One Health timeliness metrics to track and evaluate outbreak response reporting: A scoping review.

Background: As the global population soars, human behaviours are increasing the risk of epidemics. Objective performance evaluation of outbreak responses requires that metrics of timeliness, or speed in response time, be recorded and reported. We sought to evaluate how timeliness data are being conveyed for multisectoral outbreaks and make recommendations on how One Health metrics can be used to improve response success. Methods: We conducted a scoping review of outbreaks reported January 1, 2010- March 15, 2020, in organizational reports and peer-reviewed literature on PubMed and Embase databases. We tracked 11 outbreak milestones and calculated timeliness metrics, the median time in days, between the following: 1) Predict; 2) Prevent; 3) Start; 4) Detect; 5) Notify; 6) Verify; 7) Diagnostic; 8) Respond; 9) Communication; 10) End; and 11) After-Action Review. Findings: We identified 26783 outbreak reports, 1014 of which involved more than just the human health sector. Only six of the eleven milestones were mentioned in >50% of reports. The time between most milestones was on average shorter for outbreaks reporting both Predict (alert of a potential outbreak) and Prevent (response to predictive alert) events. Interpretation: Tracking progress in timeliness during outbreaks can focus efforts to prevent outbreaks from evolving into epidemics or pandemics. Response to predictive alerts demonstrated improved expediency in time to most milestones. We recommend the adoption of universally defined One Health outbreak milestones, including After Action Review, such that timeliness metrics can be used to assess outbreak response improvements over time. Funding: This study was made possible by the United States Agency for International Development's One Health Workforce-Next Generation Project (Cooperative Agreement 7200AA19CA00018).

Coronavirus and Paramyxovirus Shedding by Bats in a Cave and Buildings in Ethiopia.

Bats are important hosts of zoonotic viruses with pandemic potential, including filoviruses, MERS-Coronavirus (CoV), SARS-CoV -1, and likely SARS-CoV-2. Viral infection and transmission among wildlife are dependent on a combination of factors that include host ecology and immunology, life history traits, roosting habitats, biogeography, and external stressors. Between 2016 and 2018, four species of insectivorous bats from a readily accessed roadside cave and buildings in Ethiopia were sampled and tested for viruses using consensus PCR assays for five viral families/genera. Previously identified and novel coronaviruses and paramyxoviruses were identified in 99 of the 589 sampled bats. Bats sampled from the cave site were more likely to test positive for a CoV than bats sampled from buildings; viral shedding was more common in the wet season; and rectal swabs were the most common sample type to test positive. A previously undescribed alphacoronavirus was detected in two bat species from different taxonomic families, sampling interfaces, geographic locations, and years. These findings expand knowledge of the range and diversity of coronaviruses and paramyxoviruses in insectivorous bats in Ethiopia and reinforce that an improved understanding of viral diversity and species-specific shedding dynamics is important for designing informed zoonotic disease surveillance and spillover risk reduction efforts.

Fine scale infectious disease modeling using satellite-derived data.

Innovative tools for modeling infectious agents are essential for better understanding disease spread given the inherent complexity of changing and interacting ecological, environmental, and demographic factors. We leveraged fine-scale satellite data on urban areas to build a road-connected geospatial network upon which to model disease spread. This model was tested by simulating the spread of the 2009 pandemic influenza in Rwanda and also used to determine the effects of vaccination regimens on outbreak spread and impact. Our results were comparable to data collected during the actual pandemic in Rwanda, determining the initial places affected after outbreak introduction in Kigali. They also highlighted the effectiveness of preventing outbreaks by targeting mitigation efforts at points of outbreak origin. This modeling approach can be valuable for planning and control purposes in real-time disease situations, providing helpful baseline scenarios during initial phases of outbreaks, and can be applied to other infectious diseases where high population mobility promotes rapid disease propagation.

Fruit bats in flight: a look into the movements of the ecologically important Eidolon helvum in Tanzania.

BACKGROUND: Many ecologically important plants are pollinated or have their seeds dispersed by fruit bats, including the widely distributed African straw-colored fruit bats (Eidolon helvum). Their ability to fly long distances makes them essential for connecting plant populations across fragmented landscapes. While bats have been implicated as a reservoir of infectious diseases, their role in disease transmission to humans is not well understood. In this pilot study, we tracked E. helvum to shed light on their movement patterns in Tanzania and possible contact with other species. METHODS: Tracking devices were deployed on 25 bats captured in the Morogoro Municipal and Kilombero District area near the Udzungwa Mountains of Tanzania. Nightly flight patterns, areas corresponding to foraging bouts and feeding roosts, and new day roosts were determined from bat movement data and characterized according to their proximity to urban built-up and protected areas. Sites for additional environmental surveillance using camera traps were identified via tracking data to determine species coming in contact with fruits discarded by bats. RESULTS: Tracking data revealed variability between individual bat movements and a fidelity to foraging areas. Bats were tracked from one to six nights, with a mean cumulative nightly flight distance of 26.14 km (min: 0.33, max: 97.57) based on data from high-resolution GPS tags. While the majority of their foraging locations were in or near urban areas, bats also foraged in protected areas, of which the Udzungwa Mountains National Park was the most frequented. Camera traps in fruit orchards frequented by tracked bats showed the presence of multiple species of wildlife, with vervet monkeys (Chlorocebus pygerythrus) observed as directly handling and eating fruit discarded by bats. CONCLUSIONS: Because we observed multiple interactions of animals with fruits discarded by bats, specifically with vervet monkeys, the possibility of disease spillover risk exists via this indirect pathway. With flight distances of up to 97 km, however, the role of E. helvum in the seed dispersal of plants across both protected and urban built-up areas in Tanzania may be even more important, especially by helping connect increasingly fragmented landscapes during this Anthropocene epoch.

Spillover of ebolaviruses into people in eastern Democratic Republic of Congo prior to the 2018 Ebola virus disease outbreak.

BACKGROUND: The second largest Ebola virus disease (EVD) outbreak began in the Democratic Republic of Congo in July 2018 in North Kivu Province. Data suggest the outbreak is not epidemiologically linked to the 2018 outbreak in Equateur Province, and that independent introduction of Ebola virus (EBOV) into humans occurred. We tested for antibodies to ebolaviruses in febrile patients seeking care in North Kivu Province prior to the EVD outbreak. METHODS: Patients were enrolled between May 2017 and April 2018, before the declared start of the outbreak in eastern DRC. Questionnaires were administered to collect demographic and behavioural information to identify risk factors for exposure. Biological samples were evaluated for ebolavirus nucleic acid, and for antibodies to ebolaviruses. Prevalence of exposure was calculated, and demographic factors evaluated for associations with ebolavirus serostatus. RESULTS: Samples were collected and tested from 272 people seeking care in the Rutshuru Health Zone in North Kivu Province. All patients were negative for filoviruses by PCR. Intial screening by indirect ELISA found that 30 people were reactive to EBOV-rGP. Results were supported by detection of ebolavirus reactive linear peptides using the Serochip platform. Differential screening of all reactive serum samples against the rGP of all six ebolaviruses and Marburg virus (MARV) showed that 29 people exhibited the strongest reactivity to EBOV and one to Bombali virus (BOMV), and western blotting confirmed results. Titers ranged from 1:100 to 1:12,800. Although both sexes and all ages tested positive for antibodies, women were significantly more likely to be positive and the majority of positives were in February 2018. CONCLUSIONS: We provide the first documented evidence of exposure to Ebola virus in people in eastern DRC. We detected antibodies to EBOV in 10% of febrile patients seeking healthcare prior to the declaration of the 2018-2020 outbreak, suggesting early cases may have been missed or exposure ocurred without associated illness. We also report the first known detection of antibodies to BOMV, previously detected in bats in West and East Africa, and show that human exposure to BOMV has occurred. Our data suggest human exposure to ebolaviruses may be more frequent and geographically widespread.

epicontacts: Handling, visualisation and analysis of epidemiological contacts.

Epidemiological outbreak data is often captured in line list and contact format to facilitate contact tracing for outbreak control. epicontacts is an R package that provides a unique data structure for combining these data into a single object in order to facilitate more efficient visualisation and analysis. The package incorporates interactive visualisation functionality as well as network analysis techniques. Originally developed as part of the Hackout3 event, it is now developed, maintained and featured as part of the R Epidemics Consortium (RECON). The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub.

Sentinel California sea lions provide insight into legacy organochlorine exposure trends and their association with cancer and infectious disease.

BACKGROUND: Organochlorine contaminants (OCs), like polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethanes (DDTs), are widespread marine pollutants resulting from massive historical use and environmental persistence. Exposure to and health effects of these OCs in the marine environment may be examined by studying California sea lions (Zalophus californianus), which are long lived, apex predators capable of accumulating OCs. METHODS: We evaluated PCB and DDT levels in 310 sea lions sampled between 1992 and 2007: 204 individuals stranded along the coast of central California, 60 healthy males from Washington State, and 46 healthy females from southern California. Lipid-normalized contaminant concentrations were analyzed using general linear models and logistic regression to ascertain temporal trends; differences between stranded and healthy sea lions; and association of organochlorines with sex, age, and presence of cancer or fatal infectious disease. RESULTS: Concentrations of the contaminants in stranded adults decreased over time in the study period (adjusted for sex, as adult males had higher mean blubber concentrations than adult females and juveniles). Cancer was almost eight and six times more likely in animals with higher summed PCBs and DDTs, compared to those with lower levels (95% CI 5.55-10.51 and 4.54-7.99, respectively). Fatal infectious diseases were similarly seven and five times more likely in animals with higher contaminant burdens (95% CI 4.20-10.89 and 3.27-7.86, respectively). Mean contaminant loads were significantly higher in stranded sea lions than in healthy live captured animals (p < 0.001). CONCLUSION: Organochlorine contamination has significant associations with health outcomes in California sea lions, raising concerns for humans and other animals eating tainted seafood. While environmental exposure to these organochlorines appears to be decreasing over time based on levels in sea lion tissues, their persistence in the environment and food web for all predators, including humans, and the associated serious health risks, warrant monitoring, possibly through sentinel species like marine mammals.