Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings

The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.

COVID-19 Inmate Risk Appraisal (CIRA): development and validation of a screening tool to assess COVID-19 vulnerability in prisons

OBJECTIVES: To develop and validate a screening tool designed to identify detained people at increased risk for COVID-19 mortality, the COVID-19 Inmate Risk Appraisal (CIRA). DESIGN: Cross-sectional study with a representative sample (development) and a case-control sample (validation). SETTING: The two largest Swiss prisons. PARTICIPANTS: (1) Development sample: all male persons detained in Poschwies, Zurich (n = 365);(2) Validation sample: case-control sample of male persons detained in Champ-Dollon, Geneva (n = 192, matching 1:3 for participants at risk for severe course of COVID-19 and participants without risk factors). MAIN OUTCOME MEASURES: The CIRA combined seven risk factors identified by the World Health Organization and the Swiss Federal Office of Public Health as predictive of severe COVID-19 to derive an absolute risk increase in mortality rate: Age >=60 years, cardiovascular disease, diabetes, hypertension, chronic respiratory disease, immunodeficiency and cancer. RESULT(S): Based on the development sample, we proposed a three-level classification: average (<3.7), elevated (3.7-5.7) and high (>5.7) risk. In the validation sample, the CIRA identified all individuals identified as vulnerable by national recommendations (having at least one risk factor). The category "elevated risk" maximised sensitivity (1) and specificity (0.97). The CIRA had even higher capacity in discriminating individuals vulnerable according to clinical evaluation (a four-level risk categorisation based on a consensus of medical staff). The category "elevated risk" maximised sensitivity and specificity (both 1). When considering the individuals classified as extremely high risk by medical staff, the category "high risk" had a high discriminatory capacity (sensitivity =0.89, specificity =0.97). CONCLUSION(S): The CIRA scores have a high discriminative ability and will be important in custodial settings to support decisions and prioritise actions using a standardised valid assessment method. However, as knowledge on risk factors for COVID-19 mortality is still limited, the CIRA may be considered preliminary. Underlying data will be updated regularly on the website (http://www.prison-research.com), where the CIRA algorithm is freely available. Copyright © 2021 EMH Swiss Medical Publishers Ltd.. All rights reserved.

Is Telerehabilitation a Viable Option for People With Low Back Pain? Associations Between Telerehabilitation and Outcomes During the COVID-19 Pandemic.

OBJECTIVE: The aims of this study were to examine associations between frequency of telerehabilitation (TR) and outcomes of functional status (FS), number of visits, and patient satisfaction during COVID-19 and to compare FS outcomes by TR delivery mode for individuals with low back pain. METHODS: Propensity score matching was used to match episodes of care with or without TR exposure by the probability of receiving TR. FS, visits, and satisfaction were compared for individuals without TR and those who received care by TR for "any," "few," "most," or "all" frequencies (4 matched samples), and FS was compared for individuals receiving synchronous, asynchronous, and mixed TR modes (3 matched samples). Standardized differences were used to compare samples before and after matching. Outcomes between matched samples were compared using z tests with 95% CI. RESULTS: The sample consisted of 91,117 episodes of care from 1398 clinics located in 46 states (58% women; mean age = 55 [SD = 18]). Of those, only 5013 episodes (5.5%) involved any amount of TR. All standardized differences between matched samples were <0.1. There was no significant difference in FS points (range = 0-100, with higher representing better FS) between matched samples, except for episodes that had ``few'' (-1.7) and ``all'' (+2.0) TR frequencies or that involved the asynchronous (-2.6) TR mode. These point differences suggest limited clinical importance. Episodes with any TR frequency involved significantly fewer visits (0.7-1.3) than episodes with no TR, except that those with the "most" TR frequency had non-significantly fewer visits (0.6). A smaller proportion of individuals with TR (-4.0% to -5.0%) than of individuals with no telerehabilitation reported being very satisfied with treatment results, except for those with the "all" TR frequency. CONCLUSIONS: A positive association between TR and rehabilitation outcomes was observed, with a trend for better FS outcomes and fewer visits when all care was delivered through TR. Satisfaction tended to be lower with TR use. Overall, this observational study showed that for people with low back pain, physical therapy delivered through TR was equally effective as and more efficient than in-person care, with a trend of higher effectiveness when used for all visits during the episode of care. No differences in FS outcomes were observed between care delivered with synchronous and mixed TR delivery modes and care delivered with no TR. However, the asynchronous mode of TR was associated with worse functional outcomes than no TR. Although the majority of people were very satisfied with their treatment results with and without TR, very high satisfaction rates were reported by a slightly smaller proportion of individuals with TR versus those without TR. Our results suggest that TR is a viable option for rehabilitation care for individuals with low back pain and should also be considered in the post-COVID-19 era.

Telerehabilitation During the COVID-19 Pandemic in Outpatient Rehabilitation Settings: A Descriptive Study.

OBJECTIVE: COVID-19 has widely affected delivery of health care. In response, telerehabilitation (TR) has emerged as alternative care model. Aims were: (1) to describe baseline patient characteristics and available unadjusted outcomes for episodes of care administered during COVID-19 using TR versus traditional in-person care, and (2) to describe TR frequency levels by condition and telecommunication modes. METHODS: A descriptive retrospective observational design was used to report patient variables and outcomes including physical function, number of visits, and patient satisfaction, by TR frequency (few, most, or all visits) and telecommunication modes. Standardized differences were used to compare baseline characteristics between episodes with and without TR. RESULTS: Sample consisted of 222,680 patients (59% female; mean [SD] age = 55 [18] years). Overall TR rate was 6% decreasing from 10% to 5% between second and third quarters of 2020. Outcome measures were available for 90% to 100% of episodes. Thirty-seven percent of clinicians administered care via TR. Patients treated using TR compared with in-person care were more likely to be younger and live in large metropolitan areas. From those with TR, 55%, 20%, and 25% had TR during few, most, or all visits, respectively. TR care was administered equally across orthopedic body parts, with lower use for nonorthopedic conditions such as stroke, edema, and vestibular dysfunction. TR was primarily administered using synchronous (video or audio) modes. The rate of patients reported being very satisfied with their treatment results was 3% higher for no TR compared with TR. CONCLUSIONS: These results provide new knowledge about to whom and how TR is being administered during the pandemic in outpatient rehabilitation practices throughout the United States. The database assessed was found to be suitable for conducting studies on associations between TR and diverse outcome measures, controlling for a comprehensive set of patient characteristics, to advance best TR care models, and promote high-quality care. IMPACT: This study provided detailed and robust descriptive information using an existing national patient database containing patient health and demographic characteristics, outcome measures, and telerehabilitation (TR) administration data. Findings support the feasibility to conduct future studies on associations between TR care and patient outcomes, adjusting for a wide range of patient characteristics and clinical setting factors that may be associated with the probability of receiving TR. The finding of limited and decreasing use of TR over the study period calls for studies aimed to better understand facilitators and inhibitors of TR use by rehabilitation therapists during everyday practice to promote its use when clinically appropriate.

The Fatty Acid Lipid Metabolism Nexus in COVID-19.

Enteric symptomology seen in early-stage severe acute respiratory syndrome (SARS)-2003 and COVID-19 is evidence of virus replication occurring in the intestine, liver and pancreas. Aberrant lipid metabolism in morbidly obese individuals adversely affects the COVID-19 immune response and increases disease severity. Such observations are in line with the importance of lipid metabolism in COVID-19, and point to the gut as a site for intervention as well as a therapeutic target in treating the disease. Formation of complex lipid membranes and palmitoylation of coronavirus proteins are essential during viral replication and assembly. Inhibition of fatty acid synthase (FASN) and restoration of lipid catabolism by activation of AMP-activated protein kinase (AMPK) impede replication of coronaviruses closely related to SARS-coronavirus-2 (CoV-2). In vitro findings and clinical data reveal that the FASN inhibitor, orlistat, and the AMPK activator, metformin, may inhibit coronavirus replication and reduce systemic inflammation to restore immune homeostasis. Such observations, along with the known mechanisms of action for these types of drugs, suggest that targeting fatty acid lipid metabolism could directly inhibit virus replication while positively impacting the patient's response to COVID-19.