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

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. 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. 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. 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.

The Discovery of Bombali Virus Adds Further Support for Bats as Hosts of Ebolaviruses

Here we describe the complete genome of a new ebolavirus, Bombali virus (BOMV) detected in free-tailed bats in Sierra Leone (little free-tailed (Chaerephon pumilus) and Angolan free-tailed (Mops condylurus)). The bats were found roosting inside houses, indicating the potential for human transmission. We show that the viral glycoprotein can mediate entry into human cells. However, further studies are required to investigate whether exposure has actually occurred or if BOMV is pathogenic in humans.

Mannitol-fermenting Methicillin-Resistant Staphylococci (MRS) in Pig Abattoirs in Cameroon and South Africa: A Serious Food Safety Threat

Food animals can be reservoirs of methicillin-resistant staphylococci (MRS) and are involved in their zoonotic transmission through the food chain. In Africa, there is a dearth of information about the food safety issues associated with their dissemination in the farm-to-plate continuum. This study sought to determine and compare the carriage, antimicrobial resistance profiles and clonal relatedness of circulating MRS strains among pigs and exposed workers in Cameroon and South Africa. A total of 288 nasal and rectal pooled samples collected from 432 pigs as well as nasal and hand swabs from 82 humans were cultured on mannitol salt agar supplemented with 6 mg/l cefoxitin. Presumptive MRS were screened for methicillin resistance using the cefoxitin disc test and confirmed with the VITEK 2 system. Selected isolates underwent genomic fingerprinting via REP-PCR. Univariate and multivariate logistic regression analyses were performed to identify risk factors for MRS carriage in humans from a questionnaire survey among slaughterhouse workers. Overall, 75% and 70% of nasal and rectal pooled samples were respectively positive for MRS. The MRS prevalence in all pooled pig samples from Cameroon was higher than that of South Africa. MRS prevalence of carriage (nasal and hand) was higher in Cameroonian exposed workers compared to those from South Africa, with high statistical significance. Nasal MRS colonization was highly statistically associated with hand MRS (31.58% vs 86.21%; p = 0.000; OR = 13.54; 95% CI 3.99-45.95; p = 0.015). Recent antibiotic use, previous hospitalization, occupation of relatives, years in the employment and contact with poultry were the main risk factors identified in the emergence and spread of MRS. MRS are emerging as serious foodborne pathogens and present a food safety threat. There is an urgent need to implement stringent and effective prevention and containment measures to curb antibiotic resistance in the farm-to-plate continuum in Cameroon and South Africa.

Rapid Confirmation of the Zaire Ebola Virus in the Outbreak of the Equateur Province in the Democratic Republic of Congo: Implications for Public Health Interventions

Ten days after the declaration of the Ebola outbreak in the Democratic Republic of Congo, rapid identification of the species Zaire Ebola virus using partial gene amplification and nanopore sequencing backed up the use of the recombinant vesicular stomatitis virus–Zaire Ebola virus vaccine in the recommended ring vaccination strategy.

DNA Indicative of Human Bocaviruses Detected in Non-Human Primates in the Democratic Republic of the Congo

Bocaparvoviruses are members of the family Parvovirinae and human bocaviruses have been found to be associated with respiratory and gastrointestinal disease. There are four known human bocaviruses, as well as several distinct ones in great apes. The goal of the presented study was to detect other non-human primate (NHP) bocaviruses in NHP species in the Democratic Republic of the Congo using conventional broad-range PCR. We found bocavirus DNA in blood and tissues samples in 6 out of 620 NHPs, and all isolates showed very high identity (>97 %) with human bocaviruses 2 or 3. These findings suggest cross-species transmission of bocaviruses between humans and NHPs.

Virus-encoded miRNAs in Ebola Virus Disease

Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.

Taxonomy of the Family Arenaviridae and the Order Bunyavirales: Update 2018

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Serologic and Behavioral Risk Survey of Workers With Wildlife Contact in China

We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. A risk factor/exposure survey was administered to individuals with high levels of exposure to wildlife. Serological testing was performed to evaluate prior infection with several wildlife viral pathogens. Follow up serology was performed on a subset of the cohort as well as close contacts of individuals. 1,312 individuals were enrolled in the study. Contact with a wide range of wildlife species was reported in both occupational and occasional contexts. The overall proportion of individuals seropositive to any of the tested wildlife pathogens was approximately 4.0%. However, persons employed as butchers demonstrated a seropositivity of 9.0% to at least one pathogen of interest. By contrast, individuals working as hunters had lower rates of seropositivity. Among the study population, a number of other behaviors showed correlation with seropositivity, including contact with particular wildlife species such as field rats. These results demonstrate the need to further explore zoonotic risks of particular activities regarding wildlife contact, and to better understand risks of persons working as butchers with wildlife species.

Building a Global Atlas of Zoonotic Diseases

 

The Global Virome Project

Outbreaks of novel and deadly viruses highlight global vulnerability to emerging diseases, with many having massive health and economic impacts. Our adaptive toolkit—based largely on vaccines and therapeutics—is often ineffective because countermeasure development can be outpaced by the speed of novel viral emergence and spread. Following each outbreak, the public health community bemoans a lack of prescience, but after decades of reacting to each event with little focus on mitigation, we remain only marginally better protected against the next epidemic. Our ability to mitigate disease emergence is undermined by our poor understanding of the diversity and ecology of viral threats, and of the drivers of their emergence. We describe a Global Virome Project (GVP) aimed to launch in 2018 that will help identify the bulk of this viral threat and provide timely data for public health interventions against future pandemics.