Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada's public health laboratories.

BACKGROUND: Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. METHODS: We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. RESULTS: We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. CONCLUSIONS: These findings enable the strategic prioritization and deployment of resources to increase Canada's ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building.

Strategy of active case-finding for COVID-19 in Bogota city, 2020-2021

Introduction. With the national guidelines of the Sustainable Selective Test-Tracking-Isolation program (PRASS in spanish) and the districts strategy of Detect-Isolation-Report (DAR in spanish) from the Public Health Plan of Collective Interventions (PSPIC in spanish), during 2020 were implemented activities of active search for positive cases of SARS-CoV-2, in order to identify risk areas and implement mitigation and containment strategies for the COVID-19 pandemic in Bogota. The objective of this work is to describe the strategy of active case-finding for COVID-19 in Bogota city, 2020-2021. Materials y methods. Using descriptive statistics, we described the search sessions carried out in the city. Thus, the integrated health services subnets with their home environment public health teams, integrated by professionals and trained technicians, carried out swab sampling in the following clusters: Select groups with greater vulnerability or high exposure to the virus given their daily activities, or specific areas of the city with a high rate of virus transmissibility or apparently silent. Samples were sent to the district public health laboratory for processing using the Charite protocol RT-PCR, Berlin. They also carry out communication and education activities for health and notification of cases to the Public Health Surveillance System-SIVIGILA. Results. Between June 2020 and June 2021, were performed 9997 journeys of active search, where 1000.225 samples were taken along the 20 localities of Bogota city, with a higher concentration of samples in Ciudad Bolivar (11%), Kennedy (9%), Tunjuelito (7%), Suba (6%), Usme (6%), Puente Aranda (6%) and Bosa (6%). Acumulative positivity ratio of 20% was observed for the observed period, in the three moments with the highest frequency of positive cases for the SARS-CoV-2 virus in the city, positivity ratios of 14% were reached in the months of July and August 2020, 19% between December 2020 and January 2021 and 39% in the third peak of infections between May and June 2021, finding for the latter period time, days with positivity proportions that exceeded 45%. Conclusion. In the city, epidemiological surveillance actions are continued, such as Field Epidemiological Investigations (IEC in spanish), as well as the increasing of collective interventions in the different environments of daily life, wich are focused on the areas with the higher positivity, developing actions aimed at empowering the community in relation to care and biosecurity guidelines to reduce the COVID-19 contagion risk. © 2021 IEEE.

Laboratory response checklist for infectious disease outbreaks-preparedness and response considerations for emerging threats.

The purpose of the Laboratory Response Checklist for Infectious Disease Outbreaks (the Checklist) is to provide public health laboratories and laboratory networks operating at multiple jurisdictional levels with a useful, adaptable tool to help rapidly identify important outbreak response considerations, particularly when investigating a previously unknown infectious disease threat. The Checklist was developed by the National Microbiology Laboratory of Canada in collaboration with provincial/territorial, national and international laboratory experts, including the Canadian Public Health Laboratory Network, and the Global Health Security Action Group Laboratory Network. While the Checklist was initially designed to reflect lessons learned through National Microbiology Laboratory participation in extended national and international outbreak responses (e.g. Zika virus epidemic [2015-2016], Ebola virus epidemic, West Africa [2014-2016]), the importance of optimizing laboratory response coordination has only been underscored by the ongoing challenges presented by the coronavirus disease 2019 (COVID-19) pandemic response requirements. The Checklist identifies five highly interdependent laboratory response themes, each of which encompasses multiple considerations that may be critical to a coordinated, strategic outbreak response. As such, the comprehensive review of Checklist considerations by responding laboratory organizations may provide a valuable opportunity to quickly detect key response considerations and interdependencies, and mitigate risks with the potential to impact public health action.