A new digital surveillance methodology to overcome challenges in reported epidemic data

Background: Accurate and complete outbreak data are essential in understanding the epidemiological properties of a disease. However, the quality of epidemiological data is often hindered by reporting delays, lack of reporting standardization, limitations in the spatial resolution of data, and the geographic coverage of reporting agencies. Researchers must find ways to effectively utilize unstandardized data of variable quality from multiple sources. The compilation of data sources is particularly valuable to fully capture global and regional disease trends of pathogens that are not confined by political boundaries. We have created a digital surveillance methodology and database that combines data from over 400 reporting sources for over 200 pathogens in 225 countries and encompases over 2400 infectious disease events. Our methods address gaps in reporting frequency, completeness, reliability, and accuracy. Methods and materials: Data sources are evaluated using qualitative and quantitative metrics encompassing source reliability and availability/permanence, as well as the consistency, structure, clarity, and spatiotemporal resolution of provided data. Based on these metrics, subject matter experts determine whether a single source is satisfactory or whether additional sources are required to provide a complete representation of an infectious disease event. When conflicting information is provided by sources, subject matter experts resolve discrepancies using a systematic approach to generate an accurate and comprehensive view of the outbreak.

Quantifying preparedness for emerging infectious diseases: A new methodology to assess health security at the subnational level in African countries

Background: A growing body of evidence demonstrates that there is significant variation in national preparedness to detect and respond to infectious disease outbreaks. The same is true at the subnational level: systems for disease surveillance and response can vary dramatically across regions within a given country. Weaker systems increase the propensity for outbreaks and epidemics, and epidemics, in turn, can absorb resources and cripple health systems, creating a negative feedback loop that must be assessed and addressed. There is increasing attention to measuring health security and country preparedness through processes like WHO's Joint External Evaluation (JEE). These processes capture information on cross-national variation in preparedness and provide information to guide capacity building and investments in health systems. However, the JEE and other assessment tools are national-level metrics and do not capture potentially significant subnational variance in preparedness. Methods and materials: We report a new methodology for measuring outbreak preparedness and response capacity at the subnational level, which was developed as part of a novel outbreak response financing initiative. This methodology draws upon validated tools, including the JEE, and captures a wide range of pathogen-specific preparedness capacities from stakeholder interviews and preexisting information, including capacities specific to the detection and mitigation of zoonotic threats to human health. This approach allows for a fine-grained analysis of subregional capacity to respond to distinct health security risks and can help identify subpopulations at risk.

Human Interactions with Bat Populations in Bombali, Sierra Leone

Human contact with bats has been epidemiologically linked to several of the most recent Ebola outbreaks, including the 2014 West Africa epidemic and the 2007 Luebo, Democratic Republic of the Congo, outbreak. While fruit bats remain the likely primary reservoir for Ebola virus (Zaire ebolavirus), recent wildlife surveillance efforts have identified a new species of ebolavirus (Bombali ebolavirus) in microchiropteran insect-eating bats in West and East Africa. Given the role of bats as potential Ebola reservoirs and sources of spillover into human populations, it is critically important to understand the circumstances and behaviors that bring human populations into close contact with bats. This study explores two sites in Bombali, Sierra Leone, where human populations have had close contact with microchiropteran bats via household infestations and fruit bats by hunting practices. Through interviews and focus groups, we identify the knowledge, beliefs, perceptions, and behaviors that may potentially protect or expose individuals to zoonotic spillover through direct and indirect contact with bats. We also describe how this research was used to develop a risk reduction and outreach tool for living safely with bats.

Coronavirus surveillance in Congo basin wildlife detects RNA of multiple species circulating in bats and rodents

Coronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 Alpha- and 6 Beta-coronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.

Serology and Behavioral Perspectives on Ebola Virus Disease Among Bushmeat Vendors in Equateur, Democratic Republic of the Congo, After the 2018 Outbreak

After the 2018 Ebola outbreak in Equateur Province, Democratic Republic of the Congo, we conducted behavioral interviews and collected samples from bushmeat vendors and primates in Mbandaka to test for evidence of Ebola virus exposure. Although participants indicated being aware of Ebola, they did not consider themselves at occupational risk for infection. We found antibodies against Zaire ebolavirus in one participant despite no reported history of disease or contact with infected individuals. Our data underline concerns of possible subclinical or undiagnosed Ebola virus infections and the importance and challenges of risk communication to populations who are occupationally exposed to bushmeat. Following the 2018 Ebola outbreak in Equateur Province, Democratic Republic of the Congo, bushmeat vendors interviewed in Mbandaka indicated being aware of Ebola, but did not consider themselves at occupational risk. Antibodies against Zaire ebolavirus were detected in one participant.

Coronavirus Surveillance of Wildlife in the Lao People’s Democratic Republic Detects Viral RNA in Rodents

Coronaviruses can become zoonotic, as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia increases the risk for such incidents. We sampled and tested rodents (851) and other mammals and found betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters and are closely related to those of known rodent coronaviruses detected in the region and distantly related to those of human coronaviruses OC43 and HKU1. Considering the close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks.

Detection of First Gammaherpesvirus Sequences in Central African Bats

Herpesviruses and have been identified in many species, however, relatively few bat herpesvirus 5 are known, considering the enormous diversity of bats. We used consensus PCR to test bats from 6 the Republic of the Congo and found DNA of two different novel bat herpesviruses. One was 7 detected in a Pipistrellus nanulus, the other in a Triaenops persicus bat and both resemble 8 gammaherpesviruses. On the amino acid level the amplified sequences differ by 55% from each 9 other, and by 27% and 25% from the next closest known viruses. The findings point towards the 10 diversity of herpesviruses in Central African bats.

Pandemic Risk Protection Report 2020

While the COVID-19 pandemic is first and foremost a human tragedy, its economic impact is also deeply concerning. The stakes for businesses, nonprofit organizations, and workers are too high to defer action, and a pandemic risk insurance program will be an essential element in the response to COVID-19 and future pandemics. Marsh’s Pandemic Risk Protection: Accelerate Recovery and Build Resilience Now Through Public-Private Partnership — with contributions from Metabiota — outlines the case for a public-private pandemic risk solution, which can accelerate the US economy’s recovery and provide protection against future risks.

Evidence of Low-Level Dengue Virus Circulation in the South Region of Cameroon in 2018

Dengue fever is an understudied disease in many parts of Africa and little is known about its prevalence in Cameroon. We tested blood from 629 individuals from the South Region of Cameroon, collected over the course of one year, for flavivirus RNA using conventional broad range PCR. Flavivirus RNA corresponding to dengue virus (DENV) serotype 1 was identified in two individuals who were also diagnosed with malaria. This finding confirms previous reports that indicate the presence of low-level circulation of DENV in Cameroon and supports the concern that dengue fever may be underdiagnosed due to more prevalent diseases that have similar symptomology and insufficient diagnostic capacity.

Unmet Need for Family Planning and Experience of Unintended Pregnancy Among Female Sex Workers in Urban Cameroon: Results From a National Cross-Sectional Study

Female sex workers (FSWs) in Cameroon commonly have unmet need for contraception posing a high risk of unintended pregnancy. Unintended pregnancy leads to a range of outcomes, and due to legal restrictions, FSWs often seek unsafe abortions. Aside from the high burden of HIV, little is known about the broader sexual and reproductive health of FSWs in Cameroon. From December 2015 to October 2016, we recruited FSWs aged ≥18 years through respondent-driven sampling across 5 Cameroonian cities. Cross-sectional data were collected through a behavioral questionnaire. Modified-robust Poisson regression was used to approximate adjusted prevalence ratios (aPR) for TOP and current use of effective nonbarrier contraception. Among 2,255 FSWs (median age 28 years), 57.6% reported history of unintended pregnancy and 40.0% reported prior TOP. In multivariable analysis, TOP history was associated with current nonbarrier contraceptive use (aPR=1.23, 95% confidence interval [CI]=1.07, 1.42); ever using emergency contraception (aPR=1.34, 95% CI=1.17, 1.55); >60 clients in the past month (aPR=1.29, 95% CI= 1.07, 1.54) compared to ≤30; inconsistent condom use with clients (aPR=1.17, 95% CI=1.00, 1.37); ever experiencing physical violence (aPR=1.24, 95% CI=1.09, 1.42); and older age. Most (76.5%) women used male condoms for contraception, but only 33.2% reported consistent condom use with all partners. Overall, 26.4% of women reported currently using a nonbarrier contraceptive method, and 6.2% reported using a long-acting method. Previous TOP (aPR=1.41, 95%CI=1.16, 1.72) and ever using emergency contraception (aPR=2.70, 95% CI=2.23, 3.26) were associated with higher nonbarrier contraceptive use. Recent receipt of HIV information (aPR=0.72, 95% CI=0.59, 0.89) and membership in an FSW community-based organization (aPR=0.73, 95% CI=0.57, 0.92) were associated with lower use nonbarrier contraceptive use. Experience of unintended pregnancies and TOP is common among FSWs in Cameroon. Given the low use of nonbarrier contraceptive methods and inconsistent condom use, FSWs are at risk of repeat unintended pregnancies. Improved integration of client-centered, voluntary family planning within community-led HIV services may better support the sexual and reproductive health and human rights of FSWs consistent with the United Nations Declaration of Human Rights.