Coronaviruses Detected in Bats in Close Contact with Humans in Rwanda

Pulmonary infections in the returning traveler

PURPOSE OF REVIEW

The recent COVID-19 pandemic has shaped the epidemiology of other infectious diseases globally. International tourist arrivals are increasing and recovering to prepandemic levels. This review focuses on respiratory infections in travelers, highlighting the characteristics of the main imported viral, bacterial, fungal, and parasitic infections with pulmonary involvement.

RECENT FINDINGS

A recent systematic review estimated a prevalence of respiratory symptoms in travelers of around 35%, increasing to nearly 65% in the context of mass gatherings. Common viral and bacterial pathogens account for the majority of respiratory infections with an identified cause; however, recent data focus on the need for surveillance of emerging infections such as MERS-CoV, henipaviruses and multidrug resistant bacteria, which may be spread through travel. Fungal and parasitic respiratory infections are less common, and acquisition is usually associated with specific risk factors or exposure in endemic areas. Special risk groups, such as immunocompromised travelers, may be particularly vulnerable, presenting with severe disease or reactivation of latent infections.

SUMMARY

The next significant international epidemic could involve another new infectious agent causing respiratory disease and spreading via mobile populations. Official protocols should be adhered to, and public health interventions implemented for effective control. Continued and globally coordinated investments in research for new vaccines, therapeutic agents, disease modeling, and digital tracking strategies are essential.

Roost selection by synanthropic bats in rural Kenya: implications for human-wildlife conflict and zoonotic pathogen spillover

Many wildlife species are synanthropic and use structures built by humans, creating a high-risk interface for human-wildlife conflict and zoonotic pathogen spillover. However, studies that investigate features of urbanizing areas that attract or repel wildlife are currently lacking. We surveyed 85 buildings used by bats and 172 neighbouring buildings unused by bats (controls) in southeastern Kenya during 2021 and 2022 and evaluated the role of microclimate and structural attributes in building selection. We identified eight bat species using buildings, with over 25% of building roosts used concurrently by multiple species. Bats selected taller cement-walled buildings with higher water vapour pressure and lower presence of permanent human occupants. However, roost selection criteria differed across the most common bat species: molossids selected structures like those identified by our main dataset whereas Cardioderma cor selected buildings with lower presence of permanent human occupants. Our results show that roost selection of synanthropic bat species is based on specific buildings attributes. Further, selection criteria that facilitate bat use of buildings are not homogeneous across species. These results provide information on the general mechanisms of bat-human contact in rural settings, as well as specific information on roost selection for synanthropic bats in urbanizing Africa.

Viral Co-Infection in Bats: A Systematic Review

Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.

Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis

The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.

Human interactions with bats and bat coronaviruses in rural Côte d'Ivoire

Bats are presumed reservoirs of diverse α- and β- coronaviruses (CoVs) and understanding the diversity of bat-CoVs and the role bats play in CoV transmission is highly relevant in the context of the current COVID pandemic. We sampled bats in Côte d'Ivoire (2016-2018) living at ecotones between anthropogenic and wild habitats in the Marahoué National Park, a recently encroached protected area, to detect and characterize the CoVs circulating in bats and humans. A total of 314 bats were captured, mostly during the rainy season (78%), and CoV RNA was detected in three of the bats (0.96%). A CoV RNA sequence similar to Chaerephon bat coronavirus/Kenya/KY22/2006 (BtKY22) was found in a Chaerephon cf. pumilus and a Mops sp. fecal swab, while a CoV RNA sequence similar to the two almost identical Kenya bat coronaviruses BtKY55 and BtKY56 (BtKY55/56) was detected in an Epomops buettikoferi oral swab. Phylogenetic analyses indicated differences in the degree of evolutionary host-virus co-speciation for BtKY22 and BtKY55/56. To assess potential for human exposure to these viruses, we conducted human syndromic and community-based surveillance in clinics and high-risk communities. We collected data on participant characteristics, livelihoods, animal contact, and high-risk behaviors that may be associated with exposure to zoonotic diseases. We then collected biological samples for viral testing from 401 people. PCR testing of these biological samples revealed no evidence of CoV infection among the enrolled individuals. We identified higher levels of exposure to bats in people working in crop production and in hunting, trapping and fishing. Finally, we used the 'Spillover' risk-ranking tool to assess the potential for viral spillover and concluded that, while there is no evidence to suggest imminent risk of spillover for these CoVs, their host range and other traits suggest caution and vigilance are warranted in people with high exposure risk.

Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies

The human immune repertoire retains the molecular memory of a very great diversity of target antigens (epitopes) and can recall this upon a second encounter with epitopes against which it has previously been primed. Although genetically diverse, proteins of coronaviruses exhibit sufficient conservation to lead to antigenic cross-reactions. In this review, our goal is to question whether pre-existing immunity against seasonal human coronaviruses (HCoVs) or exposure to animal CoVs has influenced the susceptibility of human populations to SARS-CoV-2 and/or had an impact upon the physiopathological outcome of COVID-19. With the hindsight that we now have regarding COVID-19, we conclude that although antigenic cross-reactions between different coronaviruses exist, cross-reactive antibody levels (titers) do not necessarily reflect on memory B cell frequencies and are not always directed against epitopes which confer cross-protection against SARS-CoV-2. Moreover, the immunological memory of these infections is short-term and occurs in only a small percentage of the population. Thus, in contrast to what might be observed in terms of cross-protection at the level of a single individual recently exposed to circulating coronaviruses, a pre-existing immunity against HCoVs or other CoVs can only have a very minor impact on SARS-CoV-2 circulation at the level of human populations.

A systematic review to describe patterns of animal and human viral research in Rwanda

Rwanda is located in the Central East African region where several viral pathogens with global importance were originally described, including human immunodeficiency virus (HIV), Ebola, Zika, Rift Valley Fever (RVF), dengue and a long list of other neglected tropical viral pathogens. Due to many factors, this region has the potential to become a global hotspot for viral emergence. In Rwanda, viral diseases are underreported and the question is whether this is due to the absence of these viruses or a lack of investigation. Like many developing countries, capabilities in Rwanda need improvement despite research efforts throughout the years. This review describes the status of human and animal virus research in Rwanda and identifies relevant research and operational gaps. A comprehensive search was conducted in PubMed for virus research in Rwanda: 233 primary studies on viruses/viral diseases are indexed with connection to Rwanda. From 1958 to 2020, yearly publications generally increased and HIV/acquired immunodeficiency syndrome is the most studied virus. Compared with human viruses, few studies focus on animal and/or zoonotic viruses. The occurrence of the current severe acute respiratory syndrome coronavirus 2 pandemic shows strengthening warning and surveillance systems is critical to efficient preparedness and response. We recommend investment in human capacity, laboratory facilities and research to inform policy for viral surveillance in Rwanda.

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.

Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Central and West African Populations

For more than two years after the emergence of COVID-19 (Coronavirus Disease-2019), significant regional differences in morbidity persist. These differences clearly show lower incidence rates in several regions of the African and Asian continents. The work reported here aimed to test the hypothesis of a pre-pandemic natural immunity acquired by some human populations in central and western Africa, which would, therefore, pose the hypothesis of an original antigenic sin with a virus antigenically close to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). To identify such pre-existing immunity, sera samples collected before the emergence of COVID-19 were tested to detect the presence of IgG reacting antibodies against SARS-CoV-2 proteins of major significance. Sera samples from French blood donors collected before the pandemic served as a control. The results showed a statistically significant difference of antibodies prevalence between the collected samples in Africa and the control samples collected in France. Given the novelty of our results, our next step consists in highlighting neutralizing antibodies to evaluate their potential for pre-pandemic protective acquired immunity against SARS-CoV-2. In conclusion, our results suggest that, in the investigated African sub-regions, the tested populations could have been potentially and partially pre-exposed, before the COVID-19 pandemic, to the antigens of a yet non-identified Coronaviruses.

Seasonal shedding of coronavirus by straw-colored fruit bats at urban roosts in Africa

The straw-colored fruit bat (Eidolon helvum) is a pteropodid whose conservation is crucial for maintaining functional connectivity of plant populations in tropical Africa. Land conversion has pushed this species to adapt to roosting in urban centers across its range. These colonies often host millions of individuals, creating intensive human-bat contact interfaces that could facilitate the spillover of coronaviruses shed by these bats. A better understanding of coronavirus dynamics in these roosts is needed to identify peak times of exposure risk in order to propose evidence-based management that supports safe human-bat coexistence, as well as the conservation of this chiropteran. We studied the temporal patterns of coronavirus shedding in E. helvum, by testing thousands of longitudinally-collected fecal samples from two spatially distant urban roosts in Ghana and Tanzania. Shedding of coronaviruses peaked during the second part of pup weaning in both roosts. Assuming that coronavirus shedding is directly related to spillover risk, our results indicate that exposure mitigation should target reducing contact between people and E. helvum roosts during the pup “weaning” period. This recommendation can be applied across the many highly-populated urban sites occupied by E. helvum across Africa.

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.

Science's Response to CoVID-19

CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.

Transmission of SARS-CoV-2 virus and ambient temperature: a critical review

The coronavirus disease 2019 (COVID-19) pandemic has brought unprecedented public health, and social and economic challenges. It remains unclear whether seasonal changes in ambient temperature will alter spreading trajectory of the COVID-19 epidemic. The probable mechanism on this is still lacking. This review summarizes the most recent research data on the effect of ambient temperature on the COVID-19 epidemic characteristic. The available data suggest that (i) mesophilic traits of viruses are different due to their molecular composition; (ii) increasing ambient temperature decreases the persistence of some viruses in aquatic media; (iii) a 1°C increase in the average monthly minimum ambient temperatures (AMMAT) was related to a 0.72% fewer mammalian individuals that would be infected by coronavirus; (iv) proportion of zoonotic viruses of mammals including humans is probably related to their body temperature difference; (v) seasonal divergence between the northern and southern hemispheres may be a significant driver in determining a waved trajectory in the next 2 years. Further research is needed to understand its effects and mechanisms of global temperature change so that effective strategies can be adopted to curb its natural effects. This paper mainly explores possible scientific hypothesis and evidences that local communities and authorities should consider to find optimal solutions that can limit the transmission of SARS-CoV-2 virus.

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.

Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations

The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.

Wide Diversity of Coronaviruses in Frugivorous and Insectivorous Bat Species: A Pilot Study in Guinea, West Africa

Zoonoses can constitute a threat for public health that can have a global importance, as seen with the current COVID-19 pandemic of severe acute respiratory syndrome coronavirus (SARS-CoV2). Bats have been recognized as an important reservoir of zoonotic coronaviruses (CoVs). In West Africa, where there is a high diversity of bat species, little is known on the circulation of CoVs in these hosts, especially at the interface with human populations. In this study, in Guinea, we tested a total of 319 bats belonging to 14 genera and six families of insectivorous and frugivorous bats across the country, for the presence of coronaviruses. We found CoVs in 35 (11%) of the tested bats—in three insectivorous bat species and five fruit bat species that were mostly captured close to human habitat. Positivity rates varied from 5.7% to 100%, depending on bat species. A wide diversity of alpha and beta coronaviruses was found across the country, including three sequences belonging to SarbeCoVs and MerbeCoVs subgenera known to harbor highly pathogenic human coronaviruses. Our findings suggest that CoVs are widely spread in West Africa and their circulation should be assessed to evaluate the risk of exposure of potential zoonotic CoVs to humans.

Self-disseminating vaccines to suppress zoonoses

The SARS-CoV-2 epidemic is merely the most recent demonstration that our current approach to emerging zoonotic infectious disease is ineffective. SARS, MERS, Ebola, Nipah and an array of arenavirus infections sporadically spillover into human populations and are often contained only as a result of their poor transmission in human hosts, coupled with intense public health control efforts in the early stages of an emerging epidemic. It is now more apparent than ever that we need a better and more proactive approach. One possibility is to eliminate the threat of spillover before it occurs using vaccines capable of autonomously spreading through wild animal reservoirs. We are now poised to begin developing self-disseminating vaccines targeting a wide range of human pathogens, but important decisions remain about how they can be most effectively designed and used to target pathogens with a high risk of spillover and/or emergence. In this Perspective, we first review the basic epidemiological theory establishing the feasibility and utility of self-disseminating vaccines. We then outline a road map for overcoming remaining technical challenges: identifying high-risk pathogens before they emerge, optimizing vaccine design with an eye to evolution, behaviour and epidemiology, and minimizing the risk of unintended consequences.