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.

Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories.

With emergence of pandemic COVID-19, rapid and accurate diagnostic testing is essential. This study compared laboratory-developed tests (LDTs) used for the detection of SARS-CoV-2 in Canadian hospital and public health laboratories, and some commercially available real-time RT-PCR assays. Overall, analytical sensitivities were equivalent between LDTs and most commercially available methods.

A Web-Based System for Mapping Laboratory Networks: Analysis of GLaDMap Application.

Public health emergencies such as H1N1 and SARS pandemics have demonstrated and validated the necessity of a strong and cohesive laboratory response system that is able to respond to threats in an efficient and timely manner. Individual laboratories, through connection with other laboratories or networks, are able to enhance their capacity for preparedness and response to emergencies. Efficient networks often establish standards and maintain best practices within member laboratories. The Global Laboratory Directory Mapping tool (GLaDMap) supports the efforts of laboratory networks to improve their connectivity by providing a simple and efficient tool to profile laboratories by geographic location, function or expertise. The purpose of this paper is to evaluate the effectiveness of the GLaDMap search tool and the completeness of the descriptive content of networks and laboratories that are currently contained within the GLaDMap database. We determined the extent of information volunteered and how the system is being used. Although the system aims to attract an array of users from around the globe, our analysis reveals minimal participation and information sharing and that the low profile participation rate limits the tool's functionality. The Global Laboratory Directory platform has addressed barriers to participation by adding optional functionality such as restricted access to laboratory profiles to protect private information and by implementing additional functional applications complementary to GLaDMap.

The limitations of point of care testing for pandemic influenza: what clinicians and public health professionals need to know.

As the world prepares for the next influenza pandemic, governments have made significant funding commitments to vaccine development and antiviral stockpiling. While these are essential components to pandemic response, rapid and accurate diagnostic testing remains an often neglected cornerstone of pandemic influenza preparedness. Clinicians and Public Health Practitioners need to understand the benefits and drawbacks of different influenza tests in both seasonal and pandemic settings. Culture has been the traditional gold standard for influenza diagnosis but requires from 1-10 days to generate a positive result, compared to nucleic acid detection methods such as real time reverse transcriptase polymerase chain reaction (RT-PCR). Although the currently available rapid antigen detection kits can generate results in less than 30 minutes, their sensitivity is suboptimal and they are not recommended for the detection of novel influenza viruses. Until point-of-care (POC) tests are improved, PILPN recommends that the best option for pandemic influenza preparation is the enhancement of nucleic acid-based testing capabilities across Canada.

Household transmission of SARS, 2003.

BACKGROUND: In the 2003 outbreak in Toronto (in Ontario, Canada) of severe acute respiratory syndrome (SARS), about 20% of cases resulted from household transmission. The purpose of our study was to determine characteristics associated with the transmission of SARS within households. METHODS: A retrospective cohort of SARS-affected households was studied to determine risk factors for household transmission. Questionnaires addressed characteristics of the index case, the household and behaviours among household members. Potential risk factors for secondary transmission of infection were assessed in regression models appropriate to the outcome (secondary cases) and nonindependence of household members. RESULTS: The 74 households that participated included 18 secondary cases and 158 uninfected household members in addition to the 74 index cases. The household secondary attack rate was 10.2% (95% confidence interval [CI] 6.7%-23.5%). There was a linear association between the time the index patient spent at home after symptom onset and the secondary attack rate. Infected health care workers who were index cases had lower rates of household transmission. INTERPRETATION: SARS transmission in households is complex and increases with the length of time an ill person spends at home. Risk of transmission was lower when the index case was a health care worker. Rapid case identification is the public health measure most useful in minimizing exposure in the home.

Risk of ruling out severe acute respiratory syndrome by ruling in another diagnosis: variable incidence of atypical bacteria coinfection based on diagnostic assays.

BACKGROUND: Severe acute respiratory syndrome (SARS) caused the first epidemic of the 21st century and continues to threaten the global community. OBJECTIVE: To assess the incidence of coinfection in patients confirmed to have SARS-associated coronavirus (SARS-CoV) infection, and thus, to determine the risk of ruling out SARS by ruling in another diagnosis. METHODS: The present report is a retrospective study evaluating the incidence and impact of laboratory-confirmed SARS-CoV and other pulmonary pathogens in 117 patients. These patients were evaluated in a Toronto, Ontario, community hospital identified as the epicentre for the second SARS outbreak. RESULTS: Coinfection with other pulmonary pathogens occurred in patients with SARS. Seventy-three per cent of the patient population evaluated had laboratory-confirmed SARS-CoV infection. Serology showing acute or recent Chlamydophila pneumoniae or Mycoplasma pneumoniae infection revealed an incidence of 30% and 9%, respectively, in those with SARS. These rates are similar to previously published studies on coinfection in pneumonia. All nucleic acid diagnostic assays were negative for C pneumoniae and M pneumoniae in respiratory samples from patients with SARS having serological evidence for these atypical pathogens. CONCLUSIONS: Diagnostic assays for well-recognized pulmonary pathogens have limitations, and ruling out SARS-CoV by ruling in another pulmonary pathogen carries significant risk. Despite positive serology for atypical pathogens, in a setting where clinical suspicion for SARS is high, specific tests for SARS should be performed to confirm or exclude a diagnosis.