SIERRA LEONE One Health in action (2016-2020) Tracing the origins of Ebola SIERRA LEONE EBOLA HOST PROJECT

estled in the heart of neighboring Guinea and Liberia, to (Bombali ebolavirus) in insect-eating coastal West Africa, find the animal source of this and bats; the first time an ebolavirus was NSierra Leone is a shining other devastating filoviruses, and discovered before causing human example of resilience and strength to investigate human behaviors or animal illness or death. A few in the face of unprecedented health associated with virus spillover. A months later, our team together challenges. With nearly 5.7 million robust community engagement with colleagues at the U.S. Centers people living in a gradient of dense strategy was also undertaken, for Disease Control and Prevention urban to very rural deep forest engaging over 400 stakeholders from (CDC) and Njala University, environments, Sierra Leone has long the national, district, chiefdom, and detected a deadly known virus been recognized as a zoonotic virus local community levels. Additionally, (Marburg virus) in fruit-eating bats, emergence hot spot. During 2013- our team worked closely with the first time this virus had been 2016, what was initially thought to government officials in six districts detected in West Africa. be a limited Ebola virus outbreak to launch district-level One Health PREDICT’s full impact in Sierra began along the Sierra Leone- Platforms. Leone will take years to fully Guinea-Liberia border. However, Through the University of Makeni appreciate. Through analysis of over the next three years the and partners in the Ministries project data and findings, PREDICT disease spread through nearly the of Health and Sanitation and was able to identify risks and entire three countries–leaving over Agriculture and Forestry, PREDICT educate communities and 28,000 people infected and more strengthened national capabilities health professionals on behavior than 11,000 dead. for virus surveillance in wildlife, change and intervention strategies This was the largest Ebola outbreak safely and humanely collecting designed to protect people and in history and further catalyzed samples from over 9,500 animals, wildlife from disease threats. Our efforts to identify the animal (bats, rodents, livestock, dogs, cats, staff continue to promote One source, or reservoir, of Ebola to and non-human primates) across Health as a key approach to obtaining prevent future outbreaks. To meet >50 independent locations. health security through their roles as this challenge, PREDICT designed leaders in health, agriculture, and the In 2018, as proof of concept for and implemented the Ebola Host environment. PREDICT’s approach, we detected Project in Sierra Leone, along with an entirely new species of ebolavirus

LOCAL PARTNERS • University of Makeni • Ministry of Health and Sanitation • Minsitry of Agriculture and Forestry LABORATORY STRENGTHENING · University of Makeni · UC Davis One Health Institute

29,160 TESTS

Global Health Security Agenda MOHAMED “It has been a pleasure working with PREDICT. I have learned a lot. I am not actually a scientist – I am an IT person, but I have TURAY build my system to love the science. I love my work that I am doing, Field Ecologist it is nice and I am learning a lot. It gives me what it takes to reach to communities, offer what I have to offer. I love what I am doing.” University of Makeni

“I have had an amazing work experience with PREDICT. The project FATMATA was not all about us collecting animal samples but PREDICT gave back BAIROH to me by building my capacity in lab and biosafety training. I can now identify the different species of bats through their external feature and Field Ecologist their inhabitants. Ultimately with PREDICT, I became a better person University of Makeni when it came to team work.”

ACHIEVEMENTS

• Discovered an entirely new species of ebolavirus of six district-level One Health Platforms, a (Bombali ebolavirus) in bats before any known human collaboration between Ministry of Health and or animal illnesses or deaths (Goldstein et al., Nature Sanitation, Ministry of Agriculture and Forestry, and Microbiology October 2018) the Environmental Protection Agency to sustain multi-sectoral coordination and bolster national • Discovered a known and deadly human pathogen health security (Marburg virus) in bats for the first time in West Africa, more than 2,400km from any • Catalyzed efforts within the Ministry of Health and known endemic area (Amman et al., Nature Sanitation’s Health Education Division leading to Communications January 2020) the development of formalized risk messaging and communication campaigns for living safely with • Supported outbreak response efforts for a pig animals and preventing zoonotic disease transmission die-off and coordinated efforts between the Government of Sierra Leone’s Central Veterinary • Served as a functional platform and role model of Laboratory, USAID, and US Department of technical assistance that led to the the establishment Agriculture to facilitate diagnostic testing for samples of an emerging Zoonotic Disease Surveillance Task collected from dead animals. These efforts and Force within the Ministry of Health and Sanitation’s confirmatory USDA testing led to the diagnosis of Emergency Operations Center, a monumental step African Swine Fever, the first occurrence of this towards proactive solutions to emerging pathogens disease in Sierra Leone, which was swiftly reported at the national level. to OIE in February 2020. • Trained >160 district-level government officials in One Health skills and supported the development ONE HEALTH SURVEILLANCE FINDING THE ELUSIVE WILDLIFE HOSTS OF EBOLAVIRUSES AND OTHER VIRAL THREATS

In collaboration with in-country partners, an extensive surveillance program was implemented in Sierra Leone to successfully identify the animal source and reservoir of Ebola virus and other closely related filoviruses (ebolaviruses and marburgviruses). Across >50 locations in six districts, biological specimens were safely and humanely collected from >9,500 animals (bats, rodents, nonhuman primates, livestock, and domesticated animals such as dogs, cats, goats and sheep) before being released. VIRUS TABLE # OF POSITIVE INDIVIDUALS VIRAL FAMILY VIRUS SPECIES SAMPLING LOCATION TOTAL WET DRY SEASON SEASON Filovirus Bombali virus (BOMV) Angolan Free-Tailed Bat, Gbindi, Kamabai, Robuya, 6 5 1 Little Free-Tailed Bat Rosanda, Yelisanda Marburg virus (MARV) Egyptian Fruit Bat Kakoya, Koema, Peidu 5 2 3 Coronavirus Bat coronavirus HKU9 Egyptian Fruit Bat Kakoya, Peidu 5 5 0 Coronavirus 229E Noack’s Roundleaf Bat Koema 1 1 0 (Bat strain) Paramyxovirus PREDICT_PMV-180 Angolan Fruit Bat Koema 1 1 0 PREDICT_PMV-183 Jones’s Roundleaf Bat Koema 1 1 0 Arenavirus Lassa mammarenavirus Natal Multimammate Blama Puila, Kamaseh 5 4 1 Mouse

Total 24 19 5 VIRUS DETECTION Our team discovered an entirely new sector (laboratories, hospitals, and one in a Jones’s Roundleaf Bat species of ebolavirus in Angolan Free- emergency response teams) and (Hipposideros jonesi) and one in tailed Bats and Little Free-tailed Bats the general population to raise an Angolan Fruit Bat (Lissonycteris (Mops condylurus, n=1; Chaerephon awareness of this new health threat. angolensis). There is no evidence pumilus, n=5), insect-eating bats in the that PREDICT_PMV-183 poses a Samples from over 300 domestic Bombali district that were sampled in threat to human health. Genetically, animals (cats and dogs) were tested and around people’s homes and the PREDICT_PMV-180 is related to using consensus PCR (cPCR) to broader community. This discovery henipaviruses, several of which are screen for filoviruses, no viruses in 2018 marked the first time ever known to cause disease in animals were detected.Samples collected that an ebolavirus was found before and people (e.g., Nipah virus, Hendra from wildlife were also tested using causing any reported human or virus) and genome sequencing is cPCR to screen for filoviruses, with animal illnesses or deaths. ongoing to further characterize this a subset of samples screened for virus and the zoonotic risks it may This new virus (Bombali ebolavirus) is arenaviruses, coronaviruses, and pose, if any. now recognized as the sixth species of paramyxoviruses. Virus findings ebolavirus. Further characterization were confirmed through genome FINDINGS IN of the virus is ongoing to understand sequencing and interpreted to better the zoonotic potential . Despite this understand the relationship of the RODENTS finding and more than 40 years of detected sequence to those from Lassa mammarenavirus was found research, data on the true reservoir known animal and human pathogens. in five Natal Multimammate Mice host for the virus that caused the A total of seven viruses, 4 historically (Mastomys natalensis). This strain is West African 2013-2016 outbreak known and 3 PREDICT -discovered known to cause Lassa hemorrhagic (Zaire ebolavirus) remains elusive, viruses, were detected in 24 animals. fever in humans. Testing for this though our team did detect Zaire virus was performed as part of the ebolavirus in bats sampled in Liberia. FINDINGS IN BATS separately funded PREEMPT project, The discovery of Bombali virus The bat coronavirus HKU9 was which is strengthening capacity and detection of Zaire ebolavirus found in five Egyptian Fruit Bats for surveillance and detection of contributes to the growing body (Rousettus aegyptiacus). There is to Lassa virus in Sierra Leone and of evidence that bats are the likely date, also no evidence to suggest that working with an international team hosts of this deadly group of viruses. this virus poses a threat to human to develop Lassa virus risk models, A few months after this discovery, health. prevention strategies and potential countermeasures to combat this PREDICT and partners with Njala This virus is not related to the public health threat. University and the US Centers for novel coronavirus strain (HCoV- Disease Control and Prevention 19SARS-CoV2) causing Coronavirus (US CDC) detected the known Disease (COVID-19) and leading and highly-lethal Marburg virus in to thea public health emergency of five Egyptian fruit bats (Rousettus international concern. Additionally, aegyptiacus) sampled at roosting coronavirus 229E, known to cause sites in the Koinadugu, Kono, and respiratory illness in people, was Moyamba districts. This finding was found in one Noack’s Roundleaf Bat significant, as the closest known (Hipposideros ruber). This particular endemic area for Marburg virus was strain virus infects bats but does not more than 2,400km east in Gabon. cause respiratory illness in people Following the discovery, PREDICT, and is not considered a public health CDC, and Njala worked closely with threat. the Government of Sierra Leone to risk communication and messaging Additionally, two new unique strategies for the public health paramyxoviruses were detected, IDENTIFYING BEHAVIORAL RISKS FOR VIRUS SPILLOVER & SPREAD HUMAN-ANIMAL IN-DEPTH BEHAVIORAL CONTACT RISK INTERVIEWS QUESTIONNAIRE Additionally, our team conducted six Our team conducted interviews to focus group discussions and 94 in- learn more about human behaviors depth ethnographic interviews in four that may be associated with zoonotic communities within the districts of disease transmission or virus spillover. Bombali, Koinadugu, and the Western A standardized questionnaire was Area to explore risky human behaviors used in interviews with 588 individuals and people’s interactions with wildlife. (304 females and 284 males) at 20 This formative ethnographic research sites (19 rural and one urban) across led our team to identify communities five districts, sites that our team also at high-risk for contact with bats in the targeted for animal surveillance activities. Bombali district, where we then focused A total of 82% of respondents in these investigations on two sites. In Bombali we communities reported raising animals conducted focus group discussions and with 77% reporting sharing water in-depth interviews with 28 individuals sources with animals for washing. The with direct or indirect contact with majority (64%) reported observing bats, including bat hunters. It was clear animal feces in or near food supplies, that the interviewees were not aware and 69% reported eating food after it of the potential health risks posed from was touched or damaged by animals. human-bat contact. Interviewees shared Twenty six percent (26%) reported that insectivorous bats were seen as being scratched or bitten by an animal in pests, were commonly found roosting in the past year and 23% reported trapping roofs of homes, and their excreta (urine or hunting animals. These findings are and feces) were contaminating food and particularly concerning as several of water supplies. these communities are in areas known Through interviews with the fruit bat as hotspots for zoonotic diseases such as hunters, we learned of more high-risk Lassa fever, a deadly virus transmitted to exposure to bats. While individuals were people by mice rodents in and around aware that bats were implicated in the people’s homes and food supplies, and Ebola epidemic, they did not have an where concentrated efforts have been adequate understanding of how zoonotic focused for years on awareness, risk diseases are transmitted or of the health eduction, and behavior change. risks that bats pose. Members of both communities heard public health messages concerning bats and wildlife during the Sometimes we find their droppings in our water, we throw the water away and other Ebola epidemic, but they seemed unsure of the messages’ veracity or relevance. times we use the water to bathe, etc. The infrequency of zoonotic spillover events presents a particular challenge They do fry them and sell them, for health communication around sometimes they can cook them in Ebola and wildlife. Furthermore, the the form of a soup, while sometimes knowledge-focused health interventions it’s being prepared as the way they implemented during the Ebola outbreak prepare chicken and put it in the seem to have fallen short of motivating tray for sale. But what I normally long-term behavior change, as virtually all see is the fried bats being sold. of the hunters had resumed bat hunting by the resolution of the outbreak. COMMUNITY OUTREACH RISK COMMUNICATION Following the discovery of the Bombali This new resource, Living Safely with Bats, communication campaign utilizing Living virus in bats, PREDICT worked closely leveraged the subject matter expertise of Safely with Bats reached an estimated with USAID, the Ministry of Health and PREDICT’s interdisciplinary One Health 1,000 individuals in 90% of communities Sanitation, and Ministry of Agriculture team who contributed technical content. engaged during the project. During and Forestry to swiftly develop a All illustrations were developed by a team the campaign, our team emphasized communications plan and a behavior member trained in animal biology and that while bats may harbor potentially change intervention resource to help raise infectious pathogens, they also play a awareness among community members very important role in the ecosystem about ways to reduce disease risks by pollinating crops and reducing insects associated with human-to-bat contact. To that can spread other diseases, such as identify the most culturally appropriate, mosquitoes. To reduce the risk of human feasible, and effective intervention resource exposure to potential pathogens, it was format, our team developed a framework stressed that people should avoid direct for assessing potential materials, channels contact with bats, their droppings or of communications, respective audiences, fluids, and food materials that have been and core messaging. A moderated picture fed upon by bats and other wildlife. In book format, delivered by a trusted addition, our team shared messages community leader, was selected as the visual arts to ensure accurate, consistent, for reducing risks of contact between best tool to put into the hands of our and compelling visual representations bats and domestic animals and livestock, local team and in-country stakeholders. throughout the book. Our Sierra Leone especially through indirect contact with A communications plan was developed team took this resource into communities bat excreta in animal feed, animal pens, with ministry partners to ensure a well- where the viruses were detected and and under orchards where animals graze coordinated effort and timely discussions met directly with each community and and forage. with community stakeholders, following their respective district level government , the release of the new ebolavirus finding. and chiefdom officials. This behavioral risk STRENGTHENING CAPACITY PREDICT worked diligently to increase collection and sampling, and safe transport of Sierra Leone in combating SARS- capacity for surveillance in animals and of biological specimens from remote CoV-2, the virus causing the COVID-19 to strengthen testing capacity for filovirus locations to virus detection laboratories pandemic. Currently, PREDICT-trained detection in the country. Moreover, with appropriate cold-chain. officers are working within four districts PREDICT recognized the importance to support the tracking of COVID-19 PREDICT also provided comprehensive of broader regional capacity with other cases in-country. These individuals have training for district-level wildlife, medical, nearby West Africa countries. In October been instrumental in providing technical and government officers on community 2017, PREDICT hosted a 10-day multi- support to the WHO-Sierra Leone engagement, risk communication, and national continuing education training, Surveillance Pillars at both the national wildlife and livestock sampling across all reaching more than 20 multi-disciplinary and district levels, and in contact tracing 16 districts in Sierra Leone. PREDICT staff from Senegal and Guinea and case investigation of COVID-19 at the University of Makeni. Participants The training of One Health individuals positive individuals to mitigate viral spread. were trained on safe and humane animal that began with PREDICT has directly , capture techniques, biological specimen befitted the government and citizens PRACTICAL IMPLICATIONS Further testing of newly discovered into practice at national, district, and of Health and Sanitation developed filoviruses, like Bombali virus, will greatly community levels, Sierra Leone is now and refined a communication campaign enhance our collective understanding better positioned to improve national and related to animal bites and living safely of ‘pre-emergent’ viral diversity and the global health security through zoonotic with animals. Initiatives focused on risk associated risks to human health. There viral surveillance. messaging will continue to strengthen remains much to understand about the prevention and preparedness for zoonotic Communication about risks was an specific factors leading to spill-over of diseases throughout the country. essential component of PREDICT´s these types of viruses and the threat they approach to zoonotic disease surveillance, The power of the PREDICT approach may pose if people become infected. and it is encouraged that these efforts to disease surveillance and preparedness Working with partner institutions in the remain a central element for future was recognized by the government of US government and other universities, vigilance efforts in Sierra Leone. Sierra Leone and stimulated tThe creation PREDICT is working to determine the of a Zoonotic Disease Surveillance Task potential mechanisms used by Bombali The Living Safely with Bats risk messaging Force within the Ministry of Health and virus could use to avoid immune responses book was highly valuable for community Sanitation’s Emergency Operations leading to spread and possibly disease in interventions to reduce and prevent Center. This was a monumental step bats and people. Understanding these exposures to potential pandemic viruses. towards proactive solutions to emerging “pathways of pathogenesis” are critical to Moreover, USAID’s Breakthrough Action pathogens in the country. With more develop effective countermeasures like project and the Sierra Leone Ministry of attention, resources, and effort placed vaccines or anti-viral drugs to augment Health and Sanitation Health Education into One Health surveillance, the country our preparedness in the face of potential Division collaborated to adapt and and by extension the West Africa region future outbreaks. PREDICT proved that broaden the message of the bat book by will be further ahead of any potential by putting extensive cross-sectoral and developing a Living Safely with Animals, risk zoonotic disease outbreaks. transdisciplinary One Health collaboration messaging book. Similarly, the Ministry REFERENCES • Goldstein, T., Anthony, S. J., Gbakima, A., et al. (2018). The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses. Nature Microbiology, 3(10), 1084-1089. https://doi.org/10.1038/s41564-018-0227-2 • Amman, B.R., Bird, B.H., Bakarr, I.A. et al. (2020). Isolation of Angola-like Marburg virus from Egyptian rousette bats from West Africa. Nat Commun 11, 510. https://doi.org/10.1038/s41467-020-14327-8

For more information view the interactive report at p2.predict.global FILOVIRUS SURVEILLANCE IN SPECIAL FEATURES SIERRA LEONE

Following the epidemic, PREDICT launched the Ebola Host Project (EHP) to conduct Ebola virus surveillance in livestock and wildlife in the three West African countries most affected by the outbreak. In 2018, EHP found a novel species of ebolavirus (Bombali ebolavirus) in Bombali, Sierra Leone in two species of insect-eating bats that were roosting in people’s homes. Learn more at https://bit.ly/2SURLaC

INSIGHTS ON THE GEOGRAPHIC DISTRIBUTION OF MOLOSSID BATS IN WEST AFRICA

In direct response to the detection of Bombali virus in Molossid bats and in recognition of the limited data available regarding bat distribution in the region, the Government of Guinea requested assistance identifying areas in the country and greater West Africa region at highest risk for virus spillover from bats. Learn more at https://bit.ly/3fH56Nw

VIRUS X HUNTERS: OPERATIONALIZING ONE HEALTH IN EMERGENCY RESPONSE & SURVEILLANCE

In Sierra Leone, the Ebola Host Project (EHP), which is part of the larger PREDICT project, was implemented to identify the animals that may act as reservoirs or transmission hosts for Ebola and other filoviruses, to further understand the spread of the virus and recommend prevention measures as well as strengthen in-country capacity to prevent, detect and respond to emerging threats. Learn more at https://bit.ly/3bpb0zw