Clinical Manifestations of an Outbreak of Monkeypox Virus in Captive Chimpanzees in Cameroon, 2016.

Monkeypox virus (MPXV) is a reemerging virus of global concern. An outbreak of clade I MPXV affected 20 captive chimpanzees in Cameroon in 2016. We describe the epidemiology, virology, phylogenetics, and clinical progression of this outbreak. Clinical signs included exanthema, facial swelling, perilaryngeal swelling, and eschar. Mpox can be lethal in captive chimpanzees, with death likely resulting from respiratory complications. We advise avoiding anesthesia in animals with respiratory signs to reduce the likelihood of death. This outbreak presented a risk to animal care staff. There is a need for increased awareness and a One Health approach to preparation for outbreaks in wildlife rescue centers in primate range states where MPXV occurs. Control measures should include quarantining affected animals, limiting human contacts, surveillance of humans and animals, use of personal protective equipment, and regular decontamination of enclosures.

Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia.

The white-bellied pangolin (Phataginus tricuspis) is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon's southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.

Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats.

Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.

Predicting the potential for zoonotic transmission and host associations for novel viruses.

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.

Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E.

Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.

Enterovirus Sequence Data Obtained from Primate Samples in Central Africa Suggest a High Prevalence of Enteroviruses.

Enteroviruses infect humans and animals and can cause disease, and some may be transmitted across species barriers. We tested Central African wildlife and found Enterovirus RNA in primates (17) and rodents (2). Some sequences were very similar, while others were dissimilar to known species, highlighting the underexplored enterovirus diversity in wildlife.

Coronavirus surveillance in wildlife from two Congo basin countries 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 betacoronaviruses, 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.

Sequences of Previously Unknown Rhabdoviruses Detected in Bat Samples from the Republic of the Congo.

The family Rhabdoviridae contains diverse viruses, including vector-borne and nonvector-borne viruses, some that are human pathogens, including rabies virus and also nonpathogenic viruses. Bats, which are a known reservoir of viruses with zoonotic potential including coronaviruses, also carry multiple rhabdoviruses such as but not limited to lyssaviruses. We collected samples from 193 insectivorous and frugivorous bats in the Republic of the Congo and tested them for rhabdovirus RNA. Four samples were found positive for viral RNA representing sequences of four different, not previously described rhabdoviruses. Although phylogenetic and taxonomic placement of the novel sequences is uncertain, similarities with previously detected rhabdovirus sequences in bats suggest that these could represent vertebrate viruses. Considering the pathogenic risks some rhabdoviruses pose for humans, these results highlight the need for more research and surveillance regarding rhabdoviruses and bats.

Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity.

Adenoviruses (AdVs) are diverse pathogens of humans and animals, with several dozen bat AdVs already identified. Considering that over 100 human AdVs are known, and the huge diversity of bat species, many bat AdVs likely remain undiscovered. To learn more about AdV prevalence, diversity and evolution, we sampled and tested bats in Cameroon using several PCR assays for viral and host DNA. AdV DNA was detected in 14 % of the 671 sampled animals belonging to 37 different bat species. There was a correlation between species roosting in larger groups and AdV DNA detection. The detected AdV DNA belonged to between 28 and 44 different, mostly previously unknown, mastadenovirus species. The novel isolates are phylogenetically diverse and while some cluster with known viruses, others appear to form divergent new clusters. The phylogenetic tree of novel and previously known bat AdVs does not mirror that of the various host species, but does contain structures consistent with a degree of virus-host co-evolution. Given that closely related isolates were found in different host species, it seems likely that at least some bat AdVs have jumped species barriers, probably in the more recent past; however, the tree is also consistent with such events having taken place throughout bat AdV evolution. AdV diversity was highest in bat species roosting in large groups. The study significantly increased the diversity of AdVs known to be harboured by bats, and suggests that host behaviours, such as roosting size, may be what limits some AdVs to one species rather than an inability of AdVs to infect other related hosts.

Market characteristics and zoonotic disease risk perception in Cameroon bushmeat markets.

Behavioral practices are one of the key factors facilitating zoonotic disease transmission, especially in individuals who have frequent contact with wild animals, yet practices of those who work and live in high-risk animal-human interfaces, such as wild animal 'bushmeat' markets in the Congo Basin are not well documented in the social, health and medical sciences. This region, where hunting, butchering, and consumption of wild animal meat is frequent, represents a hotspot for disease emergence, and has experienced zoonotic disease spillover events, traced back to close human-animal contact with bats and non-human primates. Using a One Health approach, we conducted wildlife surveillance, human behavioral research, and concurrent human and animal biological sampling to identify and characterize factors associated with zoonotic disease emergence and transmission. Research was conducted through the USAID Emerging Pandemic Threats program between 2010 and 2019 including qualitative studies of bushmeat markets, with selected study sites prioritized based on proximity to bushmeat markets. Sites included two hospitals where we conducted surveillance of individuals with syndromes of acute febrile illness, community sites where we enrolled actors of the animal value chain (ie. hunters, middlemen, transporters), and bushmeat markets, where we enrolled bushmeat vendors, butchers, market managers, cleaners, and shoppers. Mixed methods research was undertaken at these sites and included investigation of bushmeat market dynamics through observational research, focus group discussions, quantitative questionnaires, and interviews. Participants were asked about their risk perception of zoonotic disease transmission and specific activities related to bushmeat trade, local market conditions, and regulations on bushmeat trade in Cameroon. Risks associated with blood contact and animal infection were not well understood by most market actors. As bushmeat markets are an important disease interface, as seen with CoVID19, risk mitigation measures in markets and bushmeat alternative strategies are discussed.

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.

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.

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.

Antimicrobial resistance from a one health perspective in Cameroon: a systematic review and meta-analysis.

BACKGROUND: Antimicrobial resistance (AMR) is widely acknowledged as a global health problem, yet in many parts of the world its magnitude is not well elucidated. A baseline assessment of the AMR prevalence is a priority for implementation of laboratory-based AMR surveillance This review, focused on a One health approach, aimed at describing the current status of AMR in Cameroon. METHODS: PubMed, Google Scholar and African Journals Online databases were searched for articles published in English and French in accordance with the PRISMA guidelines. Retrieval and screening of article was done using a structured search string with strict inclusion/exclusion criteria. Free-text and grey literature were obtained by contacting the authors directly. The pooled prevalence and 95% confidence intervals were calculated for each pathogen-antibiotic pairs using random-effects models. RESULT: Amongst 97 full-text articles reviewed, 66 met the eligibility criteria. The studies originated from the Centre (24; 36.4%), South-West (16; 24.2%), West (13; 19.7%), Littoral (9; 13.6%) and other (4; 6.1%) regions of Cameroon. These studies reported AMR in human (45; 68.2%), animals (9; 13.6%) and the environment (12; 18.2%). Overall, 19 species of bacteria were tested against 48 antibiotics. These organisms were resistant to all classes of antibiotics and showed high levels of multidrug resistance. Escherichia coli, Klebsiella pneumoniae and Staphylococcus spp were reported in 23, 19 and 18 of the human studies and revealed multidrug resistance (MDR) rates of 47.1% [95% CI (37.3-57.2%)], 51.0% [95% CI (42.0-59.9)] and 45.2% [95% CI (38.0-54.7)], respectively. Salmonella spp was reported in 6 of the animal studies and showed a MDR rate of 46.2% [95% CI (39.2-53.5%)] while Staphylococcus spp in 8 of environment studies showed MDR rate of 67.1% [95% CI (55.2-77.2%)]. CONCLUSION: This review shows that resistance to commonly prescribed antibiotics in Cameroon is high. The findings emphasize the urgent need to address gaps in the standardization of AMR diagnostics, reporting and use of available information to optimize treatment guidelines for the arsenal of antibiotics. Effective AMR surveillance through continued data sharing, large-scale collaboration, and coordination of all stakeholders is essential to understand and manage the AMR national burden.

DNA of diverse adenoviruses detected in Cameroonian rodent and shrew species.

Rodent adenoviruses are important models for human disease. In contrast to the over 70 adenovirus types isolated from humans, few rodent adenoviruses are known, despite the vast diversity of rodent species. PCR and Sanger sequencing were used to investigate adenovirus diversity in wild rodents and shrews in Cameroon. Adenovirus DNA was detected in 13.8% of animals (n = 218). All detected sequences differ from known adenovirus types by more than 10% at the amino acid level, thus indicating up to 14 novel adenovirus species. These results highlight the diversity of rodent adenoviruses, their phylogeny, and opportunities for studying alternative adenovirus rodent models.

High Herpesvirus Diversity in Wild Rodent and Shrew Species in Central Africa.

OBJECTIVE: Herpesviruses belong to a diverse order of large DNA viruses that can cause diseases in humans and animals. With the goal of gathering information about the distribution and diversity of herpesviruses in wild rodent and shrew species in central Africa, animals in Cameroon and the Democratic Republic of the Congo were sampled and tested by PCR for the presence of herpesvirus DNA. METHODS: A broad range PCRs targeting either the Polymerase or the terminase gene were used for virus detection. Amplified products from PCR were sequenced and isolates analysed for phylogenetic placement. RESULTS: Overall, samples of 1,004 animals of various rodent and shrew species were tested and 24 were found to be positive for herpesvirus DNA. Six of these samples contained strains of known viruses, while the other positive samples revealed DNA sequences putatively belonging to 11 previously undescribed herpesviruses. The new isolates are beta- and gammaherpesviruses and the shrew isolates appear to form a separate cluster within the Betaherpesvirinae subfamily. CONCLUSION: The diversity of viruses detected is higher than in similar studies in Europe and Asia. The high diversity of rodent and shrew species occurring in central Africa may be the reason for a higher diversity in herpesviruses in this area.

Knowledge, attitude and practices of snakebite management amongst health workers in Cameroon: Need for continuous training and capacity building.

BACKGROUND: Snakebite has only recently been recognized as a neglected tropical disease by the WHO. Knowledge regarding snakebites and its care is poor both at the population level, and at the health care staff level. The goal of this study was to describe the level of knowledge and clinical practice regarding snakebite among health care staff from Cameroon. METHODS: A two-day training dedicated to snakebite and its care was organized in 2015 in Yaoundé, capital city of Cameroon. A total of 98 health care staff from all over Cameroon attended the training. Prior to and after the training, an evaluation quantified the attendees' level of knowledge. Pre- and post-training evaluations were compared to assess knowledge improvement. RESULTS: Overall, prior to the training knowledge regarding snakebite and care was poor, and wrong beliefs that "pierre noire" or tourniquet were useful in case of snakebite were common. Knowledge was statistically improved after the training. CONCLUSION: Trainings dedicated to all type of health care staff towards snakebite to improve care are needed, this training must take into consideration the context and the targeted population.

Highly pathogenic avian influenza A/H5N1 Clade 2.3.2.1c virus in poultry in Cameroon, 2016-2017.

In May 2016, highly pathogenic avian influenza virus of the subtype A/H5N1 was detected in Cameroon in an industrial poultry farm at Mvog-Betsi, Yaoundé (Centre region), with a recorded sudden increase of deaths among chickens, and an overall mortality rate of 75%. The virus spread further and caused new outbreaks in some parts of the country. In total, 21 outbreaks were confirmed from May 2016 to March 2017 (six in the Centre, six in the West, eight in the South and one in the Adamaoua regions). This resulted in an estimated total loss of 138,252 birds (44,451 deaths due to infection and 93,801 stamped out). Only domestic birds (chickens, ducks and geese) were affected in farms as well as in poultry markets. The outbreaks occurred in three waves, the first from May to June 2016, the second in September 2016 and the last wave in March 2017. The topology of the phylogeny based on the haemagglutinin gene segment indicated that the causative H5N1 viruses fall within the genetic clade 2.3.2.1c, within the same group as the A/H5N1 viruses collected in Niger in 2015 and 2016. More importantly, the gene constellation of four representative viruses showed evidence of H5N1/H9N2 intra-clade reassortment. Additional epidemiological and genetic data from affected countries in West Africa are needed to better trace the origin, spread and evolution of A/H5N1 in Cameroon. RESEARCH HIGHLIGHTS HPAI A/H5N1 was detected in May 2016 in domestic chickens in Yaoundé-Cameroon. Twenty-one outbreaks in total were confirmed from May 2016 to March 2017. The causative H5N1 viruses fall within the genetic clade 2.3.2.1c. The viral gene constellation showed evidence of H5N1/H9N2 intra-clade reassortment.