Leveraging human resources for outbreak analysis: lessons from an international collaboration to support the sub-Saharan African COVID-19 response.

Emerging infectious diseases are a growing threat in sub-Saharan African countries, but the human and technical capacity to quickly respond to outbreaks remains limited. Here, we describe the experience and lessons learned from a joint project with the WHO Regional Office for Africa (WHO AFRO) to support the sub-Saharan African COVID-19 response.In June 2020, WHO AFRO contracted a number of consultants to reinforce the COVID-19 response in member states by providing actionable epidemiological analysis. Given the urgency of the situation and the magnitude of work required, we recruited a worldwide network of field experts, academics and students in the areas of public health, data science and social science to support the effort. Most analyses were performed on a merged line list of COVID-19 cases using a reverse engineering model (line listing built using data extracted from national situation reports shared by countries with the Regional Office for Africa as per the IHR (2005) obligations). The data analysis platform The Renku Project ( https://renkulab.io ) provided secure data storage and permitted collaborative coding.Over a period of 6 months, 63 contributors from 32 nations (including 17 African countries) participated in the project. A total of 45 in-depth country-specific epidemiological reports and data quality reports were prepared for 28 countries. Spatial transmission and mortality risk indices were developed for 23 countries. Text and video-based training modules were developed to integrate and mentor new members. The team also began to develop EpiGraph Hub, a web application that automates the generation of reports similar to those we created, and includes more advanced data analyses features (e.g. mathematical models, geospatial analyses) to deliver real-time, actionable results to decision-makers.Within a short period, we implemented a global collaborative approach to health data management and analyses to advance national responses to health emergencies and outbreaks. The interdisciplinary team, the hands-on training and mentoring, and the participation of local researchers were key to the success of this initiative.

Rectal Infection With Neisseria gonorrhoeae and Chlamydia trachomatis in Men in the United States.

BACKGROUND: Centers for Disease Control and Prevention guidelines recommend at least annual rectal screening of men who have receptive anal intercourse for Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT). Only limited national data are available on the prevalence of rectal GC and CT infection among US men. METHODS: In collaboration with a large US commercial laboratory, we estimated positivity of the first rectal GC and CT test ("index" test) in men aged 15-60 years tested between January 2013 and May 2015. We estimated the frequency and positivity of pharyngeal or urine specimens tested for GC and CT on the index date, and the frequency and positivity of repeat rectal testing or any follow-up testing at any anatomic site after the index date. RESULTS: Of 52 063 tested men aged 15-60 years, approximately 6.1% were positive for GC only, 8.3% for CT only, and 2.7% for both GC and CT on their index date. On that date, 86.5% had either urine or pharyngeal specimens collected, and 56.1% had both specimens collected. Pharyngeal GC infection was highly associated with rectal GC infection. Follow-up testing after 12 months ranged from 42.4% among uninfected men to 56.7% among infected men on the index date. Positivity was at least 5.7% in rectal GC, rectal CT, or pharyngeal GC at their last test. CONCLUSIONS: This analysis of a large number of male rectal specimens tested for GC and CT suggest that routine testing and timely repeat rectal GC and CT testing should be prioritized among men who report receptive rectal sex.