ABSTRACT
INTRO: Viruses, including SARS-CoV-2, which causes COVID-19, are constantly changing. These genetic changes (aka mutations) occur over time and can lead to the emergence of new variants that may have different characteristics. After the first SARS-CoV-2 genome was published in early 2020, scientists all over the world soon realized the immediate need to obtain as much genetic information from as many strains as possible. However, understanding the functional significance of the mutations harbored by a variant is important to assess its impact on transmissibility, disease severity, immune escape, and the effectiveness of vaccines and therapeutics. METHODS: Here in Canada, we have developed an interactive framework for visualizing and reporting mutations in SARS-CoV-2 variants. This framework is composed of three stand-alone yet connected components;an interactive visualization (COVID-MVP), a manually curated functional annotation database (pokay), and a genomic analysis workflow (nf-ncov-voc). Findings: COVID-MVP provides (i) an interactive heatmap to visualize and compare mutations in SARS-CoV-2 lineages classified across different VOCs, VOIs, and VUMs;(ii) mutation profiles including the type, impact, and contextual information;(iii) annotation of biological impacts for mutations where functional data is available in the literature;(iv) summarized information for each variant and/or lineage in the form of a surveillance report;and (v) the ability to upload raw genomic sequence(s) for rapid processing and annotating for real-time classification. DISCUSSION: This comprehensive comparison allows microbiologists and public health practitioners to better predict how the mutations in emerging variants will impact factors such as infection severity, vaccine resistance, hospitalization rates, etc. CONCLUSION: This framework is cloud-compatible & standalone, which makes it easier to integrate into other genomic surveillance tools as well. COVID-MVP is integrated into the Canadian VirusSeq data portal (https://virusseqdataportal.ca) - a national data hub for SARS-COV-2 genomic data. COVID-MVP is also used by the CanCOGeN and CoVaRR networks in national COVID-19 genomic surveillance.
ABSTRACT
Objectives: The first confirmed case of Middle East respiratory syndrome (MERS) in Oman was in 2013. This report describes the nosocomial spread of MERS-coronavirus (CoV) in two regional hospitals in Oman (2019) and highlights opportunities for rapid containment in the future. Method(s): An outbreak epidemiological description and analysis of contributing factors was undertaken, with infection prevention and control challenges highlighted. A transmission map was created to trace hospital contacts and symptomatic contacts were screened using RT-PCR. Environment decontamination was carried out. Awareness programmes including training and education were augmented and infection prevention and control guidelines were revised, especially those related to the implementation of risk assessment for contact screenings. Result(s): Between 23 January and 16 February 2019, 13 confirmed cases were reported from two hospitals. Seven out of 13 were secondary transmitted cases, including two healthcare workers. Symptoms included fever in six (46%) patients, respiratory symptoms in six (46%), and gastrointestinal symptoms in four (31%). Four out of 13 patients died. High traffic in affected wards, poor adherence to infection control measures, lack of awareness, delay in the diagnosis of primary cases, and inadequate terminal cleaning were identified as contributory factors to the outbreak. Both affected healthcare workers and two secondary patients were missed during contact screenings. Conclusion(s): Lapses in the implementation of infection control measures within a facility can facilitate nosocomial transmission of MERS-CoV. There is a need to revise risk assessment tools for contacts within hospitals so that positive cases can be detected earlier.