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.

Sexually Transmitted Infection Risks and Symptoms Heightened Among Female Sex Workers who Started Selling Sex Before the Age of 18 in Five Cities in Cameroon.

Many adolescents under 18 years old who sell sex are at elevated risk for sexually transmitted infection (STI) acquisition, which may persist into adulthood. There has been limited study of the burden of the risks and vulnerabilities among women who started selling sex as adolescents across Sub-Saharan Africa. In this study, a Adult female sex workers (FSW) recruited through respondent-driven sampling in five cities in Cameroon from December 2015 to October 2016 completed a questionnaire and human immunodeficiency virus (HIV) and syphilis testing. Multivariable logistic regression analysis controlling for age was used to identify factors associated with reporting selling sex before age 18. Selling sex before age 18 was reported by 11.5% (256/2,220) of FSW. Initiation of selling sex as an adolescent was positively associated with experiencing dysuria (adjusted odds ratio [aOR]:1.50, 95% confidence interval [CI]:1.08-2.10) or genital warts (aOR:1.78, 95% CI:1.08-2.94) and negatively associated with prior recent testing for HIV (aOR:0.71, 95% CI:0.53-0.96) or STIs (aOR:0.65, 95% CI:0.44-0.96). Consistent condom use with clients was negatively associated with early initiation of selling sex (aOR:0.58, 95% CI:0.42-0.80), while experience of recent sexual violence was positively associated with early initiation (aOR:1.74, 95% CI:1.15-2.63). There were no independent significant differences in HIV (24.5%) or syphilis (8.3%) prevalence. Given the limited use of HIV and STI testing services by women who sold sex as adolescents, the prevalence of forced sex, condomless sex, and STI symptoms were high. Programs serving FSW should more vigorously aim to serve adolescents and adults who began selling sex early.

Modeling the potential impact of pre-exposure prophylaxis for HIV among men who have sex with men in Cameroon.

BACKGROUND: Men who have sex with men (MSM) are consistently burdened by HIV at higher levels than other adults. While HIV prevention programs for MSM are growing in coverage and quality, HIV incidence remains high. In response, pre-exposure prophylaxis (PrEP) was introduced in 2019 to support HIV risk reduction among MSM in Cameroon. Understanding how PrEP initiation programs will change the HIV prevalence among MSM in Cameroon is important to developing effective programs. METHODS: This study uses a mathematical model to simulate population-level HIV transmission among MSM in the cities of Yaoundé and Douala, Cameroon. PrEP is incorporated into the model at rates that equal 25%, 50%, or 75% coverage after twenty years to assess the potential effects on HIV prevalence among MSM, requiring annual initiation rates of 2.5%, 6.8%, and 17.2% for Yaoundé and 2.2%, 5.6%, and 13.4% for Douala, respectively. The data utilized for this model are from a cross sectional study which recruited MSM through respondent-driven sampling of MSM in two major cities in Cameroon: Yaoundé and Douala. RESULTS: The model estimated an HIV prevalence of 43.2% among MSM, annual HIV diagnoses of 300 per 10,000 MSM and antiretroviral therapy (ART) coverage of 53.9% in Yaoundé. In Douala, estimated prevalence is 26.5% among MSM, 167 per 10,000 MSM annual diagnoses and ART coverage of 72.0%. Standalone PrEP interventions aimed at 50% coverage at the end of a 20-year program would reduce the prevalence from 43.2% to 35.4% in Yaoundé and from 26.5 to 20.1% in Douala. Combining PrEP with a 10% increase in HIV testing would decrease the number of MSM living with HIV and unaware of their status from 9.8 to 6.0% in Yaoundé and from 8.7 to 4.6% in Douala. CONCLUSIONS: PrEP would be beneficial in reducing prevalence even at varying initiation and coverage levels. Combination of PrEP and increased HIV testing further decreased the number of undiagnosed MSM. This study supports the utility of implementing PrEP as part of comprehensive HIV prevention programming among MSM in Cameroon.

Disclosure of same-sex practices and experiences of healthcare stigma among cisgender men who have sex with men in five sub-Saharan African countries.

BACKGROUND: For men who have sex with men (MSM) across sub-Saharan Africa (SSA), disclosure of same-sex practices to family and healthcare workers (HCWs) can facilitate access to HIV prevention services and support, but can also lead to experiences of stigma. METHODS: We performed mixed-effects regressions on pooled data from MSM in Cameroon, Senegal, Côte d'Ivoire, Lesotho, and eSwatini to assess associations between disclosure and sexual behavior stigma in healthcare contexts; we used logistic regressions to analyze country-specific data. RESULTS: Compared to participants who had not disclosed to either family or HCWs, those who had disclosed only to family were more likely to have been gossiped about by HCWs (aOR = 1.70, CI = 1.18, 2.45); the association between having disclosed to family and having felt mistreated in a health center approached, but did not achieve, statistical significance (aOR = 1.56, CI = 0.94, 2.59). Those who had disclosed only to HCWs were more likely to have feared to seek health services (aOR = 1.60, CI = 1.14, 2.25), avoided health services (aOR = 1.74, CI = 1.22, 2.50), and felt mistreated in a health center (aOR = 2.62, CI = 1.43, 4.81). Those who had disclosed to both were more likely to have feared to seek health services (aOR = 1.71, CI = 1.16, 2.52), avoided health services (aOR = 1.59, CI = 1.04, 2.42), been gossiped about by HCWs (aOR = 3.78, CI = 2.38, 5.99), and felt mistreated in a health center (aOR = 3.39, CI = 1.86, 6.20). Country-specific analyses suggested that data from Cameroon drove several of these associations. CONCLUSIONS: Research to determine the factors driving disclosure's differential effect on healthcare stigma across contexts is needed. Ultimately, supportive environments enabling safe disclosure is critical to understanding HIV-acquisition risks and informing differentiated HIV-prevention, treatment, and testing services for MSM across SSA.

Characterizing Cross-Culturally Relevant Metrics of Stigma Among Men Who Have Sex With Men Across 8 Sub-Saharan African Countries and the United States.

Overcoming stigma affecting gay, bisexual, and other men who have sex with men (MSM) is a foundational element of an effective response to the human immunodeficiency virus (HIV) pandemic. Quantifying the impact of stigma mitigation interventions necessitates improved measurement of stigma for MSM around the world. In this study, we explored the underlying factor structure and psychometric properties of 13 sexual behavior stigma items among 10,396 MSM across 8 sub-Saharan African countries and the United States using cross-sectional data collected between 2012 and 2016. Exploratory factor analyses were used to examine the number and composition of underlying stigma factors. A 3-factor model was found to be an adequate fit in all countries (root mean square error of approximation = 0.02-0.05; comparative fit index/Tucker-Lewis index = 0.97-1.00/0.94-1.00; standardized root mean square residual = 0.04-0.08), consisting of "stigma from family and friends," "anticipated health-care stigma," and "general social stigma," with internal consistency estimates across countries of α = 0.36-0.80, α = 0.72-0.93, and α = 0.51-0.79, respectively. The 3-factor model of sexual behavior stigma cut across social contexts among MSM in the 9 countries. These findings indicate commonalities in sexual behavior stigma affecting MSM across sub-Saharan Africa and the United States, which can facilitate efforts to track progress on global stigma mitigation interventions.

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.

Phyloepidemiological Analysis Reveals that Viral Divergence Led to the Paucity of Simian Immunodeficiency Virus SIVmus/gsn/mon Infections in Wild Populations.

Human immunodeficiency virus type 1 (HIV-1) is the result of cross-species transmission of simian immunodeficiency virus from chimpanzees (SIVcpz). SIVcpz is a chimeric virus which shares common ancestors with viruses infecting red-capped mangabeys and a subset of guenon species. The epidemiology of SIV infection in hominoids is characterized by low prevalences and an uneven geographic distribution. Surveys in Cameroon indicated that two closely related members of the guenon species subset, mustached guenons and greater spot-nosed guenons, infected with SIVmus and SIVgsn, respectively, also have low rates of SIV infections in their populations. Compared to that for other monkeys, including red-capped mangabeys and closely related guenon species, such an epidemiology is unusual. By intensifying sampling of geographically distinct populations of mustached and greater spot-nosed guenons in Gabon and including large sample sets of mona guenons from Cameroon, we add strong support to the hypothesis that the paucity of SIV infections in wild populations is a general feature of this monophyletic group of viruses. Furthermore, comparative phylogenetic analysis reveals that this phenotype is a feature of this group of viruses infecting phylogenetically disparate hosts, suggesting that this epidemiological phenotype results from infection with these HIV-1-related viruses rather than from a common host factor. Thus, these HIV-1-related viruses, i.e., SIVcpz and the guenon viruses which share an ancestor with part of the SIVcpz genome, have an epidemiology distinct from that found for SIVs in other African primate species.IMPORTANCE Stable virus-host relationships are established over multiple generations. The prevalence of viral infections in any given host is determined by various factors. Stable virus-host relationships of viruses that are able to cause persistent infections and exist with high incidences of infection are generally characterized by a lack of morbidity prior to host reproduction. Such is the case for cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections of humans. SIV infections of most African primate species also satisfy these criteria, with these infections found at a high prevalence and with rare cases of clinical disease. In contrast, SIVcpz, the ancestor of HIV-1, has a different epidemiology, and it has been reported that infected animals suffer from an AIDS-like disease in the wild. Here we conclusively demonstrate that viruses which are closely related to SIVcpz and infect a subset of guenon monkeys show an epidemiology resembling that of SIVcpz.

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.

Female sex workers' empowerment strategies amid HIV-related socioeconomic vulnerabilities in Cameroon.

Research has consistently demonstrated that female sex workers use a variety of empowerment strategies to protect one another and their families. This study examines the strategies Cameroonian sex workers employ to do so. In-depth interviews and focus-group discussions were conducted with 100 sex workers. Coded texts were analysed for recurring themes. Sex workers reported being concerned with physical violence and sexual assault and demands from authorities for bribes to avoid fines and/or imprisonment. Women described strategies such as 'looking out for' each other when faced with security threats. Many reported staying in sex work to provide for their children through education and other circumstances to allow them to lead a better life. Sex worker mothers reported not using condoms when clients offered higher pay, or with intimate partners, even when they understood the risk of HIV transmission to themselves. Concern for their children's quality of life took precedence over HIV-related risks, even when sex workers were the children's primary carers. A sex worker empowerment programme with a focus on family-oriented services could offer an effective and novel approach to increasing coverage of HIV prevention, treatment and care in Cameroon.

Gender-based violence against female sex workers in Cameroon: prevalence and associations with sexual HIV risk and access to health services and justice.

BACKGROUND/OBJECTIVES: Female sex workers (FSWs) are at risk for HIV and physical and sexual gender-based violence (GBV). We describe the prevalence of lifetime GBV and its associations with HIV risk behaviour, access to health services and barriers in accessing justice among FSWs in Cameroon. METHODS: FSWs (n=1817) were recruited for a cross-sectional study through snowball sampling in seven cities in Cameroon. We examined associations of lifetime GBV with key outcomes via adjusted logistic regression models. RESULTS: Overall, 60% (1098/1817) had experienced physical or sexual violence in their lifetime. GBV was associated with inconsistent condom use with clients (adjusted OR (AOR) 1.49, 95% CI 1.18 to 1.87), being offered more money for condomless sex (AOR 2.09, 95% CI 1.56 to 2.79), having had a condom slip or break (AOR 1.53, 95% CI 1.25 to 1.87) and difficulty suggesting condoms with non-paying partners (AOR 1.47, 95% CI 1.16 to 1.87). Violence was also associated with fear of health services (AOR 2.25, 95% CI 1.61 to 3.16) and mistreatment in a health centre (AOR 1.66, 95% CI 1.01 to 2.73). Access to justice was constrained for FSWs with a GBV history, specifically feeling that police did not protect them (AOR 1.41, 95% CI 1.12 to 1.78). DISCUSSION: Among FSWs in Cameroon, violence is prevalent and undermines HIV prevention and access to healthcare and justice. Violence is highly relevant to FSWs' ability to successfully negotiate condom use and engage in healthcare. In this setting of criminalised sex work, an integrated, multisectoral GBV-HIV strategy that attends to structural risk is needed to enhance safety, HIV prevention and access to care and justice.

Reorganization and expansion of the nidoviral family Arteriviridae.

The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American "types" of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.

The Detection of Influenza Virus Before and During the COVID-19 Pandemic in Cameroon.

BACKGROUND: Influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are both respiratory viruses with similar clinical manifestations and modes of transmission. This study describes influenza data before and during the coronavirus disease pandemic (COVID-19) in Cameroon and SARS-CoV-2 data during the pandemic period. METHODS: The study ran from 2017 to 2022, and data were divided into two periods: before (2017-2019) and during (2020-2022) the COVID-19 pandemic. Nasopharyngeal samples collected from persons with respiratory illness were tested for influenza using the Centers for Disease Control and Prevention (CDC) typing and subtyping assays. During the COVID-19 pandemic, the respiratory specimens were simultaneously tested for SARS-CoV-2 using the DaAn gene protocol or the Abbott real-time SARS-CoV-2 assay. The WHO average curve method was used to compare influenza virus seasonality before and during the pandemic. RESULTS: A total of 6246 samples were tested. Influenza virus detection rates were significantly higher in the pre-pandemic period compared to the pandemic period (30.8% vs. 15.5%; p < 0.001). Meanwhile, the SARS-CoV-2 detection rate was 2.5%. A change in the seasonality of influenza viruses was observed from a bi-annual peak before the pandemic to no clear seasonal pattern during the pandemic. The age groups 2-4 and 5-14 years were significantly associated with higher influenza positivity rates in both pre-pandemic and pandemic periods. For SARS-CoV-2, all age groups above 15 years were the most affected population. CONCLUSION: The COVID-19 pandemic had a significant impact on the seasonal influenza by changing the seasonality of the virus and reducing its detection rates.

Associations between punitive policies and legal barriers to consensual same-sex sexual acts and HIV among gay men and other men who have sex with men in sub-Saharan Africa: a multicountry, respondent-driven sampling survey.

BACKGROUND: Few assessments of associations between structural-level factors and HIV among gay men and other men who have sex with men (MSM) have been conducted, especially in sub-Saharan Africa. Our objective was to examine HIV testing history, HIV status, and stigmas among MSM living in ten countries with heterogeneous legal environments. METHODS: This study used pooled data from ten country-specific, cross-sectional studies done in 25 sites in Burkina Faso, Cameroon, Côte d'Ivoire, The Gambia, Guinea-Bissau, Nigeria, Senegal, Eswatini, Rwanda, and Togo. MSM were recruited by respondent-driven sampling and were eligible if they met country-specific requirements for age, area of residence, and self reported being assigned male sex at birth and having anal sex with a man in the past 12 months. Policy related to same-sex sexual behaviour for each country was categorised as not criminalised or criminalised. Countries were also categorised on the basis of recent reports of prosecutions related to same-sex sexual acts. Legal barriers were defined as those that legally prevented registration or operation of sexual orientation related civil society organisations (CSOs). Individual data on HIV testing history, HIV status, and stigma were collected via interviewer-administered sociobehavioural questionnaires and HIV testing. Multilevel logistic regression with random intercepts was used to assess the association between policies, recent prosecutions, legal barriers to CSOs, and HIV-related factors with adjusted odds ratios (aORs) and 95% CIs. FINDINGS: Between Aug 3, 2011, and May 27, 2020, we recruited 8047 MSM with a median age of 23 years (IQR 21-27). 4886 (60·7%) lived in countries that criminalise same-sex sexual acts. HIV prevalence among MSM was higher in criminalised settings than non-criminalised settings (aOR 5·15, 95% CI 1·12-23·57); higher in settings with recent prosecutions than in settings without prosecutions (12·06, 7·19-20·25); and higher in settings with barriers to CSOs than without barriers to CSOs (9·83, 2·00-48·30). HIV testing or status awareness was not associated with punitive policies or practices. Stigma was associated with HIV status but did not consistently vary across legal environments. Disparities in HIV prevalence between MSM and other adult men were highest in punitive settings. INTERPRETATION: Structural risks including discriminatory country-level policies, prosecutions, and legal barriers might contribute to higher HIV prevalence among MSM. Taken together, these data highlight the importance of decriminalisation and decreasing enforcement, alongside stigma reduction, as central to effective control for HIV. FUNDING: National Institutes of Health. TRANSLATION: For the French translation of the abstract see Supplementary Materials section.

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.

High seroprevalence of enterovirus infections in apes and old world monkeys.

To estimate population exposure of apes and Old World monkeys in Africa to enteroviruses (EVs), we conducted a seroepidemiologic study of serotype-specific neutralizing antibodies against 3 EV types. Detection of species A, B, and D EVs infecting wild chimpanzees demonstrates their potential widespread circulation in primates.

Novel simian foamy virus infections from multiple monkey species in women from the Democratic Republic of Congo.

BACKGROUND: Zoonotic transmission of simian retroviruses in Central Africa is ongoing and can result in pandemic human infection. While simian foamy virus (SFV) infection was reported in primate hunters in Cameroon and Gabon, little is known about the distribution of SFV in Africa and whether human-to-human transmission and disease occur. We screened 3,334 plasmas from persons living in rural villages in central Democratic Republic of Congo (DRC) using SFV-specific EIA and Western blot (WB) tests. PCR amplification of SFV polymerase sequences from DNA extracted from buffy coats was used to measure proviral loads. Phylogenetic analysis was used to define the NHP species origin of SFV. Participants completed questionnaires to capture NHP exposure information. RESULTS: Sixteen (0.5%) samples were WB-positive; 12 of 16 were from women (75%, 95% confidence limits 47.6%, 92.7%). Sequence analysis detected SFV in three women originating from Angolan colobus or red-tailed monkeys; both monkeys are hunted frequently in DRC. NHP exposure varied and infected women lived in distant villages suggesting a wide and potentially diverse distribution of SFV infections across DRC. Plasmas from 22 contacts of 8 WB-positive participants were all WB negative suggesting no secondary viral transmission. Proviral loads in the three women ranged from 14 - 1,755 copies/105 cells. CONCLUSIONS: Our study documents SFV infection in rural DRC for the first time and identifies infections with novel SFV variants from Colobus and red-tailed monkeys. Unlike previous studies, women were not at lower risk for SFV infection in our population, providing opportunities for spread of SFV both horizontally and vertically. However, limited testing of close contacts of WB-positive persons did not identify human-to-human transmission. Combined with the broad behavioral risk and distribution of NHPs across DRC, our results suggest that SFV infection may have a wider geographic distribution within DRC. These results also reinforce the potential for an increased SFV prevalence throughout the forested regions of Africa where humans and simians co-exist. Our finding of endemic foci of SFV infection in DRC will facilitate longitudinal studies to determine the potential for person-to-person transmissibility and pathogenicity of these zoonotic retroviral infections.

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.

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.