Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa

Next-generation sequencing (NGS) has the potential to transform the discovery of viruses causing unexplained acute febrile illness (UAFI) because it does not depend on culturing the pathogen or a priori knowledge of the pathogen’s nucleic acid sequence. More generally, it has the potential to elucidate the complete human virome, including viruses that cause no overt symptoms of disease, but may have unrecognized immunological or developmental consequences. We have used NGS to identify RNA viruses in the blood of 195 patients with UAFI and compared them with those found in 328 apparently healthy (i.e., no overt signs of illness) control individuals, all from communities in southeastern Nigeria. Among UAFI patients, we identified the presence of nucleic acids from several well-characterized pathogenic viruses, such as HIV-1, hepatitis, and Lassa virus. In our cohort of healthy individuals, however, we detected the nucleic acids of two novel rhabdoviruses. These viruses, which we call Ekpoma virus-1 (EKV-1) and Ekpoma virus-2 (EKV-2), are highly divergent, with little identity to each other or other known viruses. The most closely related rhabdoviruses are members of the genus Tibrovirus and Bas-Congo virus (BASV), which was recently identified in an individual with symptoms resembling hemorrhagic fever. Furthermore, by conducting a serosurvey of our study cohort, we find evidence for remarkably high exposure rates to the identified rhabdoviruses. The recent discoveries of novel rhabdoviruses by multiple research groups suggest that human infection with rhabdoviruses might be common. While the prevalence and clinical significance of these viruses are currently unknown, these viruses could have previously unrecognized impacts on human health; further research to understand the immunological and developmental impact of these viruses should be explored. More generally, the identification of similar novel viruses in individuals with and without overt symptoms of disease highlights the need for a broader understanding of the human virome as efforts for viral detection and discovery advance

Diverse HIV viruses are targeted by a conformationally dynamic antiviral

Rhesus macaque TRIMCyp (RhTC) is a potent primate antiviral host protein that inhibits the replication of diverse HIV viruses. Here we show that it has acquired the ability to target multiple viruses by evolving an active site that interconverts between multiple conformations. Mutations that have relieved active site constraints allow RhTC to dynamically sample conformational space, including radically different conformers that target both HIV-1 and HIV-2 viruses. Introduction of a reversible constraint into RhTC allows specificity to be switched between a single conformation specific for HIV-1 and a dynamic ensemble that targets multiple viruses. These results show that conformational diversity can be used to expand the target diversity of innate immune receptors by supplementing their limited genetic variability with variability in protein structure

Sequencing results and schematic representation of the EKV-1 and -2 genome organization.

<p>(<b>A</b>) Overview of the data generated for each novel rhabdovirus. (<b>B</b>) A schematic showing the assembled genomes, consisting of the following genes: <i>nucleoprotein</i> (N), <i>phosphoprotein</i> (P), <i>matrix</i> (M), <i>U1</i>/<i>U2</i>/<i>U3</i> (uncharacterized accessory proteins), <i>glycoprotein</i> (G), and <i>polymerase</i> (L). We indicate in orange (EKV-1) and blue (EKV-2) segments of the viral genomes that could not be assembled from Illumina reads and instead Sanger sequenced. (<b>C</b>) Coverage plots of the final viral genomes.</p

Sero-positivity to EKV-1 and EKV-2.

<p>A serosurvey for EKV-1 and EKV-2 was performed on Nigerian samples (n = 320). Cut-off values were based on the mean of US normals (n = 137) plus either 3xSD or 5xSD (SD = standard deviation).</p><p>Sero-positivity to EKV-1 and EKV-2.</p

Examples of rhabdoviruses reported in Africa.

<p>A map depicting examples of rhabdoviruses isolated in sub-Saharan Africa. This map does not depict the current distribution of rhabdoviruses in Sub-Saharan Africa, nor is it meant as a comprehensive listing of all rhabdoviruses isolated in Africa; rather its purpose is to illustrate that many rhabdoviruses have been discovered throughout Africa over the past half-century. Country refers to the sample’s country of origin. Abbreviations: CAR, Central African Republic; DRC, Democratic Republic of Congo.</p

The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE—detected in the Yoruba population of Nigeria—conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the “emerging” nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz’s critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts