Publications by authors named "Sharmistha Mishra"

106 Publications

Exploring the dynamics of workplace typologies for sex workers in Eastern Ukraine.

Glob Public Health 2021 Aug 17:1-20. Epub 2021 Aug 17.

Institute for Global Public Health, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.

We examine the typologies of workplaces for sex workers in Dnipro, Ukraine as part of the larger Dynamics Study, which explores the influence of conflict on sex work. We conducted a cross-sectional survey with 560 women from September 2017 to October 2018. The results of our study demonstrate a diverse sex work environment with heterogeneity across workplace typologies in terms of remuneration, workload, and safety. Women working in higher prestige typologies earned a higher hourly wage, however client volume also varied which resulted in comparable monthly earnings from sex work across almost all workplace types. While sex workers in Dnipro earn a higher monthly wage than the city mean, they also report experiencing high rates of violence and a lack of personal safety at work. Sex workers in all workplaces, with the exception of those working in art clubs, experienced physical and sexual violence perpetrated by law enforcement officers and sex partners. By understanding more about sex work workplaces, programmes may be better tailored to meet the needs of sex workers and respond to changing work environments due to ongoing conflict and COVID-19 pandemic.
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http://dx.doi.org/10.1080/17441692.2021.1965180DOI Listing
August 2021

Déterminants individuels et sociaux du test de dépistage du SRAS-CoV-2 et de l’obtention d’un résultat positif en Ontario, au Canada: une étude populationnelle.

CMAJ 2021 08;193(32):E1261-E1276

ICES Central (Sundaram, Calzavara, Hamilton, Djebli, Rosella, Watson, H. Chen, B. Chen, Kwong); Département de médecine (Mishra, Chan); Institut de gestion, d'évaluation et de politiques de santé (Mishra, Chan); Institut des sciences médicales (Mishra); École de santé publique Dalla Lana (Kustra, Chan, Hamilton, Djebli, Rosella, Watson, H. Chen, Kwong); Département des sciences statistiques (Kustra); Département de médecine familiale et communautaire (Kwong), Université de Toronto; MAP Centre for Urban Health Solutions (Mishra), Institut du savoir Li Ka Shing, Hôpital St. Michael, Unity Health Toronto; Centre des sciences de la santé Sunnybrook (Chan); Santé publique Ontario (Kwong, H. Chen); Toronto, Ont.; Département d'épidémiologie (Baral), École de santé publique Bloomberg de l'Université Johns Hopkins, Baltimore, Md.

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http://dx.doi.org/10.1503/cmaj.202608-fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386493PMC
August 2021

Increasing concentration of COVID-19 by socioeconomic determinants and geography in Toronto, Canada: an observational study.

Ann Epidemiol 2021 Jul 25. Epub 2021 Jul 25.

St. Michael's Hospital, Unity Health Toronto, Toronto, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada; ICES, Toronto, Canada; Public Health Ontario, Toronto, Canada; Department of Family and Community Medicine, Faculty of Medicine, University of Toronto, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto, Canada; Division of Infectious Diseases, Sunnybrook Health Sciences, University of Toronto, Toronto, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada; Toronto Public Health, City of Toronto, Toronto, Canada; Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Canada; Departments of Community Health Sciences and Family Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada; Capacity Planning and Analytics Division, Ontario Ministry of Health, Toronto, Canada; Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, United States.

Background: Inequities in the burden of COVID-19 were observed early in Canada and around the world suggesting economically marginalized communities faced disproportionate risks. However, there has been limited systematic assessment of how heterogeneity in risks has evolved in large urban centers over time.

Purpose: To address this gap, we quantified the magnitude of risk heterogeneity in Toronto, Ontario from January-November, 2020 using a retrospective, population-based observational study using surveillance data.

Methods: We generated epidemic curves by social determinants of health (SDOH) and crude Lorenz curves by neighbourhoods to visualize inequities in the distribution of COVID-19 and estimated Gini coefficients. We examined the correlation between SDOH using Pearson-correlation coefficients.

Results: Gini coefficient of cumulative cases by population size was 0.41 (95% confidence interval [CI]:0.36-0.47) and estimated for: household income (0.20, 95%CI: 0.14-0.28); visible minority (0.21, 95%CI:0.16-0.28); recent immigration (0.12, 95%CI:0.09-0.16); suitable housing (0.21, 95%CI:0.14-0.30); multi-generational households (0.19, 95%CI:0.15-0.23); and essential workers (0.28, 95%CI:0.23-0.34).

Conclusions: There was rapid epidemiologic transition from higher to lower income neighbourhoods with Lorenz curve transitioning from below to above the line of equality across SDOH. Moving forward necessitates integrating programs and policies addressing socioeconomic inequities and structural racism into COVID-19 prevention and vaccination programs.
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http://dx.doi.org/10.1016/j.annepidem.2021.07.007DOI Listing
July 2021

A disproportionate epidemic: COVID-19 cases and deaths among essential workers in Toronto, Canada.

Ann Epidemiol 2021 Jul 24;63:63-67. Epub 2021 Jul 24.

St. Michael's Hospital, University of Toronto, Toronto, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada. Electronic address:

Shelter-in-place mandates and closure of nonessential businesses have been central to COVID19 response strategies including in Toronto, Canada. Approximately half of the working population in Canada are employed in occupations that do not allow for remote work suggesting potentially limited impact of some of the strategies proposed to mitigate COVID-19 acquisition and onward transmission risks and associated morbidity and mortality. We compared per-capita rates of COVID-19 cases and deaths from January 23, 2020 to January 24, 2021, across neighborhoods in Toronto by proportion of the population working in essential services. We used person-level data on laboratory-confirmed COVID-19 community cases and deaths, and census data for neighborhood-level attributes. Cumulative per-capita rates of COVID-19 cases and deaths were 3.3-fold and 2.5-fold higher, respectively, in neighborhoods with the highest versus lowest concentration of essential workers. Findings suggest that the population who continued to serve the essential needs of society throughout COVID-19 shouldered a disproportionate burden of transmission and deaths. Taken together, results signal the need for active intervention strategies to complement restrictive measures to optimize both the equity and effectiveness of COVID-19 responses.
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http://dx.doi.org/10.1016/j.annepidem.2021.07.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8435380PMC
July 2021

The burden of hand, foot, and mouth disease among children under different vaccination scenarios in China: a dynamic modelling study.

BMC Infect Dis 2021 Jul 5;21(1):650. Epub 2021 Jul 5.

School of Public Health, Fudan University, Shanghai, 200032, China.

Background: Hand, foot, and mouth disease (HFMD) is a common illness in young children. A monovalent vaccine has been developed in China protecting against enterovirus-71, bivalent vaccines preventing HFMD caused by two viruses are under development.

Objective: To predict and compare the incidence of HFMD under different vaccination scenarios in China.

Methods: We developed a compartmental model to capture enterovirus transmission and the natural history of HFMD in children aged 0-5, and calibrated to reported cases in the same age-group from 2015 to 2018. We compared the following vaccination scenarios: different combinations of monovalent and bivalent vaccine; a program of constant vaccination to that of pulse vaccination prior to seasonal outbreaks.

Results: We estimate 1,982,819, 2,258,846, 1,948,522 and 2,398,566 cases from 2015 to 2018. Increased coverage of monovalent vaccine from 0 to 80% is predicted to decrease the cases by 797,262 (49.1%). Use of bivalent vaccine at an 80% coverage level would decrease the cases by 828,560. Use of a 2.0× pulse vaccination for the bivalent vaccine in addition to 80% coverage would reduce cases by over one million. The estimated R for HFMD in 2015-2018 was 1.08, 1.10, 1.35 and 1.17.

Conclusions: Our results point to the benefit of bivalent vaccine and using a pulse vaccination in specific months over routine vaccination. Other ways to control HFMD include isolation of patients in the early stage of dissemination, more frequent hand-washing and ventilation, and better treatment options for patients.
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http://dx.doi.org/10.1186/s12879-021-06157-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8259139PMC
July 2021

Patient perspectives on the implementation of routinised syphilis screening with HIV viral load testing: Qualitative process evaluation of the Enhanced Syphilis Screening Among HIV-positive Men trial.

BMC Health Serv Res 2021 Jun 30;21(1):625. Epub 2021 Jun 30.

MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, M5B 1W8, Toronto, Ontario, Canada.

Background: Syphilis infections have been on the rise, affecting men living with HIV in urban centres disproportionately. Since individuals in HIV care undergo routine blood testing, HIV clinics provide practical opportunities to conduct regular and frequent syphilis testing. Following the implementation of a routine syphilis testing intervention in HIV outpatient clinics, we conducted a qualitative process evaluation of patient experiences to measure patient acceptability, barriers to implementation, and facilitators of successful uptake.

Methods: Upon completion of the trial, which took place at four HIV outpatient clinics in Toronto and Ottawa, Canada, we recruited male patients attending these clinics from November 2017 to April 2018. Interviews were conducted on-site and were audio-recorded and transcribed verbatim. All participants provided written informed consent. Interview data were analyzed using grounded theory, assessing qualitative modulators of effective uptake of routinised syphilis testing.

Results: A total of 21 male patients were interviewed. Overall, interviewees found the clinical intervention acceptable, endorsing the practice of routinising syphilis testing alongside regular viral load bloodwork. Some men preferred, based on their self-assessment of syphilis risk, to opt out of testing; we considered this as a potential barrier to uptake of population-wide routinised syphilis testing. Interviewees also identified multiple facilitators of successful uptake, including the de-stigmatising of STI testing as a consequence of the universal nature of routinised testing. Participants recommended a routinised syphilis screening intervention to give patients peace of mind surrounding their sexual health. Participants identified HIV care clinics as comfortable and efficient locations to offer testing.

Conclusions: Overall, most men were in support of implementing routinised syphilis testing as part of standard HIV care. From the patient perspective, HIV care clinics are convenient places to be tested for syphilis, and the routine approach was viewed to have a de-stigmatisng effect on syphilis testing.

Trial Registration: ClinicalTrials.gov NCT02019043; registered December 23, 2013.
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http://dx.doi.org/10.1186/s12913-021-06602-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243864PMC
June 2021

Estimating the epidemic consequences of HIV prevention gaps among key populations.

J Int AIDS Soc 2021 Jul;24 Suppl 3:e25739

Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA.

Introduction: HIV epidemic appraisals are used to characterize heterogeneity and inequities in the context of the HIV pandemic and the response. However, classic measures used in appraisals have been shown to underestimate disproportionate risks of onward transmission, particularly among key populations. In response, a growing number of modelling studies have quantified the consequences of unmet prevention and treatment needs (prevention gaps) among key populations as a transmission population attributable fraction over time (tPAF ). To aid its interpretation and use by programme implementers and policy makers, we outline and discuss a conceptual framework for understanding and estimating the tPAF via transmission modelling as a measure of onward transmission risk from HIV prevention gaps; and discuss properties of the tPAF .

Discussion: The distribution of onward transmission risks may be defined by who is at disproportionate risk of onward transmission, and under which conditions. The latter reflects prevention gaps, including secondary prevention via treatment: the epidemic consequences of which may be quantified by the tPAF . Steps to estimating the tPAF include parameterizing the acquisition and onward transmission risks experienced by the subgroup of interest, defining the most relevant counterfactual scenario, and articulating the time-horizon of analyses and population among whom to estimate the relative difference in cumulative transmissions; such steps could reflect programme-relevant questions about onward transmission risks. Key properties of the tPAF include larger onward transmission risks over longer time-horizons; seemingly mutually exclusive tPAF measures summing to greater than 100%; an opportunity to quantify the magnitude of disproportionate onward transmission risks with a per-capita tPAF ; and that estimates are conditional on what has been achieved so far in reducing prevention gaps and maintaining those conditions moving forward as the status quo.

Conclusions: The next generation of HIV epidemic appraisals has the potential to support a more specific HIV response by characterizing heterogeneity in disproportionate risks of onward transmission which are defined and conditioned on the past, current and future prevention gaps across subsets of the population.
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http://dx.doi.org/10.1002/jia2.25739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242976PMC
July 2021

Routinised Syphilis Screening among Men Living with HIV: A stepped wedge cluster randomised controlled trial.

Clin Infect Dis 2021 Jun 27. Epub 2021 Jun 27.

Public Health Ontario Laboratories, Public Health Ontario, Toronto, Ontario, Canada.

Background: Frequent syphilis screening may increase early detection and decrease transmission. We implemented an opt-out clinic-based intervention pairing syphilis tests with routine HIV viral load testing. The primary objective was to determine the degree to which this intervention increased the detection of early syphilis.

Methods: The Enhanced Syphilis Screening among HIV-positive Men (ESSAHM) Trial was a stepped wedge cluster-randomised controlled trial involving four urban HIV clinics in Ontario, Canada, from 2015 to 2017. Population: HIV-positive adult males. Intervention (I): standing orders for syphilis serological testing with viral loads. Control (C): usual practice. Outcome: early syphilis diagnosis. We obtained test results via linkage with the centralized provincial laboratory and defined cases using a standardized clinical worksheet and medical chart review. We employed a generalized linear mixed model with a logit link to estimate odds ratios (OR) and 95% confidence intervals (CI) of the intervention.

Findings: 3,895 men were followed over 7,471 person-years (PY). The mean number of syphilis tests increased from 0.53 to 2.02 tests per person per year. There were 217 new diagnoses of syphilis (C: 81; I: 136), for which 147 (68%) were cases of early syphilis (C:61 (75%); I:86 (63%)). The annualized proportion with newly-detected early syphilis increased from 0.009 to 0.032 with implementation of the intervention; the corresponding time-adjusted OR was 1.25 (CI 0.71, 2.20).

Interpretation: The implementation of standing orders for syphilis testing with HIV viral loads was feasible and increased testing yet produced less-than-expected increases in case detection compared to past uncontrolled pre-post trials.
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http://dx.doi.org/10.1093/cid/ciab582DOI Listing
June 2021

SARS-CoV-2 variants and considerations of inferring causality on disease severity.

Lancet Infect Dis 2021 Jun 22. Epub 2021 Jun 22.

Department of Medicine, St Michael's Hospital, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1016/S1473-3099(21)00338-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219487PMC
June 2021

Individual and social determinants of SARS-CoV-2 testing and positivity in Ontario, Canada: a population-wide study.

CMAJ 2021 05 27;193(20):E723-E734. Epub 2021 Apr 27.

ICES Central (Sundaram, Calzavara, Hamilton, Djebli, Rosella, Watson, H. Chen, B. Chen, Kwong); Department of Medicine (Mishra, Chan); Institute of Health Policy, Management and Evaluation (Mishra, Chan); Institute of Medical Science (Mishra); Dalla Lana School of Public Health (Kustra, Chan, Hamilton, Djebli, Rosella, Watson, H. Chen, Kwong); Department of Statistical Sciences (Kustra); and Department of Family and Community Medicine (Kwong), University of Toronto; MAP Centre for Urban Health Solutions (Mishra), Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto; Sunnybrook Health Sciences Centre (Chan); Public Health Ontario (Kwong, H. Chen); University Health Network (Kwong), Toronto, Ont.; Department of Epidemiology (Baral), Johns Hopkins Bloomberg School of Public Health, Baltimore, Md

Background: Optimizing the public health response to reduce the burden of COVID-19 necessitates characterizing population-level heterogeneity of risks for the disease. However, heterogeneity in SARS-CoV-2 testing may introduce biased estimates depending on analytic design. We aimed to explore the potential for collider bias in a large study of disease determinants, and evaluate individual, environmental and social determinants associated with SARS-CoV-2 testing and diagnosis among residents of Ontario, Canada.

Methods: We explored the potential for collider bias and characterized individual, environmental and social determinants of being tested and testing positive for SARS-CoV-2 infection using cross-sectional analyses among 14.7 million community-dwelling people in Ontario, Canada. Among those with a diagnosis, we used separate analytic designs to compare predictors of people testing positive versus negative; symptomatic people testing positive versus testing negative; and people testing positive versus people not testing positive (i.e., testing negative or not being tested). Our analyses included tests conducted between Mar. 1 and June 20, 2020.

Results: Of 14 695 579 people, we found that 758 691 were tested for SARS-CoV-2, of whom 25 030 (3.3%) had a positive test result. The further the odds of testing from the null, the more variability we generally observed in the odds of diagnosis across analytic design, particularly among individual factors. We found that there was less variability in testing by social determinants across analytic designs. Residing in areas with the highest household density (adjusted odds ratio [OR] 1.86, 95% confidence interval [CI] 1.75-1.98), highest proportion of essential workers (adjusted OR 1.58, 95% CI 1.48-1.69), lowest educational attainment (adjusted OR 1.33, 95% CI 1.26-1.41) and highest proportion of recent immigrants (adjusted OR 1.10, 95% CI 1.05-1.15) were consistently related to increased odds of SARS-CoV-2 diagnosis regardless of analytic design.

Interpretation: Where testing is limited, our results suggest that risk factors may be better estimated using population comparators rather than test-negative comparators. Optimizing COVID-19 responses necessitates investment in and sufficient coverage of structural interventions tailored to heterogeneity in social determinants of risk, including household crowding, occupation and structural racism.
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http://dx.doi.org/10.1503/cmaj.202608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8177943PMC
May 2021

Cryptococcose disséminée chez une greffée rénale de longue date.

CMAJ 2021 Apr;193(16):E585-E588

Divisions de médecine interne générale (Li), de néphrologie (Khan) et d'infectiologie (Mishra, Zhabokritsky), Département de médecine, Faculté de médecine, Université de Toronto; Division d'infectiologie (Mishra), Service de médecine, Hôpital St. Michael, Unity Health Toronto, Toronto, Ont.

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http://dx.doi.org/10.1503/cmaj.200825-fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8084560PMC
April 2021

Simulation-Based Estimation of SARS-CoV-2 Infections Associated With School Closures and Community-Based Nonpharmaceutical Interventions in Ontario, Canada.

JAMA Netw Open 2021 03 1;4(3):e213793. Epub 2021 Mar 1.

Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada.

Importance: Resurgent COVID-19 cases have resulted in the reinstitution of nonpharmaceutical interventions, including school closures, which can have adverse effects on families. Understanding the associations of school closures with the number of incident and cumulative COVID-19 cases is critical for decision-making.

Objective: To estimate the association of schools being open or closed with the number of COVID-19 cases compared with community-based nonpharmaceutical interventions.

Design, Setting, And Participants: This decision analytical modelling study developed an agent-based transmission model using a synthetic population of 1 000 000 individuals based on the characteristics of the population of Ontario, Canada. Members of the synthetic population were clustered into households, neighborhoods, or rural districts, cities or rural regions, day care facilities, classrooms (ie, primary, elementary, or high school), colleges or universities, and workplaces. Data were analyzed between May 5, 2020, and October 20, 2020.

Exposures: School reopening on September 15, 2020, vs schools remaining closed under different scenarios for nonpharmaceutical interventions.

Main Outcomes And Measures: Incident and cumulative COVID-19 cases between September 1, 2020, and October 31, 2020.

Results: Among 1 000 000 simulated individuals, the percentage of infections among students and teachers acquired within schools was less than 5% across modeled scenarios. Incident COVID-19 case numbers on October 31, 2020, were 4414 (95% credible interval [CrI], 3491-5382) cases in the scenario with schools remaining closed and 4740 (95% CrI, 3863-5691) cases in the scenario for schools reopening, with no other community-based nonpharmaceutical intervention. In scenarios with community-based nonpharmaceutical interventions implemented, the incident case numbers on October 31 were 714 (95% CrI, 568-908) cases for schools remaining closed and 780 (95% CrI, 580-993) cases for schools reopening. When scenarios applied the case numbers observed in early October in Ontario, the cumulative case numbers were 777 (95% CrI, 621-993) cases for schools remaining closed and 803 (95% CrI, 617-990) cases for schools reopening. In scenarios with implementation of community-based interventions vs no community-based interventions, there was a mean difference of 39 355 cumulative COVID-19 cases by October 31, 2020, while keeping schools closed vs reopening them yielded a mean difference of 2040 cases.

Conclusions And Relevance: This decision analytical modeling study of a synthetic population of individuals in Ontario, Canada, found that most COVID-19 cases in schools were due to acquisition in the community rather than transmission within schools and that the changes in COVID-19 case numbers associated with school reopenings were relatively small compared with the changes associated with community-based nonpharmaceutical interventions.
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http://dx.doi.org/10.1001/jamanetworkopen.2021.3793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8013816PMC
March 2021

Decentralizing PrEP delivery: Implementation and dissemination strategies to increase PrEP uptake among MSM in Toronto, Canada.

PLoS One 2021 18;16(3):e0248626. Epub 2021 Mar 18.

Division of Infectious Diseases, St. Michael's Hospital, Toronto, Ontario, Canada.

Pre-exposure prophylaxis (PrEP) is traditionally prescribed by HIV specialist physicians. Given finite specialist resources, there is a need to scale up PrEP delivery by decentralizing services via other healthcare professionals. We aimed to assess the feasibility of delivering PrEP to men who have sex with men (MSM) through primary care physicians and sexual health clinic nurses. We piloted a multi-component, implementation and dissemination research program to increase provision of PrEP through primary care physicians and sexual health clinic nurses in Toronto, Canada. Community-based organizations (CBOs) provided prospective participants with information cards that contained links to an online module on engaging providers in a conversation about PrEP. In our patient-initiated continuing medical education (PICME) strategy, participants saw their family doctors and gave them the card, which also contained a link to a Continuing Medical Education module. In the nurse-led strategy, participants visited one of two participating clinics to obtain PrEP. We administered an optional online questionnaire to patients and providers at baseline and six months. CBOs distributed 3043 cards. At least 339 men accessed the online module and 196 completed baseline questionnaires. Most (55%) intended to visit nurses while 21% intended to consult their physicians. Among 45 men completing follow-up questionnaires at 6 months, 31% reported bringing cards to their physicians and obtaining PrEP through them; sexual health clinics delivered PrEP to 244 patients. Participants who went through the PICME approach reported no changes in relationships with their providers. Nurses showed fidelity to PrEP prescribing guidelines. Nurse-led PrEP and patient-initiated continuing medical education (PICME) for primary care physicians are feasible strategies to increase PrEP uptake. Nurse-led PrEP delivery was preferred by most patients.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0248626PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971529PMC
March 2021

Implementing Implementation Research: Teaching Implementation Research to HIV Researchers.

Curr HIV/AIDS Rep 2021 06 11;18(3):186-197. Epub 2021 Mar 11.

Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA.

Purpose Of Review: Given the growth in HIV-related implementation research, there is a need to expand the workforce and rigor through implementation science (IS) training and mentorship. Our objective is to review IS training opportunities for HIV-focused researchers and describe the approach and lessons learned from a recent HIV-related implementation research training initiative.

Recent Findings: IS training opportunities range from degree programs to short- and longer-term professional development institutes and community-focused institutional trainings. Until recently, there have not been extensive dedicated opportunities for implementation research training for HIV-focused investigators. To meet this gap, an inter-Center for AIDS Research IS Fellowship for early-stage investigators was launched in 2019, building on lessons learned from dissemination and implementation training programs. Key components of the HIV-focused IS fellowship include didactic training, mentorship, grant-writing, and development of HIV-IS collaborative networks. Fellows to-date were two-thirds junior faculty and one-third post-doctoral fellows, the majority (69%) with prior public health training. Perceived value of the program was high, with a median rating of 9 [IQR 8-9] on a 10-point scale. Overall, 22/27 (81%) Fellows from the first cohort submitted IS-related grants within 12 months of Fellowship completion, and by 1 year 13 grants had been funded among 10 investigators, 37% overall among Fellows. Mentors identified framing of IS questions as the top-ranked training priority for HIV-investigators. Increasing knowledge of the utility of IS may support more grants focused on optimal implementation of HIV treatment and prevention strategies. Experiences from mentors and trainees engaged in an IS-focused fellowship for HIV investigators demonstrate the demand and value of a dedicated training program and reinforce the importance of mentorship.
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http://dx.doi.org/10.1007/s11904-021-00551-4DOI Listing
June 2021

Cohort profile: St. Michael's Hospital Tuberculosis Database (SMH-TB), a retrospective cohort of electronic health record data and variables extracted using natural language processing.

PLoS One 2021 3;16(3):e0247872. Epub 2021 Mar 3.

Department of Medicine, University of Toronto, Toronto, Ontario, Canada.

Background: Tuberculosis (TB) is a major cause of death worldwide. TB research draws heavily on clinical cohorts which can be generated using electronic health records (EHR), but granular information extracted from unstructured EHR data is limited. The St. Michael's Hospital TB database (SMH-TB) was established to address gaps in EHR-derived TB clinical cohorts and provide researchers and clinicians with detailed, granular data related to TB management and treatment.

Methods: We collected and validated multiple layers of EHR data from the TB outpatient clinic at St. Michael's Hospital, Toronto, Ontario, Canada to generate the SMH-TB database. SMH-TB contains structured data directly from the EHR, and variables generated using natural language processing (NLP) by extracting relevant information from free-text within clinic, radiology, and other notes. NLP performance was assessed using recall, precision and F1 score averaged across variable labels. We present characteristics of the cohort population using binomial proportions and 95% confidence intervals (CI), with and without adjusting for NLP misclassification errors.

Results: SMH-TB currently contains retrospective patient data spanning 2011 to 2018, for a total of 3298 patients (N = 3237 with at least 1 associated dictation). Performance of TB diagnosis and medication NLP rulesets surpasses 93% in recall, precision and F1 metrics, indicating good generalizability. We estimated 20% (95% CI: 18.4-21.2%) were diagnosed with active TB and 46% (95% CI: 43.8-47.2%) were diagnosed with latent TB. After adjusting for potential misclassification, the proportion of patients diagnosed with active and latent TB was 18% (95% CI: 16.8-19.7%) and 40% (95% CI: 37.8-41.6%) respectively.

Conclusion: SMH-TB is a unique database that includes a breadth of structured data derived from structured and unstructured EHR data by using NLP rulesets. The data are available for a variety of research applications, such as clinical epidemiology, quality improvement and mathematical modeling studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0247872PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7928444PMC
March 2021

Assessing the Potential Impact of Disruptions Due to COVID-19 on HIV Among Key and Lower-Risk Populations in the Largest Cities of Cameroon and Benin.

J Acquir Immune Defic Syndr 2021 07;87(3):899-911

MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom.

Background: The COVID-19 pandemic indirectly impacts HIV epidemiology in Central/West Africa. We estimated the potential impact of COVID-19-related disruptions to HIV prevention/treatment services and sexual partnerships on HIV incidence and HIV-related deaths among key populations including female sex workers (FSW), their clients, men who have sex with men, and overall.

Setting: Yaoundé (Cameroon) and Cotonou (Benin).

Methods: We used mathematical models of HIV calibrated to city population-specific and risk population-specific demographic/behavioral/epidemic data. We estimated the relative change in 1-year HIV incidence and HIV-related deaths for various disruption scenarios of HIV prevention/treatment services and decreased casual/commercial partnerships, compared with a scenario without COVID-19.

Results: A 50% reduction in condom use in all partnerships over 6 months would increase 1-year HIV incidence by 39%, 42%, 31%, and 23% among men who have sex with men, FSW, clients, and overall in Yaoundé, respectively, and 69%, 49%, and 23% among FSW, clients, and overall, respectively, in Cotonou. Combining a 6-month interruption of ART initiation and 50% reduction in HIV prevention/treatment use would increase HIV incidence by 50% and HIV-related deaths by 20%. This increase in HIV infections would be halved by a simultaneous 50% reduction in casual and commercial partnerships.

Conclusions: Reductions in condom use after COVID-19 would increase infections among key populations disproportionately, particularly FSW in Cotonou, who need uninterrupted condom provision. Disruptions in HIV prevention/treatment services have the biggest impacts on HIV infections and deaths overall, only partially mitigated by equal reductions in casual/commercial sexual partnerships. Maintaining ART provision must be prioritized to minimize short-term excess HIV-related deaths.
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http://dx.doi.org/10.1097/QAI.0000000000002663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8191475PMC
July 2021

Disseminated cryptococcal infection in a patient with a remote renal transplant.

CMAJ 2021 Feb;193(6):E211-E214

Divisions of General Internal Medicine (Li), Nephrology (Khan) and Infectious Diseases (Mishra, Zhabokritsky), Department of Medicine, Faculty of Medicine, University of Toronto; Division of Infectious Diseases (Mishra), Department of Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, Ont.

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http://dx.doi.org/10.1503/cmaj.200825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954546PMC
February 2021

Mathematical modelling of the influence of serosorting on the population-level HIV transmission impact of pre-exposure prophylaxis.

AIDS 2021 06;35(7):1113-1125

MAP-Centre for Urban Health Solutions, St. Michael's Hospital, Unity Health Toronto.

Objectives: HIV pre-exposure prophylaxis (PrEP) may change serosorting patterns. We examined the influence of serosorting on the population-level HIV transmission impact of PrEP, and how impact could change if PrEP users stopped serosorting.

Design: We developed a compartmental HIV transmission model parameterized with bio-behavioural and HIV surveillance data among MSM in Canada.

Methods: We separately fit the model with serosorting and without serosorting [counterfactual; sero-proportionate mixing (random partner-selection proportional to availability by HIV status)], and reproduced stable HIV epidemics with HIV-prevalence 10.3-24.8%, undiagnosed fraction 4.9-15.8% and treatment coverage 82.5-88.4%. We simulated PrEP-intervention reaching stable pre-specified coverage by year-one and compared absolute difference in relative HIV-incidence reduction 10 years post-intervention (PrEP-impact) between models with serosorting vs. sero-proportionate mixing; and counterfactual scenarios when PrEP users immediately stopped vs. continued serosorting. We examined sensitivity of results to PrEP-effectiveness (44-99%; reflecting varying dosing or adherence levels) and coverage (10-50%).

Results: Models with serosorting predicted a larger PrEP-impact than models with sero-proportionate mixing under all PrEP-effectiveness and coverage assumptions [median (interquartile range): 8.1% (5.5-11.6%)]. PrEP users' stopping serosorting reduced PrEP-impact compared with when PrEP users continued serosorting: reductions in PrEP-impact were minimal [2.1% (1.4-3.4%)] under high PrEP-effectiveness (86-99%); however, could be considerable [10.9% (8.2-14.1%)] under low PrEP effectiveness (44%) and high coverage (30-50%).

Conclusion: Models assuming sero-proportionate mixing may underestimate population-level HIV-incidence reductions due to PrEP. PrEP-mediated changes in serosorting could lead to programmatically important reductions in PrEP-impact under low PrEP-effectiveness. Our findings suggest the need to monitor sexual mixing patterns to inform PrEP implementation and evaluation.
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http://dx.doi.org/10.1097/QAD.0000000000002826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8183492PMC
June 2021

Estimating the contribution of key populations towards HIV transmission in South Africa.

J Int AIDS Soc 2021 01;24(1):e25650

Population Health Sciences, University of Bristol, Bristol, United Kingdom.

Introduction: In generalized epidemic settings, there is insufficient understanding of how the unmet HIV prevention and treatment needs of key populations (KPs), such as female sex workers (FSWs) and men who have sex with men (MSM), contribute to HIV transmission. In such settings, it is typically assumed that HIV transmission is driven by the general population. We estimated the contribution of commercial sex, sex between men, and other heterosexual partnerships to HIV transmission in South Africa (SA).

Methods: We developed the "Key-Pop Model"; a dynamic transmission model of HIV among FSWs, their clients, MSM, and the broader population in SA. The model was parameterized and calibrated using demographic, behavioural and epidemiological data from national household surveys and KP surveys. We estimated the contribution of commercial sex, sex between men and sex among heterosexual partnerships of different sub-groups to HIV transmission over 2010 to 2019. We also estimated the efficiency (HIV infections averted per person-year of intervention) and prevented fraction (% IA) over 10-years from scaling-up ART (to 81% coverage) in different sub-populations from 2020.

Results: Sex between FSWs and their paying clients, and between clients with their non-paying partners contributed 6.9% (95% credibility interval 4.5% to 9.3%) and 41.9% (35.1% to 53.2%) of new HIV infections in SA over 2010 to 2019 respectively. Sex between low-risk groups contributed 59.7% (47.6% to 68.5%), sex between men contributed 5.3% (2.3% to 14.1%) and sex between MSM and their female partners contributed 3.7% (1.6% to 9.8%). Going forward, the largest population-level impact on HIV transmission can be achieved from scaling up ART to clients of FSWs (% IA = 18.2% (14.0% to 24.4%) or low-risk individuals (% IA = 20.6% (14.7 to 27.5) over 2020 to 2030), with ART scale-up among KPs being most efficient.

Conclusions: Clients of FSWs play a fundamental role in HIV transmission in SA. Addressing the HIV prevention and treatment needs of KPs in generalized HIV epidemics is central to a comprehensive HIV response.
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http://dx.doi.org/10.1002/jia2.25650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7855076PMC
January 2021

The Relationship Between the Global Burden of Influenza From 2017 to 2019 and COVID-19: Descriptive Epidemiological Assessment.

JMIR Public Health Surveill 2021 03 2;7(3):e24696. Epub 2021 Mar 2.

Department of Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.

Background: SARS-CoV-2 and influenza are lipid-enveloped viruses with differential morbidity and mortality but shared modes of transmission.

Objective: With a descriptive epidemiological framing, we assessed whether recent historical patterns of regional influenza burden are reflected in the observed heterogeneity in COVID-19 cases across regions of the world.

Methods: Weekly surveillance data reported by the World Health Organization from January 2017 to December 2019 for influenza and from January 1, 2020 through October 31, 2020, for COVID-19 were used to assess seasonal and temporal trends for influenza and COVID-19 cases across the seven World Bank regions.

Results: In regions with more pronounced influenza seasonality, COVID-19 epidemics have largely followed trends similar to those seen for influenza from 2017 to 2019. COVID-19 epidemics in countries across Europe, Central Asia, and North America have been marked by a first peak during the spring, followed by significant reductions in COVID-19 cases in the summer months and a second wave in the fall. In Latin America and the Caribbean, COVID-19 epidemics in several countries peaked in the summer, corresponding to months with the highest influenza activity in the region. Countries from regions with less pronounced influenza activity, including South Asia and sub-Saharan Africa, showed more heterogeneity in COVID-19 epidemics seen to date. However, similarities in COVID-19 and influenza trends were evident within select countries irrespective of region.

Conclusions: Ecological consistency in COVID-19 trends seen to date with influenza trends suggests the potential for shared individual, structural, and environmental determinants of transmission. Using a descriptive epidemiological framework to assess shared regional trends for rapidly emerging respiratory pathogens with better studied respiratory infections may provide further insights into the differential impacts of nonpharmacologic interventions and intersections with environmental conditions. Ultimately, forecasting trends and informing interventions for novel respiratory pathogens like COVID-19 should leverage epidemiologic patterns in the relative burden of past respiratory pathogens as prior information.
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http://dx.doi.org/10.2196/24696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7927952PMC
March 2021

Competing Health Risks Associated with the COVID-19 Pandemic and Response: A Scoping Review.

medRxiv 2021 Jan 8. Epub 2021 Jan 8.

Background: COVID-19 has rapidly emerged as a global public health threat with infections recorded in nearly every country. Responses to COVID-19 have varied in intensity and breadth, but generally have included domestic and international travel limitations, closure of non-essential businesses, and repurposing of health services. While these interventions have focused on testing, treatment, and mitigation of COVID-19, there have been reports of interruptions to diagnostic, prevention, and treatment services for other public health threats. We conducted a scoping review to characterize the impact of COVID-19 on HIV, tuberculosis, malaria, sexual and reproductive health, and malnutrition.

Methods: A scoping literature review was completed using searches of PubMed and preprint servers (medRxiv/bioRxiv) from January 1 to October 31 , 2020, using Medical Subject Headings (MeSH) terms related to SARS-CoV-2 or COVID-19 and HIV, tuberculosis, malaria, sexual and reproductive health, and malnutrition. Empiric studies reporting original data collection and mathematical models were included, and available data synthesized by region. Studies were excluded if they were not written in English.

Results: A total of 1604 published papers and 205 preprints met inclusion criteria, including 8.2% (132/1604) of published studies and 10.2% (21/205) of preprints: 7.3% (68/931) on HIV, 7.1% (24/339) on tuberculosis, 11.6% (26/224) on malaria, 7.8% (13/166) on sexual and reproductive health, and 12.1% (16/132) on malnutrition. Thematic results were similar across competing health risks, with substantial indirect effects of the COVID-19 pandemic and response on diagnostic, prevention, and treatment services for HIV, tuberculosis, malaria, sexual and reproductive health, and malnutrition.

Discussion: COVID-19 emerged in the context of existing public health threats that result in millions of deaths every year. Thus, effectively responding to COVID-19 while minimizing the negative impacts of COVID-19 necessitates innovation and integration of existing programs that are often siloed across health systems. Inequities have been a consistent driver of existing health threats; COVID-19 has worsened disparities, reinforcing the need for programs that address structural risks. Data reviewed here suggest that effective strengthening of health systems should include investment in public health with adequate funding to ensure continuity of care for emergent and existing public health threats.
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http://dx.doi.org/10.1101/2021.01.07.21249419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805463PMC
January 2021

Validating International Classification of Disease 10th Revision algorithms for identifying influenza and respiratory syncytial virus hospitalizations.

PLoS One 2021 7;16(1):e0244746. Epub 2021 Jan 7.

ICES, Toronto, Ontario, Canada.

Objective: Routinely collected health administrative data can be used to efficiently assess disease burden in large populations, but it is important to evaluate the validity of these data. The objective of this study was to develop and validate International Classification of Disease 10th revision (ICD -10) algorithms that identify laboratory-confirmed influenza or laboratory-confirmed respiratory syncytial virus (RSV) hospitalizations using population-based health administrative data from Ontario, Canada.

Study Design And Setting: Influenza and RSV laboratory data from the 2014-15, 2015-16, 2016-17 and 2017-18 respiratory virus seasons were obtained from the Ontario Laboratories Information System (OLIS) and were linked to hospital discharge abstract data to generate influenza and RSV reference cohorts. These reference cohorts were used to assess the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the ICD-10 algorithms. To minimize misclassification in future studies, we prioritized specificity and PPV in selecting top-performing algorithms.

Results: 83,638 and 61,117 hospitalized patients were included in the influenza and RSV reference cohorts, respectively. The best influenza algorithm had a sensitivity of 73% (95% CI 72% to 74%), specificity of 99% (95% CI 99% to 99%), PPV of 94% (95% CI 94% to 95%), and NPV of 94% (95% CI 94% to 95%). The best RSV algorithm had a sensitivity of 69% (95% CI 68% to 70%), specificity of 99% (95% CI 99% to 99%), PPV of 91% (95% CI 90% to 91%) and NPV of 97% (95% CI 97% to 97%).

Conclusion: We identified two highly specific algorithms that best ascertain patients hospitalized with influenza or RSV. These algorithms may be applied to hospitalized patients if data on laboratory tests are not available, and will thereby improve the power of future epidemiologic studies of influenza, RSV, and potentially other severe acute respiratory infections.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244746PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7790248PMC
May 2021

Validation of a Clinical Prediction Rule to Predict Asymptomatic Chlamydia and Gonorrhea Infections Among Internet-Based Testers.

Sex Transm Dis 2021 07;48(7):481-487

From the British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.

Background: Clinical prediction rules (CPRs) can be used in sexually transmitted infection (STI) testing environments to prioritize individuals at the highest risk of infection and optimize resource allocation. We previously derived a CPR to predict asymptomatic chlamydia and/or gonorrhea (CT/NG) infection among women and heterosexual men at in-person STI clinics based on 5 predictors. Population differences between clinic-based and Internet-based testers may limit the tool's application across settings. The primary objective of this study was to assess the validity, sensitivity, and overall performance of this CPR within an Internet-based testing environment (GetCheckedOnline.com).

Methods: We analyzed GetCheckedOnline online risk assessment and laboratory data from October 2015 to June 2019. We compared the STI clinic population used for CPR derivation (data previously published) and the GetCheckedOnline validation population using χ2 tests. Calibration and discrimination were assessed using the Hosmer-Lemeshow goodness-of-fit test and the area under the receiver operating curve, respectively. Sensitivity and the fraction of total screening tests offered were quantified for CPR-predicted risk scores.

Results: Asymptomatic CT/NG infection prevalence in the GetCheckedOnline population (n = 5478) was higher than in the STI clinic population (n = 10,437; 2.4% vs. 1.8%, P = 0.007). When applied to GetCheckedOnline, the CPR had reasonable calibration (Hosmer-Lemeshow, P = 0.90) and discrimination (area under the receiver operating characteristic, 0.64). By screening only individuals with total risk scores ≥4, we would detect 97% of infections and reduce screening by 14%.

Conclusions: The application of an existing CPR to detect asymptomatic CT/NG infection is valid within an Internet-based STI testing environment. Clinical prediction rules applied online can reduce unnecessary STI testing and optimize resource allocation within publicly funded health systems.
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http://dx.doi.org/10.1097/OLQ.0000000000001340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208089PMC
July 2021

Modeling the coronavirus disease 2019 pandemic: A comprehensive guide of infectious disease and decision-analytic models.

J Clin Epidemiol 2021 04 7;132:133-141. Epub 2020 Dec 7.

Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada; Toronto Health Economics and Technology Assessment (THETA) Collaborative, University Health Network, Toronto, Canada; Public Health Ontario, Toronto, Canada; ICES, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jclinepi.2020.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7837043PMC
April 2021

Leveraging epidemiological principles to evaluate Sweden's COVID-19 response.

Ann Epidemiol 2021 02 23;54:21-26. Epub 2020 Nov 23.

Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Harvard Medical School, Boston, MA.

In the response to COVID-19, countries have implemented response strategies along a continuum of population- and venue-level specificity ranging from suppression to mitigation strategies. Suppression strategies generally include population-wide shelter-in-place mandates or lockdowns, closure of nonessential physical venues, travel bans, testing and contact tracing, and quarantines. Sweden followed a mitigation strategy focused on risk-tailored approaches to mitigate specific acquisition risks among the elderly, minimizing the disruption to education and the delivery of other health care services, and recommendations for social distancing to minimize the disease burden. To date, Sweden has reported higher case counts and attributable mortality than other Scandinavian countries and lower than other Northern European countries. However, there are several limitations with comparison given heterogeneity in testing strategies, suspected and confirmed case definitions, and assessment of attributable mortality. The decisions in Sweden also reflect social priorities such as equity being a foundational principle of Swedish social systems. Consistently, in-person education for those aged less than 16 years continued throughout. Notably, the mitigation strategy did not eliminate the inequitable impacts of COVID-19 cases and mortality in Sweden with higher-exposure and generally lower-income occupations being associated with higher risks intersecting with these communities often residing in more dense multigenerational households. From January 1 to November 15, there has been a 1.8% increase in all-cause mortality in 2020 compared with the average of 2015-2019, representing an excess of 14.3 deaths per 100,000 population. However, the final assessment of excess deaths in Sweden in 2020 including stratification by age and integration of secular trends can only be calculated in the coming years. In response to increasing cases in the fall of 2020, Sweden has continued to leverage business-oriented regulations and public-oriented guidelines for social distancing rather than police-enforced mandates. Ultimately, pandemics present no winners. Countries have implemented a range of different COVID-19 prevention and mitigation strategies responsive to their own priorities and legal systems including equity and the balancing of competing health priorities. Given these varied approaches, countries that pursued elimination, suppression, or mitigation strategies can collaboratively learn from both successes and challenges of the different strategies to inform COVID-19 and future pandemic responses.
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http://dx.doi.org/10.1016/j.annepidem.2020.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7682427PMC
February 2021

Quantifying the Evolving Contribution of HIV Interventions and Key Populations to the HIV Epidemic in Yaoundé, Cameroon.

J Acquir Immune Defic Syndr 2021 04;86(4):396-405

Department of Infectious Disease Epidemiology, Imperial College London, HPTN Modelling Centre, London, United Kingdom.

Background: Key populations (KP) including men who have sex with men (MSM), female sex workers (FSW), and their clients are disproportionately affected by HIV in Sub-Saharan Africa. We estimated the evolving impact of past interventions and contribution of unmet HIV prevention/treatment needs of key populations and lower-risk groups to HIV transmission.

Setting: Yaoundé, Cameroon.

Methods: We parametrized and fitted a deterministic HIV transmission model to Yaoundé-specific demographic, behavioral, HIV, and intervention coverage data in a Bayesian framework. We estimated the fraction of incident HIV infections averted by condoms and antiretroviral therapy (ART) and the fraction of all infections over 10-year periods directly and indirectly attributable to sex within and between each risk group.

Results: Condom use and ART together may have averted 43% (95% uncertainty interval: 31-54) of incident infections over 1980-2018 and 72% (66-79) over 2009-2018. Most onward transmissions over 2009-2018 stemmed from sex between lower-risk individuals [47% (32-61)], clients [37% (23-51)], and MSM [35% (20-54)] with all their partners. The contribution of commercial sex decreased from 25% (8-49) over 1989-1998 to 8% (3-22) over 2009-2018, due to higher intervention coverage among FSW.

Conclusion: Condom use and recent ART scale-up mitigated the HIV epidemic in Yaoundé and changed the contribution of different partnerships to onward transmission over time. Findings highlight the importance of prioritizing HIV prevention and treatment for MSM and clients of FSW whose unmet needs now contribute most to onward transmission, while maintaining services that successfully reduced transmissions in the context of commercial sex.
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http://dx.doi.org/10.1097/QAI.0000000000002580DOI Listing
April 2021

Comprendre l’hétérogénéité pour guider la réponse de la santé publique à la COVID-19 au Canada.

CMAJ 2020 11;192(46):E1502-E1504

MAP Centre for Urban Health Solutions (Mishra), Institut du savoir Li Ka Shing, Hôpital St. Michael's, Réseau universitaire de santé de Toronto; Département de médecine (Mishra), Hôpital St. Michael's, Université de Toronto; Institut pour les politiques, la gestion et l'évaluation de la santé (Mishra), École Dalla Lana de santé publique, Université de Toronto; Institut de recherche en sciences cliniques (Kwong); Département de médecine familiale et communautaire (Kwong), Université de Toronto; École Dalla Lana de santé publique (Kwong), Université de Toronto; Division d'infectiologie (Chan), Département de médecine, Centre des sciences de la santé Sunnybrook; Division de la santé publique clinique et Institut pour les politiques, la gestion et l'évaluation de la santé (Chan), École Dalla Lana de santé publique, Université de Toronto, Toronto, Ont.; Département d'épidémiologie (Baral), Université Johns Hopkins, Baltimore, Md.; Institut du savoir Li Ka Shing (Baral), Hôpital St. Michael's, Toronto, Ont.

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http://dx.doi.org/10.1503/cmaj.201112-fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7682994PMC
November 2020

Estimating effective reproduction number using generation time versus serial interval, with application to covid-19 in the Greater Toronto Area, Canada.

Infect Dis Model 2020 1;5:889-896. Epub 2020 Nov 1.

Institute of Medical Science, University of Toronto, Canada.

Background: The effective reproduction number () is a critical measure of epidemic potential. () can be calculated in near real time using an incidence time series and the generation time distribution: the time between infection events in an infector-infectee pair. In calculating (), the generation time distribution is often approximated by the serial interval distribution: the time between symptom onset in an infector-infectee pair. However, while generation time must be positive by definition, serial interval can be negative if transmission can occur before symptoms, such as in covid-19, rendering such an approximation improper in some contexts.

Methods: We developed a method to infer the generation time distribution from parametric definitions of the serial interval and incubation period distributions. We then compared estimates of () for covid-19 in the Greater Toronto Area of Canada using: negative-permitting versus non-negative serial interval distributions, versus the inferred generation time distribution.

Results: We estimated the generation time of covid-19 to be Gamma-distributed with mean 3.99 and standard deviation 2.96 days. Relative to the generation time distribution, non-negative serial interval distribution caused overestimation of () due to larger mean, while negative-permitting serial interval distribution caused underestimation of () due to larger variance.

Implications: Approximation of the generation time distribution of covid-19 with non-negative or negative-permitting serial interval distributions when calculating () may result in over or underestimation of transmission potential, respectively.
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http://dx.doi.org/10.1016/j.idm.2020.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7604055PMC
November 2020

The role of case importation in explaining differences in early SARS-CoV-2 transmission dynamics in Canada-A mathematical modeling study of surveillance data.

Int J Infect Dis 2021 Jan 25;102:254-259. Epub 2020 Oct 25.

Department of Epidemiology, Biostatistics, and Occupational Health, School of Population and Global Health, McGill University, Montréal, Quebec, Canada. Electronic address:

Objective: The North American coronavirus disease-2019 (COVID-19) epidemic exhibited distinct early trajectories. In Canada, Quebec had the highest COVID-19 burden and its earlier March school break, taking place two weeks before those in other provinces, could have shaped early transmission dynamics.

Methods: We combined a semi-mechanistic model of SARS-CoV-2 transmission with detailed surveillance data from Quebec and Ontario (initially accounting for 85% of Canadian cases) to explore the impact of case importation and timing of control measures on cumulative hospitalizations.

Results: A total of 1544 and 1150 cases among returning travelers were laboratory-confirmed in Quebec and Ontario, respectively (symptoms onset ≤03-25-2020). Hospitalizations could have been reduced by 55% (95% CrI: 51%-59%) if no cases had been imported after Quebec's March break. However, if Quebec had experienced Ontario's number of introductions, hospitalizations would have only been reduced by 12% (95% CrI: 8%-16%). Early public health measures mitigated the epidemic spread as a one-week delay could have resulted in twice as many hospitalizations (95% CrI: 1.7-2.1).

Conclusion: Beyond introductions, factors such as public health preparedness, responses and capacity could play a role in explaining interprovincial differences. In a context where regions are considering lifting travel restrictions, coordinated strategies and proactive measures are to be considered.
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http://dx.doi.org/10.1016/j.ijid.2020.10.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585716PMC
January 2021

Prevalence and patterns of gender-based violence across adolescent girls and young women in Mombasa, Kenya.

BMC Womens Health 2020 10 12;20(1):229. Epub 2020 Oct 12.

Institute for Global Public Health, University of Manitoba, Winnipeg, Canada.

Background: We sought to estimate the prevalence and describe heterogeneity in experiences of gender-based violence (GBV) across subgroups of adolescent girls and young women (AGYW).

Methods: We used data from a cross-sectional bio-behavioural survey among 1299 AGYW aged 14-24 in Mombasa, Kenya in 2015. Respondents were recruited from hotspots associated with sex work, and self-selected into one of three subgroups: young women engaged in casual sex (YCS), young women engaged in transactional sex (YTS), and young women engaged in sex work (YSW). We compared overall and across subgroups: prevalence of lifetime and recent (within previous year) self-reported experience of physical, sexual, and police violence; patterns and perpetrators of first and most recent episode of physical and sexual violence; and factors associated with physical and sexual violence.

Results: The prevalences of lifetime and recent physical violence were 18.0 and 10.7% respectively. Lifetime and recent sexual violence respectively were reported by 20.5 and 9.8% of respondents. Prevalence of lifetime and recent experience of police violence were 34.7 and 25.8% respectively. All forms of violence were most frequently reported by YSW, followed by YTS and then YCS. 62%/81% of respondents reported having sex during the first episode of physical/sexual violence, and 48%/62% of those sex acts at first episode of physical/sexual violence were condomless. In the most recent episode of violence when sex took place levels of condom use remained low at 53-61%. The main perpetrators of violence were intimate partners for YCS, and both intimate partners and regular non-client partners for YTS. For YSW, first-time and regular paying clients were the main perpetrators of physical and sexual violence. Alcohol use, ever being pregnant and regular source of income were associated with physical and sexual violence though it differed by subgroup and type of violence.

Conclusions: AGYW in these settings experience high vulnerability to physical, sexual and police violence. However, AGYW are not a homogeneous group, and there are heterogeneities in prevalence and predictors of violence between subgroups of AGYW that need to be understood to design effective programmes to address violence.
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http://dx.doi.org/10.1186/s12905-020-01081-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7549220PMC
October 2020
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