Search

Mosquito-based surveillance is a practical way to estimate the risk of transmission of West Nile virus (WNV) to people. Variations in temperature and precipitation play a role in driving mosquito infection rates and transmission of WNV, motivating efforts to predict infection rates based on prior weather conditions. Weather conditions and sequential patterns of meteorological events can have particularly important, but regionally distinctive, consequences for WNV transmission, with high temperatures and low precipitation often increasing WNV mosquito infection. Predictive models that incorporate weather can thus be used to provide early indications of the risk of WNV infection. The purpose of this study was first, to assess the ability of a previously published model of WNV mosquito infection to predict infection for an area within the region for which it was developed, and second, to improve the predictive ability of this model by incorporating new weather factors that may affect mosquito development. The legacy model captured the primary trends in mosquito infection, but it was improved considerably when calibrated with local mosquito infection rates. The use of interaction terms between precipitation and temperature improved model performance. Specifically, temperature had a stronger influence than rainfall, so that lower than average temperature greatly reduced the effect of low rainfall on increased infection rates. When rainfall was lower, high temperature had an even stronger positive impact on infection rates. The final model is practical, stable, and operationally valid for predicting West Nile virus infection rates in future weeks when calibrated with local data., Journal of Medical Entomology, 53(4), pp.935-944; 2016

In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates—even in our closest living relatives, chimpanzees and bonobos ( Pan troglodytes and P. paniscus )—are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees ( P. t. schweinfurthii ), using metagenomics to characterize viromes (full viral communities) in the faeces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We identified 12 viruses from at least four viral families possessing genomes of both single-stranded RNA and single-stranded DNA. Faecal viromes of both sexes varied with chimpanzee age, but viral richness increased with age only in males. This effect was largely due to three viruses, salivirus, porprismacovirus and chimpanzee stool-associated RNA virus (chisavirus), which occurred most frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Faecal viromes are therefore useful for studying processes related to the divergent reproductive strategies of males and females, ageing, and sex differences in longevity. This article is part of the theme issue ‘Evolution of the primate ageing process'.

Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.

Reference intervals (RIs) for biochemical analytes provide baseline values for assessing physiologic status and health. We established RIs for commonly assessed blood-based analytes for polar bears from the southern Beaufort Sea. These RIs fill a knowledge gap that will inform assessments of polar bear health in a changing Arctic., Accurate reference intervals (RIs) for commonly measured blood-based analytes are essential for health monitoring programmes. Baseline values for a panel of analytes can be used to monitor physiologic and pathophysiologic processes such as organ function, electrolyte balance and protein catabolism. Our reference population includes 651 serum samples from polar bears (Ursus maritimus) from the southern Beaufort Sea (SB) subpopulation sampled in Alaska, USA, between 1983 and 2016. To establish RI for 13 biochemical analytes, we defined specific criteria for characterizing the reference population and relevant subgroups. To account for differences in seasonal life history characteristics, we determined separate RI for the spring and fall seasons, when prey availability and energetic requirements of bears differ. We established RI for five subgroups in spring based on sex, age class and denning status, and three subgroups in fall based on sex and age class in females only. Alkaline phosphatase activities were twice as high in subadult as in adult polar bears in spring (zmales = 4.08, Pmales

Bats host diverse viruses due to their unique ecology, behavior, and immunology. However, the role of other organisms with which bats interact in nature is understudied as a contributor to bat viral diversity. We discovered five viruses in the blood of fruit bats (Hypsignathus monstrosus) from the Republic of Congo. Of these five viruses, four have phylogenetic and genomic features suggesting an arthropod origin (a dicistrovirus, a nodavirus, and two tombus-like viruses), while the fifth (a hepadnavirus) is clearly of mammalian origin. We also report the parallel discovery of related tombus-like viruses in fig wasps and primitive crane flies from bat habitats, as well as high infection rates of bats with haemosporidian parasites (Hepatocystis sp.). These findings suggest transmission between arthropods and bats, perhaps through ingestion or hyperparasitism (viral infection of bat parasites). Some "bat-associated" viruses may be epidemiologically linked to bats through their ecological associations with invertebrates.

Antibiotic resistance is a global concern, although it has been studied most extensively in developed countries. We studied Escherichia coli and class 1 integrons in western Uganda by analyzing 1,685 isolates from people, domestic animals, and wild nonhuman primates near two national parks. Overall, 499 isolates (29.6%) were resistant to at least one of 11 antibiotics tested. The frequency of resistance reached 20.3% of isolates for trimethoprim-sulfamethoxazole but was nearly zero for the less commonly available antibiotics ciprofloxacin (0.4%), gentamicin (0.2%), and ceftiofur (0.1%). The frequency of resistance was 57.4% in isolates from people, 19.5% in isolates from domestic animals, and 16.3% in isolates from wild nonhuman primates. Isolates of livestock and primate origin displayed multidrug resistance patterns identical to those of human-origin isolates. The percentage of resistant isolates in people was higher near Kibale National Park (64.3%) than near Bwindi Impenetrable National Park (34.6%), perhaps reflecting local socioeconomic or ecological conditions. Across antibiotics, resistance correlated negatively with the local price of the antibiotic, with the most expensive antibiotics (nalidixic acid and ciprofloxacin) showing near-zero resistance. Among phenotypically resistant isolates, 33.2% harbored class 1 integrons containing 11 common resistance genes arranged into nine distinct gene cassettes, five of which were present in isolates from multiple host species. Overall, these results show that phenotypic resistance and class 1 integrons are distributed broadly among E. coli isolates from different host species in this region, where local socioeconomic and ecological conditions may facilitate widespread diffusion of bacteria or resistance-conferring genetic elements. IMPORTANCE Antibiotic resistance is a global problem. This study, conducted in rural western Uganda, describes antibiotic resistance patterns in Escherichia coli bacteria near two forested national parks. Resistance was present not only in people, but also in their livestock and in nearby wild nonhuman primates. Multidrug resistance and class 1 integrons containing genes that confer resistance were common and were similar in people and animals. The percentage of resistant isolates decreased with increasing local price of the antibiotic. Antibiotic resistance in this setting likely reflects environmental diffusion of bacteria or their genes, perhaps facilitated by local ecological and socioeconomic conditions.

Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to human immunodeficiency virus in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.

International audience; In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales 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.

Respiratory illnesses have caused significant mortality in African great ape populations. While much effort has been given to identifying the responsible pathogens, little is known about the factors that influence disease transmission or individual susceptibility. In the Kanyawara community of wild chimpanzees, respiratory illness has been the leading cause of mortality over 31 years, contributing to 27% of deaths. Deaths were common in all age groups except juveniles. Over 22 years of health observations, respiratory signs were rare among infants and most common among older adults of both sexes. Respiratory signs were also common among males during the transition to adulthood (ages 10–20 years), particularly among those of low rank. Respiratory signs peaked conspicuously in March, a pattern that we could not explain after modelling climatic factors, group sizes, diet or exposure to humans. Furthermore, rates of respiratory illness in the chimpanzees did not track seasonal rates of illness in the nearby village. Our data indicate that the epidemiology of chimpanzee respiratory illness warrants more investigation but clearly differs in important ways from humans. Findings on individual susceptibility patterns suggest that respiratory signs are a robust indicator for investigating immunocompetence in wild chimpanzees.

Tony L. Goldberg · Samuel Angedakin · Gilbert M. Isabirye Basuta · Michelle Brown · Thomas M. Butynski · Colin A. Chapman · Lauren Chapman · Sholly Gunter · Innocent Kato · Jean-Michel Krief · Sabrina Krief · Joanna E. Lambert · Kevin E. Langergraber · John C. Mitani · Martin N. Muller · Sherry V. Nelson · Patrick Omeja · Emily Otali · Kevin B. Potts · Elizabeth A. Ross · Jessica M. Rothman · Carolyn Rowney · Eric Sande · Thomas T. Struhsaker · Dennis Twinomugisha · David P. Watts · Geoffrey Weny · Richard W. Wrangham

We previously reported fatal infection of a captive Bornean orangutan with metacestodes of a novel taeniid tapeworm, Versteria sp. New data implicate mustelids as definitive hosts of these tapeworms in North America. At least 2 parasite genetic lineages circulate in North America, representing separate introductions from Eurasia.

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.

Wild nonhuman primates are immediate sources and long-term reservoirs of human pathogens. However, ethical and technical challenges have hampered the identification of novel blood-borne pathogens in these animals. We recently examined RNA viruses in plasma from wild African monkeys and discovered several novel, highly divergent viruses belonging to the family Arteriviridae . Close relatives of these viruses, including simian hemorrhagic fever virus, have caused sporadic outbreaks of viral hemorrhagic fever in captive macaque monkeys since the 1960s. However, arterivirus infection in wild nonhuman primates had not been described prior to 2011. The arteriviruses recently identified in wild monkeys have high sequence and host species diversity, maintain high viremia, and are prevalent in affected populations. Taken together, these features suggest that the simian arteriviruses may be “preemergent” zoonotic pathogens. If not, this would imply that biological characteristics of RNA viruses thought to facilitate zoonotic transmission may not, by themselves, be sufficient for such transmission to occur.

Simian hemorrhagic fever (SHF) is lethal for macaques. Based on clinical presentation and serological diagnosis, all reported SHF outbreaks were thought to be caused by different strains of the same virus, simian hemorrhagic fever virus (SHFV; Arteriviridae ). Here we show that the SHF outbreaks in Sukhumi in 1964 and in Alamogordo in 1989 were caused not by SHFV but by two novel divergent arteriviruses. Our results indicate that multiple divergent simian arteriviruses can cause SHF.

In 49 patients with known Ebola virus disease outcomes during the ongoing outbreak in Sierra Leone, 13 were coinfected with the immunomodulatory pegivirus GB virus C (GBV-C). Fifty-three percent of these GBV-C + patients survived; in contrast, only 22% of GBV-C − patients survived. Both survival and GBV-C status were associated with age, with older patients having lower survival rates and intermediate-age patients (21 to 45 years) having the highest rate of GBV-C infection. Understanding the separate and combined effects of GBV-C and age on Ebola virus survival may lead to new treatment and prevention strategies, perhaps through age-related pathways of immune activation.

To the Editor: Hepatitis A (HAV; family Picornaviridae; genus Hepatovirus) is an ≈7.5-kb single-stranded positive-sense RNA virus that causes acute inflammation of the liver in humans and nonhuman primates. Although HAV is most commonly transmitted by food and water contaminated with feces, humans have acquired HAV from handling infected nonhuman primates in captivity (1). HAV has been detected in recently imported captive primates after spontaneous outbreaks of acute hepatitis in animal facilities, but the definitive hosts of this virus have remained obscure (2,3). We identified by next-generation sequencing HAV in the blood of a free-living olive baboon (Papio anubis) from Kibale National Park, Uganda, sampled in September 2010. Subsequent testing of a separate Kibale olive baboon troop in 2014 indicated the virus was prevalent and shed in feces. As part of a long-term study of nonhuman primate health and ecology, 23 animals were immobilized and sampled in 2010 as previously described (4). All animal protocols received prior approval from the Uganda National Council for Science and Technology (Kampala, Uganda), the Uganda Wildlife Authority (Kampala, Uganda), and the University of Wisconsin–Madison Animal Care and Use Committee (Madison, WI, USA). All samples were shipped in accordance with international laws under Convention on International Trade in Endangered Species of Wild Fauna and Flora Ugandan permit no. 002290. During May 2012, we subjected total RNA from 1 mL of blood plasma of each animal to next-generation sequencing as previously described (4); results showed HAV-like sequences in 1 of 23 baboons. De novo assembly of these reads yielded a nearly complete HAV genome, which we term KibOB-1. KibOB-1 is most similar (94.2% nt identity; Figure) to AGM-27, an HAV originally detected in an African green monkey (Chlorocebus aethiops) imported to a Russian primate facility from Kenya (3). Figure Whole-genome phylogenetic reconstruction of representative HAVs. HAVs are grouped into 6 genotypes based on 168 bp of the C-terminal extension of the viral protein 1 gene. Baboon HAV detected in Kibale National Park, Uganda, in 2010 and 2014 (GenBank ... For 11 baboons, we also collected a paired fecal sample, which we analyzed for evidence of viral shedding. Samples were preserved in RNAlater (Ambion Inc., Austin, TX, USA) at −20°C, and viral RNA was isolated by using the ZR Soil/Fecal RNA Microprep kit (Zymo Research, Irvine, CA, USA) following manufacturer’s protocols. Reverse transcription PCR (RT-PCR) of RNA was primed with random hexamers by using the RNA to cDNA Ecodry Premix (Random Hexamers) (Clontech Laboratories, Inc., Mountain View, CA, USA), and diagnostic PCR was conducted with primers flanking the C-terminal extension of the HAV viral protein (VP) 1 gene (pX) by using the High Fidelity PCR Master Mix-Ecodry Premix (Clontech Laboratories, Inc.). Five of 11 paired fecal samples tested positive for HAV by RT-PCR, indicating a higher prevalence of the virus in feces than in blood. We then surveyed a second troop of habituated olive baboons at the same field site during February–April 2014 (5). From these baboons, 7 of 19 fecal samples tested positive by RT-PCR. Confirmatory Sanger sequencing of RT-PCR amplicons was successful for 3 of these 7 animals (GenBank accession nos. {"type":"entrez-nucleotide-range","attrs":{"text":"KT819576-KT819578","start_term":"KT819576","end_term":"KT819578","start_term_id":"1036222291","end_term_id":"1036222295"}}KT819576-KT819578). Phylogenetic analyses of these sequences demonstrate monophyly and a low degree of interhost variability (>94% nt identity). The risk to humans posed by KibOb-1 remains unknown. Although human infection with HAV genotype V has not been reported, evidence suggests that HAV variants might be capable of infecting a diversity of primate hosts (6). Although it is not known whether the closely related AGM-27 strain was discovered infecting its natural host, the similarity of KibOB-1 and AGM-27 raises the possibility of a recent host transfer. Major host shifts characterize the evolutionary histories of recently discovered bat and rodent hepatoviruses (7). Host fidelity of KibOB-1 is similarly unknown, but experimental infection of several nonhuman primate species with the similar AGM-27 virus found varying pathogenicity in different species (6). In particular, the AGM-27 caused productive infection in chimpanzees, with stimulation of a broadly reactive HAV immunoglobulin response (6). Human and simian HAVs are considered a single serotype (6); thus, serosurveillance for HAV in humans might be unable to distinguish between human and zoonotic simian HAV infection, enabling the possibility of cryptic zoonotic transmission. Similarly, detection of HAV antibodies in wild primates, such as in a recent study of baboons in South Africa living in close proximity to humans (8), might not indicate anthroponotic transmission of human viruses but rather infection with an endemic HAV. Prior studies have documented cross-species transmission between the primates of Kibale National Park and neighboring human populations, especially of gastrointestinal pathogens (9). A study tracking food-crop–raiding events on 97 farms within 0.5 km of Kibale’s forest edge found that 72% of households faced baboon raids over a 23-month period, including 228 discrete baboon raids (10). This finding suggests that a major portion of the local community remains at risk for exposure to potentially infectious baboon excreta. Such exposure, in addition to the evidence presented here that HAV is prevalent in wild baboons of Uganda and is shed into the environment, merits increased attention to the zoonotic risk for simian hepatoviruses.

Arthropod-borne viruses are among the most genetically constrained RNA viruses, yet they have a remarkable propensity to adapt and emerge. We studied wild birds and mosquitoes naturally infected with West Nile virus (WNV) in a ‘hot spot’ of virus transmission in Chicago, IL, USA. We generated full coding WNV genome sequences from spatiotemporally matched bird and mosquito samples using high-throughput sequencing, allowing a molecular evolutionary assessment with deep coverage. Mean FST among samples was 0.66 (±0.02 SE) and was bimodal, with mean nucleotide diversity being higher between samples (interhost πN = 0.001; πS = 0.024) than within them (intrahost πN 1.01 (in the PrM, NS2a, NS3, NS4b, and 5'-noncoding genomic regions) showed bird versus mosquito variant frequency differences of >30 per cent and/or polymorphisms fixed in ≥5 host or vector individuals, suggesting host tropism for these variants. However, phylogenetic analyses demonstrated a lack of grouping by bird or mosquito, most inter-sample differences were synonymous (mean interhost πN/πS = 0.04), and there was no significant difference between hosts and vectors in either their nucleotide diversities or levels of purifying selection (mean intrahost πN/πS = 0.28 in birds and πN/πS = 0.21 in mosquitoes). This finding contrasts with the ‘trade-off’ and ‘selective sieve’ hypotheses that have been proposed and tested in the laboratory, which predict strong host versus vector effects on WNV genetic variation, with heightened selective constraint in birds alternating with heightened viral diversity in mosquitoes. Overall, our data show WNV to be highly selectively constrained within and between both hosts and vectors but still able to vary at a limited number of sites across the genome. Such site-specific plasticity in the face of overall selective constraint may offer a mechanism whereby highly constrained viruses such as WNV and its relatives can still adapt and emerge.

Simian hemorrhagic fever virus (SHFV) causes a severe and almost uniformly fatal viral hemorrhagic fever in Asian macaques but is thought to be nonpathogenic for humans. To date, the SHFV life cycle is almost completely uncharacterized on the molecular level. Here, we describe the first steps of the SHFV life cycle. Our experiments indicate that SHFV enters target cells by low-pH-dependent endocytosis. Dynamin inhibitors, chlorpromazine, methyl-β-cyclodextrin, chloroquine, and concanamycin A dramatically reduced SHFV entry efficiency, whereas the macropinocytosis inhibitors EIPA, blebbistatin, and wortmannin and the caveolin-mediated endocytosis inhibitors nystatin and filipin III had no effect. Furthermore, overexpression and knockout study and electron microscopy results indicate that SHFV entry occurs by a dynamin-dependent clathrin-mediated endocytosis-like pathway. Experiments utilizing latrunculin B, cytochalasin B, and cytochalasin D indicate that SHFV does not hijack the actin polymerization pathway. Treatment of target cells with proteases (proteinase K, papain, α-chymotrypsin, and trypsin) abrogated entry, indicating that the SHFV cell surface receptor is a protein. Phospholipases A2 and D had no effect on SHFV entry. Finally, treatment of cells with antibodies targeting CD163, a cell surface molecule identified as an entry factor for the SHFV-related porcine reproductive and respiratory syndrome virus, diminished SHFV replication, identifying CD163 as an important SHFV entry component. IMPORTANCE Simian hemorrhagic fever virus (SHFV) causes highly lethal disease in Asian macaques resembling human illness caused by Ebola or Lassa virus. However, little is known about SHFV's ecology and molecular biology and the mechanism by which it causes disease. The results of this study shed light on how SHFV enters its target cells. Using electron microscopy and inhibitors for various cellular pathways, we demonstrate that SHFV invades cells by low-pH-dependent, actin-independent endocytosis, likely with the help of a cellular surface protein.

Over the past decade several studies have reported that the gut microbiomes of mammals with similar dietary niches exhibit similar compositional and functional traits. However, these studies rely heavily on samples from captive individuals and often confound host phylogeny, gut morphology, and diet. To more explicitly test the influence of host dietary niche on the mammalian gut microbiome we use 16S rRNA gene amplicon sequencing and shotgun metagenomics to compare the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely related non-folivores, evenly distributed throughout the primate order and representing a range of gut morphological specializations. While folivory results in some convergent microbial traits, collectively we show that the influence of host phylogeny on both gut microbial composition and function is much stronger than that of host dietary niche. This pattern does not result from differences in host geographic location or actual dietary intake at the time of sampling, but instead appears to result from differences in host physiology. These findings indicate that mammalian gut microbiome plasticity in response to dietary shifts over both the lifespan of an individual host and the evolutionary history of a given host species is constrained by host physiological evolution. Therefore, the gut microbiome cannot be considered separately from host physiology when describing host nutritional strategies and the emergence of host dietary niches.

Few studies have combined genetic association analyses with functional characterization of infection-associated SNPs in natural populations of nonhuman primates. Here, we investigate the relationship between host genetic variation, parasitism and natural selection in a population of red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. We collected parasitological, cellular and genomic data to test the following hypotheses: (i) MHC-DQA1 regulatory genetic variation is associated with control of whipworm (Trichuris) infection in a natural population of red colobus; (ii) infection-associated SNPs are functional in driving differential gene expression in vitro; and (iii) balancing selection has shaped patterns of variation in the MHC-DQA1 promoter. We identified two SNPs in the MHC-DQA1 promoter, both in transcription factor binding sites, and both of which are associated with decreased control of Trichuris infection. We characterized the function of both SNPs by testing differences in gene expression between the two alleles of each SNP in two mammalian cell lines. Alleles of one of the SNPs drove differential gene expression in both cell lines, while the other SNP drove differences in expression in one of the cell lines. Additionally, we found evidence of balancing selection acting on the MHC-DQA1 promoter, including extensive trans-species polymorphisms between red colobus and other primates, and an excess of intermediate-frequency alleles relative to genome-wide, coding and noncoding RADseq data. Our data suggest that balancing selection provides adaptive regulatory flexibility that outweighs the consequences of increased parasite infection intensity in heterozygotes.

Bats are natural reservoir hosts of highly virulent pathogens such as Marburg virus, Nipah virus, and SARS coronavirus. However, little is known about the role of bat ectoparasites in transmitting and maintaining such viruses. The intricate relationship between bats and their ectoparasites suggests that ectoparasites might serve as viral vectors, but evidence to date is scant. Bat flies, in particular, are highly specialized obligate hematophagous ectoparasites that incidentally bite humans. Using next-generation sequencing, we discovered a novel ledantevirus (mononegaviral family Rhabdoviridae, genus Ledantevirus) in nycteribiid bat flies infesting pteropodid bats in western Uganda. Mitochondrial DNA analyses revealed that both the bat flies and their bat hosts belong to putative new species. The coding-complete genome of the new virus, named Kanyawara virus (KYAV), is only distantly related to that of its closest known relative, Mount Elgon bat virus, and was found at high titers in bat flies but not in blood or on mucosal surfaces of host bats. Viral genome analysis indicates unusually low CpG dinucleotide depletion in KYAV compared to other ledanteviruses and rhabdovirus groups, with KYAV displaying values similar to rhabdoviruses of arthropods. Our findings highlight the possibility of a yet-to-be-discovered diversity of potentially pathogenic viruses in bat ectoparasites.

Simian arteriviruses are a diverse clade of viruses infecting captive and wild nonhuman primates. We recently reported that Kibale red colobus virus 1 (KRCV-1) causes a mild and self-limiting disease in experimentally infected crab-eating macaques, while simian hemorrhagic fever virus (SHFV) causes lethal viral hemorrhagic fever. Here we characterize how these viruses evolved during replication in cell culture and in experimentally infected macaques. During passage in cell culture, 68 substitutions that were localized in open reading frames (ORFs) likely associated with host cell entry and exit became fixed in the KRCV-1 genome. However, we did not detect any strong signatures of selection during replication in macaques. We uncovered patterns of evolution that were distinct from those observed in surveys of wild red colobus monkeys, suggesting that these species may exert different adaptive challenges for KRCV-1. During SHFV infection, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome. Overall, our data suggest that patterns of evolution differ markedly among simian arteriviruses and among host species. IMPORTANCE Certain RNA viruses can cross species barriers and cause disease in new hosts. Simian arteriviruses are a diverse group of related viruses that infect captive and wild nonhuman primates, with associated disease severity ranging from apparently asymptomatic infections to severe, viral hemorrhagic fevers. We infected nonhuman primate cell cultures and then crab-eating macaques with either simian hemorrhagic fever virus (SHFV) or Kibale red colobus virus 1 (KRCV-1) and assessed within-host viral evolution. We found that KRCV-1 quickly acquired a large number of substitutions in its genome during replication in cell culture but that evolution in macaques was limited. In contrast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins. These patterns suggest that in addition to diverse pathogenic phenotypes, these viruses may also exhibit distinct patterns of within-host evolution both in vitro and in vivo .

Infectious disease transmission is a cost of sociality in humans and other animals. Nevertheless, the mechanisms linking social behaviour to infection risk are poorly known. We conducted a field experiment to examine how host intrinsic traits, behaviour and physiology affect infection of nonhuman primates with gastrointestinal parasites. We measured rate to reinfection in a social group of red-capped mangabeys, Cercocebus torquatus, following chemotherapeutic treatment for parasite infections. By measuring behaviour, infection and glucocorticoid levels, we compared the relative effects of space sharing, directional contact and physiological stress on risk of acquiring new infections. We found that, within proximity networks, individuals that were central and well connected and that had a tendency to switch groups were at increased risk of infection with helminths. Protozoan infections, however, were acquired more uniformly across the population. In general, position in the social network and, in particular, space sharing appears to be more important than the immunosuppressive effects of physiological stress or host traits in determining risk of infection. Our results suggest that future studies of disease ecology within wildlife populations should focus on measures of network association in addition to individual host traits.

Dramatic increases in human populations and per capita consumption, climate change, overexploitation of marine and freshwater resources, and deforestation have caused a litany of negative consequences for biodiversity. Such doom-and-gloom scenarios are widely known, frequently cited and frankly depressing. Although accurate assessments of threats have clear value for intervention planning, we believe there is also a need to reflect on successes. Such reflection provides balance to negative scenarios and may shift attention towards constructive, positive action. Here we use a systematic evaluation of 90 success stories provided by conservation scientists and practitioners to explore the characteristics of the projects perceived as being associated with success. Success was deemed to have occurred for 19.4% of the projects simply because an event had occurred (e.g. a law was passed) and for 36.1% of projects quantitative data indicated success (e.g. censuses demonstrated population increase). However, for most projects (63.9%) there was no evaluation and success was defined by the subjective opinion of the respondent. Conservation community members viewed successful projects most often as those being long-term (88%), small in spatial scale (52%), with a relatively low budget (68%), and involving a protectionist approach alone or in combination with another approach. These results highlight the subjectivity of definitions of success in conservation but also the characteristics of conservation efforts that the conservation community perceives as indicative of success.

Frozen blood samples from 13 species of free-ranging birds (n = 65) and captive Chilean flamingos (Phoenicopterus chilensis) (n = 46) housed outdoors in the Chicago area were screened for Plasmodium. With the use of a modified polymerase chain reaction, 20/65 (30.8%) of free-ranging birds and 26/46 (56.5%) of flamingos were classified as positive for this parasite genus. DNA sequencing of the parasite cytochrome b gene in positive samples demonstrated that eight species of free-ranging birds were infected with five different Plasmodium spp. cytochrome b lineages, and all positive Chilean flamingos were infected with Plasmodium spp. cytochrome b lineages most closely related to organisms in the Novyella subgenus. These results show that Chilean flamingos may harbor subclinical malaria infections more frequently than previously estimated, and that they may have increased susceptibility to some Plasmodium species.

A critical failure in our preparedness for an influenza pandemic is the lack of a universal vaccine. Influenza virus strains diverge by 1 to 2% per year, and commercially available vaccines often do not elicit protection from one year to the next, necessitating frequent formulation changes. This represents a major challenge to the development of a cross-protective vaccine that can protect against circulating viral antigenic diversity. We have constructed a recombinant modified vaccinia virus Ankara (MVA) that expresses an H5N1 mosaic hemagglutinin (H5M) (MVA-H5M). This mosaic was generated in silico using 2,145 field-sourced H5N1 isolates. A single dose of MVA-H5M provided 100% protection in mice against clade 0, 1, and 2 avian influenza viruses and also protected against seasonal H1N1 virus (A/Puerto Rico/8/34). It also provided short-term (10 days) and long-term (6 months) protection postvaccination. Both neutralizing antibodies and antigen-specific CD4 + and CD8 + T cells were still detected at 5 months postvaccination, suggesting that MVA-H5M provides long-lasting immunity. IMPORTANCE Influenza viruses infect a billion people and cause up to 500,000 deaths every year. A major problem in combating influenza is the lack of broadly effective vaccines. One solution from the field of human immunodeficiency virus vaccinology involves a novel in silico mosaic approach that has been shown to provide broad and robust protection against highly variable viruses. Unlike a consensus algorithm which picks the most frequent residue at each position, the mosaic method chooses the most frequent T-cell epitopes and combines them to form a synthetic antigen. These studies demonstrated that a mosaic influenza virus H5 hemagglutinin expressed by a viral vector can elicit full protection against diverse H5N1 challenges as well as induce broader immunity than a wild-type hemagglutinin.

Zoonotic pathogens cause an estimated 70% of emerging and re-emerging infectious diseases in humans. In sub-Saharan Africa, bushmeat hunting and butchering is considered the primary risk factor for human-wildlife contact and zoonotic disease transmission, particularly for the transmission of simian retroviruses. However, hunting is only one of many activities in sub-Saharan Africa that bring people and wildlife into contact. Here, we examine human-animal interaction in western Uganda, identifying patterns of injuries from animals and contact with nonhuman primates. Additionally, we identify individual-level risk factors associated with contact. Nearly 20% (246/1,240) of participants reported either being injured by an animal or having contact with a primate over their lifetimes. The majority (51.7%) of injuries were dog bites that healed with no long-term medical consequences. The majority (76.8%) of 125 total primate contacts involved touching a carcass; however, butchering (20%), hunting (10%), and touching a live primate (10%) were also reported. Red colobus (Piliocolobus rufomitratus tephrosceles) accounted for most primate contact events. Multivariate logistic regression indicated that men who live adjacent to forest fragments are at elevated risk of animal contact and specifically primate contact. Our results provide a useful comparison to West and Central Africa where "bushmeat hunting" is the predominant paradigm for human-wildlife contact and zoonotic disease transmission.

Graphical abstract Highlights ► Co-circulating hematozoan parasites in avian amplification hosts for West Nile virus. ► Hematocrit centrifuge technique for microfilariae and trypanosomes. ► Phylogenetics describe community composition of filarioid nematodes and trypanosomes. ► Parasites have potential for direct or indirect interactions with West Nile virus., Hosts are commonly infected with a suite of parasites, and interactions among these parasites can affect the size, structure, and behavior of host–parasite communities. As an important step to understanding the significance of co-circulating parasites, we describe prevalence of co-circulating hemoparasites in two important avian amplification hosts for West Nile virus (WNV), the American robin (Turdus migratorius) and house sparrow (Passer domesticus), during the 2010–2011 in Chicago, Illinois, USA. Rates of nematode microfilariemia were 1.5% of the robins (n = 70) and 4.2% of the house sparrows (n = 72) collected during the day and 11.1% of the roosting robins (n = 63) and 0% of the house sparrows (n = 11) collected at night. Phylogenetic analysis of nucleotide sequences of the 18S rRNA and cytochrome oxidase subunit I (COI) genes from these parasites resolved two clades of filarioid nematodes. Microscopy revealed that 18.0% of American robins (n = 133) and 16.9% of house sparrows (n = 83) hosted trypanosomes in the blood. Phylogenetic analysis of nucleotide sequences from the 18s rRNA gene revealed that the trypanosomes fall within previously described avian trypanosome clades. These results document hemoparasites in the blood of WNV hosts in a center of endemic WNV transmission, suggesting a potential for direct or indirect interactions with the virus.

Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate “microbiomes” remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance.

Ticks in the nostrils of humans visiting equatorial African forests have been reported sporadically for decades, but their taxonomy and natural history have remained obscure. We report human infestation with a nostril tick in Kibale National Park, Uganda, coincident with infestation of chimpanzees in the same location with nostril ticks, as shown by high-resolution digital photography. The human-derived nostril tick was identified morphologically and genetically as a nymph of the genus Amblyomma, but the mitochondrial 12S ribosomal RNA or the nuclear intergenic transcribed spacer 2 DNA sequences of the specimen were not represented in GenBank. These ticks may represent a previously uncharacterized species that is adapted to infesting chimpanzee nostrils as a defense against grooming. Ticks that feed upon apes and humans may facilitate cross-species transmission of pathogens, and the risk of exposure is likely elevated for persons who frequent ape habitats.

a b s t r a c t Bonefish (Albula spp.) are a group of fishes that inhabit tropical and subtropical marine waters worldwide. Large gaps in our understanding of the ecology of these fishes exist despite their economic importance as a sport fish and their potential role in the ecological functioning of coastal systems. Using a passive acoustic telemetry array, we monitored the movement patterns of A. vulpes along the north coast of Cape Eleuthera, The Bahamas. During the course of the study, we successfully detected 15 individuals for periods exceeding six months that permitted us to observe several previously unknown movement pat- terns for bonefish. Data indicate that bonefish exhibit periods of site fidelity where they repeatedly visit the same tidal creeks, interspersed with transient periods (up to 339 days) in which they utilize large areas of shallow coastal habitats or disappear from the study area entirely. Relative activity space, as measured by minimum linear dispersal, median distance traveled, and mean number of receivers visited daily, did not vary with fish size. Individuals associated in schools tended to display nearly synchronous movements. School-fidelity in bonefish may be influenced by school size, the duration in which an indi- vidual has been in the school, and the frequency with which schools mix. Bonefish responded to tidal influences and tended to move out of tidal creeks on outgoing tides and into creeks or shallow habitats during incoming tides. There was also evidence of increased use of tidal creeks during daytime when con- trolling for tidal phase. Seasonal movements toward the seaward portion of the array likely correspond with spawning. In general, the movement patterns of bonefish we observed demonstrate the importance of this species in the connectivity between nearshore (e.g., mangrove tidal creeks) and offshore habitats. Moreover, because residency patterns in a given area vary greatly among individuals and over time, this work points to the need to examine population mixing and spatial ecology over larger temporal and spatial scales.

Understanding how human activities affect wild primates is critical to the design of effective conservation strategies. Despite this need, few studies have examined the physiological and behavioral effects of field research methods in the wild. Here, we examine how the stress response, i.e., fecal cortisol, and behavior of Ugandan red colobus monkeys (Procolobus rufomitratus) in Kibale National Park are affected by chemical immobilization and collaring, i.e., capture. We compare this anthropogenic stressor to a naturally occurring stressor: a chimpanzee (Pan troglodytes) predation attack. Two adult males had peak cortisol levels of 283 and 284 ng/g 2–3 d after capture, which were 190% and 182% above their baseline levels, i.e., the first sample taken immediately after capture, but these peak levels did not remain elevated. Using long-term data, i.e., 11 mo of data, we found no difference in fecal cortisol levels between 10 darted and collared individuals and 14 individuals living in the same social group that were not darted or collared. For the chimpanzee attack, peak fecal cortisol levels (147–211% above baseline) were recorded 1–4 d after the attack, but these levels also did not remain elevated for long. These data show that darting and collaring and a chimpanzee predation attempt caused an acute stress response, but neither leads to sustained elevated cortisol levels. Thus, in situations in which research contributes significantly to the conservation of primates and cannot be conducted noninvasively, capture darting appears to be a useful technique with minimal long-term effects as long as injury and mortality are avoided. However, we encourage researchers to make similar physiological and behavioral comparisons in other field studies using similar techniques to provide a better understanding of the effects of research practices on the stress physiology and social behavior of wild primates.

GB virus B (GBV-B; family Flaviviridae , genus Hepacivirus ) has been studied in New World primates as a model for human hepatitis C virus infection, but the distribution of GBV-B and its relatives in nature has remained obscure. Here, we report the discovery of a novel and highly divergent GBV-B-like virus in an Old World monkey, the black-and-white colobus ( Colobus guereza ), in Uganda. The new virus, guereza hepacivirus (GHV), clusters phylogenetically with GBV-B and recently described hepaciviruses infecting African bats and North American rodents, and it shows evidence of ancient recombination with these other hepaciviruses. Direct sequencing of reverse-transcribed RNA from blood plasma from three of nine colobus monkeys yielded near-complete GHV genomes, comprising two distinct viral variants. The viruses contain an exceptionally long nonstructural 5A (NS5A) gene, approximately half of which codes for a protein with no discernible homology to known proteins. Computational structure-based analyses indicate that the amino terminus of the GHV NS5A protein may serve a zinc-binding function, similar to the NS5A of other viruses within the family Flaviviridae . However, the 521-amino-acid carboxy terminus is intrinsically disordered, reflecting an unusual degree of structural plasticity and polyfunctionality. These findings shed new light on the natural history and evolution of the hepaciviruses and on the extent of structural variation within the Flaviviridae .

Hemoparasites of the apicomplexan family Plasmodiidae include the etiological agents of malaria, as well as a suite of non-human primate parasites from which the human malaria agents evolved. Despite the significance of these parasites for global health, little information is available about their ecology in multi-host communities. Primates were investigated in Kibale National Park, Uganda, where ecological relationships among host species are well characterized. Blood samples were examined for parasites of the genera Plasmodium and Hepatocystis using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene, followed by Sanger sequencing. To assess co-infection, “deep sequencing” of a variable region within cytochrome b was performed. Out of nine black-and-white colobus (Colobus guereza), one blue guenon (Cercopithecus mitis), five grey-cheeked mangabeys (Lophocebus albigena), 23 olive baboons (Papio anubis), 52 red colobus (Procolobus rufomitratus) and 12 red-tailed guenons (Cercopithecus ascanius), 79 infections (77.5%) were found, all of which were Hepatocystis spp. Sanger sequencing revealed 25 different parasite haplotypes that sorted phylogenetically into six species-specific but morphologically similar lineages. “Deep sequencing” revealed mixed-lineage co-infections in baboons and red colobus (41.7% and 64.7% of individuals, respectively) but not in other host species. One lineage infecting red colobus also infected baboons, but always as the minor variant, suggesting directional cross-species transmission. Hepatocystis parasites in this primate community are a diverse assemblage of cryptic lineages, some of which co-infect hosts and at least one of which can cross primate species barriers.

Reoviruses (family Reoviridae) infect vertebrate and invertebrate hosts with clinical effects ranging from inapparent to lethal. Here, we describe the discovery and characterization of Largemouth bass reovirus (LMBRV), found during investigation of a mortality event in wild largemouth bass (Micropterus salmoides) in 2015 in WI, USA. LMBRV has spherical virions of approximately 80 nm diameter containing 10 segments of linear dsRNA, aligning it with members of the genus Orthoreovirus, which infect mammals and birds, rather than members of the genus Aquareovirus, which contain 11 segments and infect teleost fishes. LMBRV is only between 24 % and 68 % similar at the amino acid level to its closest relative, Piscine reovirus (PRV), the putative cause of heart and skeletal muscle inflammation of farmed salmon. LMBRV expands the known diversity and host range of its lineage, which suggests that an undiscovered diversity of related pathogenic reoviruses may exist in wild fishes.

Nonhuman primates (NHPs) are a historically important source of zoonotic viruses and are a gold-standard model for research on many human pathogens. However, with the exception of simian immunodeficiency virus (SIV) (family Retroviridae ), the blood-borne viruses harbored by these animals in the wild remain incompletely characterized. Here, we report the discovery and characterization of two novel simian pegiviruses (family Flaviviridae ) and two novel simian arteriviruses (family Arteriviridae ) in wild African green monkeys from Zambia (malbroucks [ Chlorocebus cynosuros ]) and South Africa (vervet monkeys [ Chlorocebus pygerythrus ]). We examine several aspects of infection, including viral load, genetic diversity, evolution, and geographic distribution, as well as host factors such as age, sex, and plasma cytokines. In combination with previous efforts to characterize blood-borne RNA viruses in wild primates across sub-Saharan Africa, these discoveries demonstrate that in addition to SIV, simian pegiviruses and simian arteriviruses are widespread and prevalent among many African cercopithecoid (i.e., Old World) monkeys. IMPORTANCE Primates are an important source of viruses that infect humans and serve as an important laboratory model of human virus infection. Here, we discover two new viruses in African green monkeys from Zambia and South Africa. In combination with previous virus discovery efforts, this finding suggests that these virus types are widespread among African monkeys. Our analysis suggests that one of these virus types, the simian arteriviruses, may have the potential to jump between different primate species and cause disease. In contrast, the other virus type, the pegiviruses, are thought to reduce the disease caused by human immunodeficiency virus (HIV) in humans. However, we did not observe a similar protective effect in SIV-infected African monkeys coinfected with pegiviruses, possibly because SIV causes little to no disease in these hosts.

The history of agriculture includes many animal and plant disease events that have had major consequences for the sector, as well as for humans. At the same time, human activities beyond agriculture have often driven the emergence of diseases. The more that humans expand the footprint of the global population, encroach into natural habitats, alter these habitats to extract resources and intensify food production, as well as move animals, people and commodities along with the pathogens they carry, the greater the potential for pathogens and pests to spread and for infection to emerge or re‐emerge. While essential to human well‐being, producing food also plays a major role in disease dynamics. The risk of emergence of pests and pathogens has increased as a consequence of global changes in the way food is produced, moved and consumed. Climate change is likely to increase pressure on the availability of food and provide newly suitable conditions for invasive pests and pathogens. Human population displacements due to economic, political and humanitarian crises represent another set of potential drivers for emerging issues. The overlapping drivers of plant, animal and human disease emergence and environmental changes point towards the concept of ‘One Health’. This paradigm underlines the urgent need to understand the influence of human behaviour and incorporate this understanding into our approach to emerging risks. For this, we face two major challenges. One is cultural; the second is methodological. We have to look at systems not under the narrow view of specific hazards but with a wider approach to system dynamics, and consider a broad spectrum of potential outcomes in terms of risk. In addition, we have to make sense of the vast amounts of data that are available in the modern age. This paper aims to help in preparing for the cultural and methodological shifts needed in our approach to emerging risks.

Parasites are ubiquitous in wildlife populations, but physiological and behavioural responses of hosts to infection are difficult to measure. We experimentally treated semi-free-ranging red-capped mangabeys ( Cercocebus torquatus ) in Nigeria with antiparasitic drugs and examined subsequent changes in glucocorticoid production and individual behaviour. Because both parasites and stress impact energy balance and health, we measured (i) behavioural time re-allocation via activity budgets, (ii) social relationships (e.g. social connectivity and dominance hierarchy stability) and (iii) body condition. We collected triplicate faecal samples ( n = 441) from 49 individuals prior to and following treatment. Cortisol levels fluctuated in parallel with parasite abundance. Elevations in cortisol, but not parasitism, were related to reduced body condition. Behaviour also shifted according to infection status, with uninfected individuals spending more time foraging and less time resting and vigilant compared with when they were infected. Time spent feeding, travelling or socializing did not differ between pre- and post-treatment time periods. Group cohesion, but not dominance stability, changed following treatment, suggesting parasite-induced social avoidance. Together, these findings show a coordinated response to infection that promotes host tolerance through stress and energy conservation, reduces transmission risk and increases protection when infected hosts are vulnerable.

In western Uganda, the landscape surrounding Kibale National Park (KNP) contains households, trading centers, roads, fields, and forest fragments. The mosaic arrangement of these landscape features is thought to enhance human-primate interaction, leading to primate population declines and increased bi-directional disease transmission. Using a social-ecological systems research framework that captures the complexity of interaction among people, wildlife, and environment, we studied five forest fragments near KNP and conducted intensive on-the-ground mapping to identify locations of human-primate spatial overlap. Primate locations and human activities were distributed within, on the edges, and far beyond fragment borders. Analysis of shared spaces indicated that 5.5% of human space overlapped with primate spaces, while 69.5% of primate spaces overlapped with human spaces. Nearest neighbor analysis indicated that human activities were significantly spatially clustered within and around individual fragments, as were primate locations. Getis-Ord statistics revealed statistically significant "hotspots" of human activity and primate activity, but only one location where spatial overlap between humans and primates was statistically significant. Human activities associated with collecting fuelwood and other forest products were the primary drivers of human-primate overlap; however, primates also spent time outside of forest fragments in agricultural spaces. These results demonstrate that fragmented landscapes are not uniform with respect to human-primate overlap, and that the implications of human-primate interaction, such as primate population declines and possible cross-species disease transmission, are spatially aggregated.

Simian hemorrhagic fever virus (SHFV) is an arterivirus that causes severe disease in captive macaques. We describe two new SHFV variants subclinically infecting wild African red-tailed guenons ( Cercopithecus ascanius ). Both variants are highly divergent from the prototype virus and variants infecting sympatric red colobus ( Procolobus rufomitratus ). All known SHFV variants are monophyletic and share three open reading frames not present in other arteriviruses. Our data suggest a need to modify the current arterivirus classification.

No longer do you have to visit rural areas to find ticks; birds are flying them directly to you. When researchers sampled several thousand birds in Chicago, they found that some carried ticks and that some of these ticks carried the organism that spreads Lyme disease. Although the number of infected ticks on these birds was low, risk for their invading an area and spreading infection to humans cannot be ignored. If conditions are favorable, a few infected ticks can quickly multiply. Migratory birds also carried tick species only known to be established in Central and South America. Limited introduction and successful establishment of ticks and disease-carrying organisms pose a major health risk for humans, wildlife, and domestic animals in urban environments worldwide., Bird-facilitated introduction of ticks and associated pathogens is postulated to promote invasion of tick-borne zoonotic diseases into urban areas. Results of a longitudinal study conducted in suburban Chicago, Illinois, USA, during 2005–2010 show that 1.6% of 6,180 wild birds captured in mist nets harbored ticks. Tick species in order of abundance were Haemaphysalis leporispalustris, Ixodes dentatus, and I. scapularis, but 2 neotropical tick species of the genus Amblyomma were sampled during the spring migration. I. scapularis ticks were absent at the beginning of the study but constituted the majority of ticks by study end and were found predominantly on birds captured in areas designated as urban green spaces. Of 120 ticks, 5 were infected with Borrelia burgdorferi, spanning 3 ribotypes, but none were infected with Anaplasma phagocytophilum. Results allow inferences about propagule pressure for introduction of tick-borne diseases and emphasize the large sample sizes required to estimate this pressure.

Analysis of molecular genetic diversity in nine marker regions of five genes within the bacteriophage WO genomic region revealed high diversity of the Wolbachia pipentis strain wPip in a population of Culex pipiens L. sampled in metropolitan Chicago, IL. From 166 blood fed females, 50 distinct genetic profiles of wPip were identified. Rarefaction analysis suggested a maximum of 110 profiles out of a possible 512 predicted by combinations of the nine markers. A rank-abundance curve showed that few strains were common and most were rare. Multiple regression showed that markers associated with gene Gp2d, encoding a partial putative capsid protein, were significantly associated with ancestry of individuals either to form molestus or form pipiens, as determined by prior microsatellite allele frequency analysis. None of the other eight markers was associated with ancestry to either form, nor to ancestry to Cx. quinquefasciatus Say. Logistic regression of host choice (mammal vs. avian) as determined by bloodmeal analysis revealed that significantly fewer individuals that had fed on mammals had the Gp9a genetic marker (58.5%) compared with avian-fed individuals (88.1%). These data suggest that certain wPip molecular genetic types are associated with genetic admixturing in the Cx. pipiens complex of metropolitan Chicago, IL, and that the association extends to phenotypic variation related to host preference.

Please cite this paper as: Bearden et al. (2012) An outbreak of the 2009 influenza a (H1N1) virus in a children’s hospital. Influenza and Other Respiratory Viruses 6(5), 374–379. Context Preventing nosocomial transmission of influenza is essential to reduce the morbidity and mortality associated with this infection. In October 2009, an outbreak of the 2009 influenza A (H1N1) virus occurred in a hematology ward of a children’s hospital over a 21-day period and involved two patients and four healthcare workers. Objective To investigate nosocomial transmission of the 2009 influenza A (H1N1) virus in patients and healthcare workers. Design, setting, and participants An outbreak investigation was initiated in response to suspected nosocomial transmission of the 2009 influenza A (H1N1) virus during the peak of the 2009 pandemic. Cases were confirmed using a polymerase chain reaction (PCR) test specific for the 2009 H1N1 influenza A virus. Viruses isolated from nasopharyngeal swabs were genetically characterized using Sanger sequencing of uncloned “bulk” PCR products. Main outcome measures Virus sequencing to investigate nosocomial transmission. Results Two immunocompromised patients and four healthcare workers were found to be part of a nosocomial outbreak of the 2009 influenza A (H1N1) virus. One immunocompromised patient had a second episode of clinical influenza infection after isolation precautions had been discontinued, resulting in additional exposures. Strain-specific PCR showed that all cases were caused by infection of the 2009 H1N1 virus. Sequencing of viral genes encoding hemagglutinin and polymerase basic subunit 2 (PB2) revealed that all viruses isolated were genetically identical at these loci, including the two episodes occurring in the same immunocompromised patient. Conclusions Prompt institution of isolation precautions is essential in preventing nosocomial outbreaks of the 2009 novel influenza A (H1N1) virus. Our data suggest that isolation precautions may need to be continued for a prolonged period of time in immunocompromised patients with influenza infection.

A series of articles by W.J. Freeland published in the 1970s proposed that social organization and behavioral processes were heavily influenced by parasitic infections, which led to a number of intriguing hypotheses concerning how natural selection might act on social factors because of the benefits of avoiding parasite infections. For example, Freeland [1979] showed that all individuals within a given group harbored identical gastrointestinal protozoan faunas, which led him to postulate that social groups were akin to “biological islands” and suggest how this isolation could select specific types of ranging and dispersal patterns. Here, we reexamine the biological island hypothesis by quantifying the protozoan faunas of the same primate species examined by Freeland in the same location; our results do not support this hypothesis. In contrast, we quantified two general changes in protozoan parasite community of primates in the study area of Kibale National Park, Uganda, over the nearly 35 years between sample collections: (1) the colobines found free of parasites in the early 1970s are now infected with numerous intestinal protozoan parasites and (2) groups are no longer biological islands in terms of their protozoan parasites. Whatever the ultimate explanation for these changes, our findings have implications for studies proposing selective forces shaping primate behavior and social organization. Am. J. Primatol. 74:510–517, 2012. © 2011 Wiley Periodicals, Inc.

Culex flavivirus (CxFV) is an insect-specific flavivirus globally distributed in mosquitoes of the genus Culex. CxFV was positively associated with West Nile virus (WNV) infection in a case-control study of 268 mosquito pools from an endemic focus of WNV transmission in Chicago, United States. Specifically, WNV-positive Culex mosquito pools were four times more likely also to be infected with CxFV than were spatiotemporally matched WNV-negative pools. In addition, mosquito pools from residential sites characterized by dense housing and impermeable surfaces were more likely to be infected with CxFV than were pools from nearby urban green spaces. Further, 6/15 (40%) WNV-positive individual mosquitoes were also CxFV positive, demonstrating that both viruses can coinfect mosquitoes in nature. Phylogenetic analysis of CxFV from Chicago demonstrated a pattern similar to WNV, consisting of low global viral diversity and lack of geographic clustering. These results illustrate a positive ecological association between CxFV and WNV, and that coinfection of individual mosquitoes can occur naturally in areas of high flaviviral transmission. These conclusions represent a challenge to the hypothesis of super-infection exclusion in the CxFV/WNV system, whereby an established infection with one virus may interfere with secondary viral infection with a similar virus. This study suggests that infection with insect-specific flaviviruses such as CxFV may not exclude secondary infection with genetically distinct flaviviruses such as WNV, and that both viruses can naturally coinfect mosquitoes that are epidemic bridge vectors of WNV to humans.

Great barracuda (Sphyraena barracuda) were implanted with acoustic telemetry transmitters (n =4 2) and monitored within a stationary acoustic receiver array (n = 53 receivers) in The Bahamas to examine residency, seasonal movements, and habitat use. Barracuda were mon- itored for up to 980 days and remained within the array area »33% (median value) of the time. Most tagged barracuda were transient and would often disappear from the array for months at a time, particularly in the summer where they were usually last detected on receivers located in deeper shelf habitats, and then return at other times in the year. Habitat use across the footprint of the array diVered, with most detections occurring in coastal areas and compara- tively fewer in deeper mosaic or shelf habitats. Linear home range estimates revealed that some barracuda moved >12 km within a single day and are capable of migrating >100 km to other islands in the Bahamian Archipelago. Our results provide some of the Wrst telemetry data for this apex marine predatory Wsh and the Wrst reliable information on the residency and localized seasonal movements of adult great barracuda in the coastal waters of the Western

5 ABSTRACT. Stormwater catch basins in urban areas provide important larval habitat for Culex mosquitoes. In this study we quantified adult Culex emergence using a newly designed emergence trap deployed in catch basins in suburban Chicago, IL. Traps were deployed from late June to mid-October, 2009-10, in 19 catch basins for a total of 461 trap-days. Based on laboratory trials, the percentage of adults emerging under the trap and reaching the collection cup ranged from 37.7 6 6.5% for closed-cup and 50.5 6 3.8% for open-cup configurations. In 2009, catch basins containing immature mosquitoes produced an estimated 58.9 6 30.8 female and 86.2 6 36.4 male Culex spp. per day. Most (84.4% )w ereCulex pipiens and the remainder were Cx. restuans. The trap was also effective in documenting reductions in adult emergence following intense precipitation events that caused ''flushing'' of larvae and pupae. In general, the new emergence trap was effective for studying Culex production in catch basins and should be broadly useful in studies of container-breeding mosquitoes.