facility-level activities, policies, incentives, and communication methods associated with higher staff COVID-19 vaccination coverage. METHODS: Design. Case-control analysis. SETTING: Nationally stratified random sample of 1338 U.S. NHs participating in the Pharmacy Partnership for Long-Term Care Program. PARTICIPANTS: Nursing home leadership. MEASUREMENT: During February 4-March 2, 2021, we surveyed NHs with low (<35%), medium (40%-60%), and high (>75%) staff vaccination coverage, to collect information on facility strategies used to encourage staff vaccination. Cases were respondents with medium and high vaccination coverage, whereas controls were respondents with low coverage. We used logistic regression modeling, adjusted for county and NH characteristics, to identify strategies associated with facility-level vaccination coverage. RESULTS: We obtained responses from 413 of 1338 NHs (30.9%). Compared with facilities with lower staff vaccination coverage, facilities with medium or high coverage were more likely to have designated frontline staff champions (medium: adjusted odds ratio [aOR] 3.6, 95% CI 1.3-10.3; high: aOR 2.9, 95% CI 1.1-7.7) and set vaccination goals (medium: aOR 2.4, 95% 1.0-5.5; high: aOR 3.7, 95% CI 1.6-8.3). NHs with high vaccination coverage were more likely to have given vaccinated staff rewards such as T-shirts compared with NHs with low coverage (aOR 3.8, 95% CI 1.3-11.0). Use of multiple strategies was associated with greater likelihood of facilities having medium or high vaccination coverage: For example, facilities that used ≥9 strategies were three times more likely to have high staff vaccination coverage than facilities using <6 strategies (aOR 3.3, 95% CI 1.2-8.9). CONCLUSIONS: Use of designated champions, setting targets, and use of non-monetary awards were associated with high NH staff COVID-19 vaccination coverage.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Nursing Homes , Nursing Staff/statistics & numerical data , Vaccination/statistics & numerical data , Adult , Case-Control Studies , Female , Humans , Male , Middle Aged , Motivation , Reward , United States
7.
J Am Med Dir Assoc ; 22(11): 2240-2244, 2021 11.
Article in English | MEDLINE | ID: covidwho-1373103

ABSTRACT

OBJECTIVES: Little is known about how the COVID-19 pandemic has affected rehabilitation care in post-acute and long-term care. As part of a process to assess research priorities, we surveyed professionals in these settings to assess the impact of the pandemic and related research needs. DESIGN: Qualitative analysis of open-ended survey results. SETTING AND PARTICIPANTS: 30 clinical and administrative staff working in post-acute and long-term care. METHODS: From June 24 through July 10, 2020, we used professional connections to disseminate an electronic survey to a convenience sample of clinical and administrative staff. We conducted an inductive thematic analysis of the data. RESULTS: We identified 4 themes, related to (1) rapid changes in care delivery, (2) negative impact on patients' motivation and physical function, (3) new access barriers and increased costs, and (4) uncertainty about sustaining changes in delivery and payment. Rapid changes: Respondents described how infection control policies and practices shifted rehabilitation from group sessions and communal gyms to the bedside and telehealth. Negative impact: Respondents felt that patients' isolation, particularly in residential care settings, affected their motivation for rehabilitation and their physical function. Access and costs: Respondents expressed concerns about increased costs (eg, for personal protective equipment) and decreased patient volume, as well as access issues. Uncertainty: At the same time, respondents described how telehealth and Medicare waivers enabled new ways to connect with patients and wondered whether waivers would be extended after the public health emergency. CONCLUSIONS AND IMPLICATIONS: Survey results highlight rapid changes to rehabilitation in post-acute and long-term care during the height of the COVID-19 pandemic. Because staff vaccine coverage remains low and patients vulnerable in residential care settings, changes such as infection precautions are likely to persist. Future research should evaluate the impact on care, outcomes, and costs.


Subject(s)
COVID-19 , Pandemics , Aged , Humans , Long-Term Care , Medicare , SARS-CoV-2 , United States
8.
J Am Geriatr Soc ; 69(8): 2079-2089, 2021 08.
Article in English | MEDLINE | ID: covidwho-1218149

ABSTRACT

BACKGROUND/OBJECTIVES: The effectiveness of the BNT162b2 vaccine on preventing the spread of COVID-19 and deaths in nursing homes (NH) is unknown. DESIGN: We used zero-inflated negative binomial mixed effects regressions to model the associations of time since the vaccine clinic ending the week of December 27, 2020 (cohort 1), January 3, 2021 (cohort 2), or January 10, 2021 (cohort 3) controlling for county rate of COVID-19, bed size, urban location, racial and ethnic census, and level of registered nurses with resident cases and deaths of COVID-19 and staff cases of COVID-19. SETTING AND PARTICIPANTS: All 2501 NHs who held a vaccine clinic from the first 17 states to initiate clinics as part of the Pharmacy Partnership for Long-Term Care Program. MAIN OUTCOME(S) AND MEASURE(S): Adjusted Incidence Rate Ratio (IRR) for time in 3, 4, 5, and 6 weeks after the first vaccine clinic for resident cases and deaths of COVID-19 and staff cases of COVID-19. RESULTS: Resident and staff cases trended downward in all three cohorts following the vaccine clinics. Time following the first clinic at 5 and 6 weeks was consistently associated with fewer resident cases (IRR: 0.68 [95% CI: 0.54-0.84], IRR: 0.64 [95% CI: 0.48-0.86], respectively); resident deaths (IRR: 0.59 [95% CI: 0.45-0.77], IRR: 0.45 [95% CI: 0.31-0.65], respectively); and staff cases (IRR: 0.64 [95% CI: 0.56-0.73], IRR: 0.51 [95% CI: 0.42-0.62], respectively). Other factors associated with fewer resident and staff cases included facilities with less than 50 certified beds and high nurse staffing per resident day (>0.987). Contrary to prior research, higher Hispanic non-white resident census was associated with fewer resident cases (IRR: 0.42, 95% CI: 0.31-0.56) and deaths (IRR: 0.18, 95% CI: 0.12-0.27). CONCLUSIONS: The BNT162b2 vaccine is associated with decreased spread of SARS-CoV-2 in both residents and staff as well as decreased deaths among residents.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Health Personnel/statistics & numerical data , Nursing Homes/statistics & numerical data , Aged , COVID-19/epidemiology , COVID-19/mortality , Cohort Studies , Humans , Incidence , Male , United States/epidemiology
9.
J Am Geriatr Soc ; 69(5): 1140-1146, 2021 05.
Article in English | MEDLINE | ID: covidwho-1150156

ABSTRACT

BACKGROUND: Presently a median of 37.5% of the U.S. skilled nursing facility (SNF) workforce has been vaccinated for COVID-19. It is essential to understand vaccine hesitancy among SNF workers to inform vaccine campaigns going forward. OBJECTIVE: To describe the concerns raised among healthcare workers and staff from SNFs during town hall meetings. DESIGN: Sixty-three SNFs from four corporations were invited to send Opinion Leaders, outspoken staff from nursing, nurse aid, dietary, housekeeping or recreational therapy, to attend a 1-h virtual town hall meeting. Meetings used a similar format where the moderator solicited concerns that the attendees themselves had or had heard from others in the facility about the COVID-19 vaccine. Physicians and moderators used personal stories to address concerns and reaffirmed positive emotions. SETTING: Twenty-six video town hall meetings with SNF staff. PARTICIPANTS: Healthcare workers and staff, with physicians serving as content experts. MEASUREMENT: Questions and comments about the COVID-19 vaccines noted by physicians. RESULTS: One hundred and ninety three staff from 50 facilities participated in 26 meetings between December 30, 2020 and January 15, 2021. Most staff reported getting information about the vaccine from friends or social media. Concerns about how rapidly the vaccines were developed and side effects, including infertility or pregnancy related concerns, were frequently raised. There were no differences in concerns raised by discipline. Questions about returning to prior activities after being vaccinated were common and offered the opportunity to build on positive emotions to reduce vaccine hesitancy. CONCLUSIONS: Misinformation about the COVID-19 vaccine was widespread among SNF staff. Sharing positive emotions and stories may be more effective than sharing data when attempting to reduce vaccine hesitancy in SNF staff.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Nursing Staff/psychology , Skilled Nursing Facilities , Communication , Humans , Physicians/psychology , Vaccination Refusal/psychology
10.
J Am Med Dir Assoc ; 22(6): 1133-1137, 2021 06.
Article in English | MEDLINE | ID: covidwho-1141947

ABSTRACT

OBJECTIVE: The vaccination of skilled nursing facility (SNF) staff is a critical component in the battle against COVID-19. Together, residents and staff constitute the single most vulnerable population in the pandemic. The health of these workers is completely entangled with the health of those they care for. Vaccination of SNF staff is key to increasing uptake of the vaccine, reducing health disparities, and reopening SNFs to visitors. Yet, as the vaccine rollout begins, some SNF staff are declining to be vaccinated. The purpose of this article is to describe reasons for COVID-19 vaccine hesitancy reported by staff of skilled nursing facilities and understand factors that could potentially reduce hesitancy. DESIGN: Five virtual focus groups were conducted with staff of SNFs as part of a larger project to improve vaccine uptake. SETTING AND PARTICIPANTS: Focus groups with 58 staff members were conducted virtually using Zoom. MEASURES: Focus groups sought to elicit concerns, perspectives, and experiences related to COVID-19 testing and vaccination. RESULTS: Our findings indicate that some SNF staff are hesitant to receive the COVID-19 vaccine. Reasons for this hesitancy include beliefs that the vaccine has been developed too fast and without sufficient testing; personal fears about pre-existing medical conditions, and more general distrust of the government. CONCLUSIONS AND IMPLICATIONS: SNF staff indicate that seeing people like themselves receive the vaccination is more important than seeing public figures. We discuss the vaccination effort as a social enterprise and the need to develop long-term care provider-academic-community partnerships in response to COVID-19 and in expectation of future pandemics.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19 , Health Personnel/psychology , Skilled Nursing Facilities , Vaccination Refusal/psychology , COVID-19/prevention & control , COVID-19 Testing , Focus Groups , Humans
11.
MMWR Morb Mortal Wkly Rep ; 70(5): 178-182, 2021 Feb 05.
Article in English | MEDLINE | ID: covidwho-1063531

ABSTRACT

Residents and staff members of long-term care facilities (LTCFs), because they live and work in congregate settings, are at increased risk for infection with SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19) (1,2). In particular, skilled nursing facilities (SNFs), LTCFs that provide skilled nursing care and rehabilitation services for persons with complex medical needs, have been documented settings of COVID-19 outbreaks (3). In addition, residents of LTCFs might be at increased risk for severe outcomes because of their advanced age or the presence of underlying chronic medical conditions (4). As a result, the Advisory Committee on Immunization Practices has recommended that residents and staff members of LTCFs be offered vaccination in the initial COVID-19 vaccine allocation phase (Phase 1a) in the United States (5). In December 2020, CDC launched the Pharmacy Partnership for Long-Term Care Program* to facilitate on-site vaccination of residents and staff members at enrolled LTCFs. To evaluate early receipt of vaccine during the first month of the program, the number of eligible residents and staff members in enrolled SNFs was estimated using resident census data from the National Healthcare Safety Network (NHSN†) and staffing data from the Centers for Medicare & Medicaid Services (CMS) Payroll-Based Journal.§ Among 11,460 SNFs with at least one vaccination clinic during the first month of the program (December 18, 2020-January 17, 2021), an estimated median of 77.8% of residents (interquartile range [IQR] = 61.3%- 93.1%) and a median of 37.5% (IQR = 23.2%- 56.8%) of staff members per facility received ≥1 dose of COVID-19 vaccine through the Pharmacy Partnership for Long-Term Care Program. The program achieved moderately high coverage among residents; however, continued development and implementation of focused communication and outreach strategies are needed to improve vaccination coverage among staff members in SNFs and other long-term care settings.


Subject(s)
COVID-19 Vaccines/administration & dosage , Pharmacy/organization & administration , Public-Private Sector Partnerships , Skilled Nursing Facilities/organization & administration , Vaccination Coverage/statistics & numerical data , Aged , COVID-19/epidemiology , COVID-19/prevention & control , Centers for Disease Control and Prevention, U.S. , Humans , Long-Term Care , Program Evaluation , United States/epidemiology
12.
Cell Syst ; 12(1): 102-107.e4, 2021 01 20.
Article in English | MEDLINE | ID: covidwho-947149

ABSTRACT

Subunit vaccines induce immunity to a pathogen by presenting a component of the pathogen and thus inherently limit the representation of pathogen peptides for cellular immunity-based memory. We find that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subunit peptides may not be robustly displayed by the major histocompatibility complex (MHC) molecules in certain individuals. We introduce an augmentation strategy for subunit vaccines that adds a small number of SARS-CoV-2 peptides to a vaccine to improve the population coverage of pathogen peptide display. Our population coverage estimates integrate clinical data on peptide immunogenicity in convalescent COVID-19 patients and machine learning predictions. We evaluate the population coverage of 9 different subunits of SARS-CoV-2, including 5 functional domains and 4 full proteins, and augment each of them to fill a predicted coverage gap.


Subject(s)
COVID-19 Vaccines/immunology , COVID-19/immunology , COVID-19/prevention & control , Immunity, Cellular/immunology , Machine Learning , Vaccines, Subunit/immunology , COVID-19 Vaccines/administration & dosage , Forecasting , Humans , Immunity, Cellular/drug effects , Vaccines, Subunit/administration & dosage
13.
Cell Syst ; 11(2): 131-144.e6, 2020 08 26.
Article in English | MEDLINE | ID: covidwho-676381

ABSTRACT

We present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations for SARS-CoV-2. Our approach optimizes the presentation likelihood of a diverse set of vaccine peptides conditioned on a target human-population HLA haplotype distribution and expected epitope drift. Our proposed SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA average hits per person (≥ 1 peptide: 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our proposed MHC class II vaccine formulations provide 97.21% predicted coverage with at least five vaccine peptide-HLA average hits per person with all peptides having an observed mutation probability of ≤ 0.001. We provide an open-source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts here: https://github.com/gifford-lab/optivax.


Subject(s)
Betacoronavirus/immunology , Haplotypes , Histocompatibility Antigens Class II/genetics , Histocompatibility Antigens Class I/genetics , Sequence Analysis, DNA/methods , Vaccines, Subunit/immunology , Viral Vaccines/immunology , Betacoronavirus/genetics , COVID-19 Vaccines , Coronavirus Infections/genetics , Coronavirus Infections/immunology , Coronavirus Infections/prevention & control , Epitopes/chemistry , Epitopes/genetics , Epitopes/immunology , Histocompatibility Antigens Class I/chemistry , Histocompatibility Antigens Class I/immunology , Histocompatibility Antigens Class II/chemistry , Histocompatibility Antigens Class II/immunology , Humans , Machine Learning , SARS-CoV-2 , Sequence Analysis, DNA/standards , Vaccines, Subunit/chemistry , Vaccines, Subunit/genetics , Viral Vaccines/chemistry , Viral Vaccines/genetics
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