Antibody Survey Reveals Widespread Flavi- and Paramyxoviruses Circulating in African Fruit Bats

Bats and rodents harbor an extraordinary diversity of RNA viruses, several of which have spilled over into human populations with devastating consequences. Yet the true prevalence of these viruses in wildlife populations, and the biological factors that determine whether a reservoir-borne virus can jump to people, remain poorly understood. A new multiregional serological study, published in PLOS Neglected Tropical Diseases, offers one of the most comprehensive antibody-based snapshots to date of RNA virus exposure in African bats and rodents, and it points to large, communal fruit bat colonies as hotspots of flavivirus and paramyxovirus circulation.

The research team, led by Jackson Emanuel and Marcel A. Müller with senior collaborators including Christian Drosten and Jan Felix Drexler, set out to overcome a persistent limitation of wildlife virology. Most virus discovery efforts depend on detecting viral nucleotide sequences in tissues or swabs, an approach that is highly specific but easily missed. Viral RNA concentrations vary enormously over the course of an infection, viruses concentrate in particular organs rather than in routinely sampled secretions, field samples degrade under tropical conditions, and many infections are transient. Antibodies, by contrast, persist in blood long after a virus has been cleared, providing a retrospective record of exposure. Serology therefore captures a wider window of infection than molecular detection alone.

To exploit this advantage, the investigators deployed a multiplex immunofluorescence assay capable of screening a single specimen for reactive antibodies against 14 different human-pathogenic RNA viruses spanning seven families: Coronaviridae, Flaviviridae, Hantaviridae, Paramyxoviridae, Phenuiviridae, Pneumoviridae, and Togaviridae. The assay uses virus-infected cells fixed on slides, allowing sera to be tested in parallel against multiple antigens while preserving the ability to distinguish genuine virus-specific reactivity from nonspecific background staining. This multiplexed design makes efficient use of precious wildlife samples, which are difficult and expensive to collect across remote field sites.

The scale of the survey is one of its defining strengths. The team retrospectively analyzed 1,135 bat specimens representing 16 species and 454 rodent specimens representing 15 species. The samples were collected at 63 distinct sites across seven countries, an unusually broad geographic and taxonomic footprint for a single serological study. This breadth matters because patterns of virus circulation in wildlife are shaped by local ecology, and conclusions drawn from one region or one host species may not generalize elsewhere.

The headline finding concerns tropical bats, which exhibited strikingly high rates of seropositivity against certain virus families. Overall, 42.7 percent of the tropical bats in the dataset carried antibodies reactive with members of the family Flaviviridae, and 67.7 percent showed reactivity against Paramyxoviridae, while 7.5 percent were seropositive for Togaviridae. These figures substantially exceed the prevalence typically observed in molecular screening studies, reinforcing the argument that antibody-based surveillance reveals enzootic virus circulation that sequence-based methods systematically underestimate. In practical terms, the results indicate that flaviviruses and paramyxoviruses are not occasional visitors to African fruit bat populations but established, continuously circulating residents.

Both virus families carry substantial public health relevance. The Flaviviridae include dengue, Zika, yellow fever, and West Nile viruses, while the Paramyxoviridae encompass measles, Nipah, and Hendra viruses as well as mumps and several rodent- and bat-borne relatives. Previous work has detected paramyxovirus sequences in African Pteropodidae, the family of Old World fruit bats that includes the straw-coloured fruit bat Eidolon helvum and the Egyptian rousette Rousettus aegyptiacus. The new serological data suggest that exposure to these viruses is far more common than sequence detection alone would imply, consistent with infections that are transient in individual animals but persistent at the population level.

Beyond mapping seroprevalence, the study probed the ecological determinants of infection. The authors are careful to note that confounding factors and sparse data still complicate the identification of reliable correlates of RNA virus infection in wildlife, and the models they present are explicitly provisional. Nevertheless, multivariable logistic regression analyses of the dataset pointed to one host characteristic in particular: colony size. Species that form large colonies, exemplified by Eidolon helvum and Rousettus aegyptiacus, were more likely to show seropositivity against orthoflaviviruses and orthorubulaviruses than species with smaller or more solitary roosting habits.

This association fits a well-established epidemiological principle. In large, dense, communally roosting colonies, viruses transmitted directly between individuals or through contaminated roost environments encounter a steady supply of susceptible hosts, particularly during annual pulses of newborn pups that lack maternal antibodies. High host density and repeated mixing of individuals from across vast foraging ranges create conditions favorable to sustained viral transmission, allowing bat-adapted viruses to circulate endemically rather than burning out after localized outbreaks. Eidolon helvum, which forms colonies numbering in the millions across equatorial Africa, and Rousettus aegyptiacus, which roosts in caves in dense aggregations, are both known to undertake long-distance seasonal movements that could further disperse viruses across the continent.

The findings carry implications for how viral surveillance in wildlife should be conducted and interpreted. Because molecular and serological methods capture different phases of the infection process, the authors argue implicitly that the two approaches are complementary: sequence detection pinpoints which virus is present and enables phylogenetic reconstruction, while serology quantifies how widely hosts are exposed over time. Integrating both into long-term monitoring programs, particularly at sites where large fruit bat colonies intersect with human activities such as bushmeat hunting, agriculture, and cave tourism, could sharpen risk assessments for zoonotic emergence before outbreaks occur, rather than after.

The study also underscores the remaining uncertainties in the field. Antibody reactivity against a virus family does not always identify the exact virus species involved, since closely related viruses can elicit cross-reactive responses, and sample quality, host age, sex, and seasonal effects can all influence serological results. The authors themselves emphasize that the regression findings should be treated as provisional within this dataset rather than as definitive laws of bat virology. Even so, by combining an unusually large and geographically diverse sample set with a multiplexed assay and formal statistical modeling, the work provides a template for future reservoir studies and strengthens the evidence that African Pteropodidae, especially species forming vast communal colonies, constitute a major and ongoing reservoir of flavi- and paramyxoviruses with potential relevance to human health.

Subject of Research: Serological surveillance of RNA virus antibodies in African bats and rodents

Article Title: A multiregional serosurvey of RNA virus-reactive antibodies in bats and rodents reveals the enzootic presence of flavi- and paramyxoviruses in African Pteropodidae

Article References: A multiregional serosurvey of RNA virus-reactive antibodies in bats and rodents reveals the enzootic presence of flavi- and paramyxoviruses in African Pteropodidae. (n.d.). https://doi.org/10.1371/journal.pntd.0013689

Image Credits: AI Generated

DOI: 10.1371/journal.pntd.0013689

Keywords: bats, rodents, serosurvey, flaviviridae, paramyxoviridae, Pteropodidae, Eidolon helvum, Rousettus aegyptiacus, zoonosis, multiplex immunofluorescence, Africa, virus reservoirs