Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples.

Understanding disease burden and transmission dynamics in resource-limited, low-income countries like Nepal are often challenging due to inadequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters (hotspots) and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 22 sites in the Kathmandu Valley from June to August 2020, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heatmap was created to visualize the presence of SARS-CoV-2 infection in the community based on viral load intensity and corresponding geospatial data. Further, 47 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n = 9, 22%) were novel at the time of data analysis and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. SNP analysis revealed possibility of assessing circulating major/minor variant diversity on environmental samples based on key mutations. Our study demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.

Exemplars in vaccine delivery protocol: a case-study-based identification and evaluation of critical factors in achieving high and sustained childhood immunisation coverage in selected low-income and lower-middle-income countries.

INTRODUCTION: Increases in global childhood vaccine delivery have led to decreases in morbidity from vaccine-preventable diseases. However, these improvements in vaccination have been heterogeneous, with some countries demonstrating greater levels of change and sustainability. Understanding what these high-performing countries have done differently and how their decision-making processes will support targeted improvements in childhood vaccine delivery. METHODS AND ANALYSIS: We studied three countries-Nepal, Senegal, Zambia-with exemplary improvements in coverage between 2000 and 2018 as part of the Exemplars in Global Health Programme. We apply established implementation science frameworks to understand the 'how' and 'why' underlying improvements in vaccine delivery and coverage. Through mixed-methods research, we will identify drivers of catalytic change in vaccine coverage and the decision-making process supporting these interventions and activities. Methods include quantitative analysis of available datasets and in-depth interviews and focus groups with key stakeholders in the global, national and subnational government and non-governmental organisation space, as well as community members and local health delivery system personnel. ETHICS AND DISSEMINATION: Working as a multinational and multidisciplinary team, and under oversight from all partner and national-level (where applicable) institutional review boards, we collect data from participants who provided informed consent. Findings are disseminated through a variety of forms, including peer-reviewed manuscripts related to country-specific case studies and vaccine system domain-specific analyses, presentations to key stakeholders in the global vaccine delivery space and narrative dissemination on the Exemplars.Health website.

Who gets vaccinated in a measles-rubella campaign in Nepal?: results from a post-campaign coverage survey.

BACKGROUND: Following the 2015 earthquake, a measles-rubella (MR) supplementary immunization activity (SIA), in four phases, was implemented in Nepal in 2015-2016. A post-campaign coverage survey (PCCS) was then conducted in 2017 to assess SIA performance and explore factors that were associated with vaccine uptake. METHODS: A household survey using stratified multi-stage probability sampling was conducted to assess coverage for a MR dose in the 2015-2016 SIA in Nepal. Logistic regression was then used to identify factors related to vaccine uptake. RESULTS: Eleven thousand two hundred fifty-three households, with 4870 eligible children provided information on vaccination during the 2015-2016 MR SIA. Overall coverage of measles-rubella vaccine was 84.7% (95% CI: 82.0-87.0), but varied between 77.5% (95% CI: 72.0, 82.2) in phase-3, of 21 districts vaccinated in Feb-Mar 2016, to 97.7% (CI: 95.4, 98.9) in phase-4, of the last seven mountainous districts vaccinated in Mar-Apr 2016. Coverage in rural areas was higher at 85.6% (CI: 81.9, 88.8) than in urban areas at 79.0% (CI: 75.5, 82.1). Of the 4223 children whose caregivers knew about the SIA, 96.5% received the MR dose and of the 647 children whose caregivers had not heard about the campaign, only 1.8% received the MR dose. CONCLUSIONS: The coverage in the 2015-2016 MR SIA in Nepal varied by geographical region with rural areas achieving higher coverage than urban areas. The single most important predictor of vaccination was the caregiver being informed in advance about the vaccination campaign. Enhanced efforts on social mobilization for vaccination have been used in Nepal since this survey, notably for the most recent 2020 MR campaign.

Increased Incidence of Injury Among Runners With COVID-19.

BACKGROUND: Coronavirus disease 2019 (COVID-19) affects multiple organ systems. Whether and how COVID-19 affects the musculoskeletal system remains unknown. We aim to assess the association between COVID-19 and risk of injury. HYPOTHESIS: Runners who report having COVID-19 also report a higher incidence of injury. STUDY DESIGN: Cross-sectional study. LEVEL OF EVIDENCE: Level 4. METHODS: An electronic survey was distributed from July through September 2020, by New York Road Runners, ASICS North America, race medical directors, and through social media. Inclusion criteria were runners 18 years or older who had participated in ≥1 race (running or triathlon) in 2019. RESULTS: A total of 1947 runners participated and met inclusion criteria. Average age was 45.0 (SD, 12.2) years and 56.5% were women. A total of 123 (6.3%) runners self-reported having COVID-19; 100 (81%) reported their diagnosis was from a laboratory test (polymerase chain reaction or antibody) and 23 reported being diagnosed by a medical professional without confirmatory laboratory testing. Since March 2020, 427 (21.9%) reported an injury that prevented running for at least 1 week, including 38 of 123 (30.9%) who self-reported having COVID-19 and 389 of 1435 (21.3%) who did not report having COVID-19 (P = 0.01). After adjusting for age, sex, the number of races in 2019, and running patterns before March 2020, runners who self-reported a diagnosis of COVID-19 had a higher incidence of injury compared with those who did not (odds ratio, 1.66; 95% CI, 1.11-2.48; P = 0.01). CONCLUSION: Injuries were more often self-reported by runners with laboratory-confirmed or clinically diagnosed COVID-19 compared with those who did not report COVID-19. Given the limitations of the study, any direct role of COVID-19 in the pathophysiology of injuries among runners remains unclear. CLINICAL RELEVANCE: Direct and indirect musculoskeletal sequelae of COVID-19 should be further investigated, including the risk of exercise- and sports-related injury after COVID-19.

Running races during the COVID-19 pandemic: a 2020 survey of the running community.

OBJECTIVES: To survey runners and triathletes about their willingness to resume in-person racing during the COVID-19 pandemic, health concerns related to mass races and changes in running patterns since the start of the pandemic. DESIGN: An electronic survey was distributed from 15 July to 1 September 2020 to runners and triathletes by New York Road Runners, ASICS North America, and race medical directors, and through social media. PARTICIPANTS: Runners and triathletes 18 years of age or older who participated in at least one race in 2019. RESULTS: A total of 2278 surveys were received. Not all participants answered every question; the denominator represents the number of responses to each question. Most participants were from the USA (1620/1940, 83.5%), of which over half were from New York (812/1475, 55.1%). Regarding when respondents would feel comfortable returning to in-person racing, the most frequent response was 'Whenever local laws allow, but only if there are sufficient precautions' (954/2173, 43.9%), followed by 'Not until there is a vaccine' (540/2173, 24.9%). The most common concerns about in-person races were crowded starting corrals (1802/2084, 86.5%), the number of COVID-19 cases in the race location (1585/2084, 76.1%) and the number of participants (1517/2084, 72.8%). Comparing running patterns before the pandemic to Summer 2020, the mean weekly mileage decreased from 25.5 (SD 15.4) miles to 22.7 (16.2) miles (p<0.001). CONCLUSION: Most runners are willing to return to racing when local laws allow, though as of Summer 2020, many desired certain precautions to feel comfortable.

Multidisciplinary approach to COVID-19 risk communication: a framework and tool for individual and regional risk assessment.

The COVID-19 pandemic has exceeded over sixty-five million cases globally. Different approaches are followed to mitigate its impact and reduce its spreading in different countries, but limiting mobility and exposure have been de-facto precautions to reduce transmission. However, a full lockdown cannot be sustained for a prolonged period. An evidence-based, multidisciplinary approach on risk zoning, personal and transmission risk assessment in near real-time, and risk communication would support the optimized decisions to minimize the impact of coronavirus on our lives. This paper presents a framework to assess the individual and regional risk of COVID-19 along with risk communication tools and mechanisms. Relative risk scores on a scale of 100 represent the integrated risk of influential factors. The personal risk model incorporates age, exposure history, symptoms, local risk and existing health condition, whereas regional risk is computed through the actual cases of COVID-19, public health risk factors, socioeconomic condition of the region, and immigration statistics. A web application tool ( http://www.covira.info ) has been developed, where anyone can assess their risk and find the guided information links primarily for Nepal. This study provides regional risk for Nepal, but the framework is scalable across the world. However, personal risk can be assessed immediately from anywhere.