Novel gamma-1 herpesviruses identified in free-ranging new world monkeys (golden-handed tamarin [Saguinus midas], squirrel monkey [Saimiri sciureus], and white-faced saki [Pithecia pithecia]) in French Guiana

Detection of herpesviruses in neotropical primates from São Paulo, Brazil

Transmission of herpesvirus between humans and non-human primates represents a serious potential threat to human health and endangered species conservation. This study aimed to identify herpesvirus genomes in samples of neotropical primates (NTPs) in the state of São Paulo, Brazil. A total of 242 NTPs, including Callithrix sp., Alouatta sp., Sapajus sp., and Callicebus sp., were evaluated by pan-herpesvirus polymerase chain reaction (PCR) and sequencing. Sixty-two (25.6%) samples containing genome segments representative of members of the family Herpesviridae, including 16.1% for Callitrichine gammaherpesvirus 3, 6.1% for Human alphaherpesvirus 1, 2.1% for Alouatta macconnelli cytomegalovirus, and 0.83% for Cebus albifrons lymphocryptovirus 1. No co-infections were detected. The detection of herpesvirus genomes was significantly higher among adult animals (p = 0.033) and those kept under human care (p = 0.008671). These findings confirm the importance of monitoring the occurrence of herpesviruses in NTP populations in epizootic events.

Callitrichine gammaherpesvirus 3 and Human alphaherpesvirus 1 in New World Primate negative for yellow fever virus in Rio de Janeiro, Brazil

BACKGROUND

Herpesvirus transmission between humans and non-human primate (NHP) can occur through contact scratches with lesions, infected saliva, and mainly through contaminated food. Therefore, cross-infection can lead to severe illness or even death for both the animal and human. In 2017, during the yellow fever (YF) outbreak in Brazil, species of the New World Primates (NWP) from Rio de Janeiro state, tested negative for yellow fever virus (YFV) detection.

OBJECTIVES

To evaluate herpesvirus in the population NWP in Rio de Janeiro.

METHODS

To investigate, liver samples of 283 NWP, from several regions of the state of Rio de Janeiro, were tested for the herpesvirus family using a Pan-polymerase chain reaction (Pan-PCR) and sequencing.

FINDINGS

34.6% (98/283) tested positive for at least one herpesvirus; 29.3% (83/283) tested positive to Human alphaherpesvirus 1 (HSV-1), this virus from humans can be lethal to New World monkey; 13% (37/283) were detected Callitrichine gammaherpesvirus 3 (CalHV-3), responsible for lymphoproliferative disease that can be fatal in NWP. In addition, CalHV-3 / HSV-1 co-infection was in 11.6% (33/283) of the samples.

MAIN CONCLUSIONS

Pan-herpesvirus was useful to identify species-specific herpesviruses and virus from human that can infect animals. Furthermore, during an outbreak of YF other infections should be monitored.

Leukemic histiocytic sarcoma in a captive common squirrel monkey (Saimiri sciureus) with Saimiriine Gammaherpesvirus 2 (Rhadinovirus), Saimiri sciureus lymphocryptovirus 2 (Lymphocryptovirus) and Squirrel monkey retrovirus (β-Retrovirus) coinfection

Hematopoietic neoplasia other than lymphoma and leukemia is uncommon among non-human primates. Herein, we provide the first evidence of occurrence of leukemic histiocytic sarcoma in a captive common squirrel monkey with Saimiriine Gammaherpesvirus 2 (Rhadinovirus), Saimiri sciureus lymphocryptovirus 2 (Lymphocryptovirus), and Squirrel monkey retrovirus (β-Retrovirus) coinfection.

DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics

Over the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to the Cytomegalovirus genus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCE Investigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.

Non-human Primate Lymphocryptoviruses: Past, Present, and Future

Epstein-Barr virus (EBV) orthologues from non-human primates (NHPs) have been studied for nearly as long as EBV itself. Cross-reactive sera and DNA hybridization studies provided the first glimpses of the closely related herpesviruses that belonged to the same gamma-1 herpesvirus, or lymphocryptovirus, genus, as EBV. Over the years, detailed molecular and sequence analyses of LCVs that infect humans and other NHPs revealed similar colinear genome structures and homologous viral proteins expressed during latent and lytic infection. Despite these similarities, experimental infection of NHPs with EBV did not result in acute symptoms or persistent infection as observed in humans, suggesting some degree of host species restriction. Genome sequencing and a molecular clone of an LCV isolate from naturally infected rhesus macaques combined with domestic colonies of LCV-naïve rhesus macaques have opened the door to a unique experimental animal model that accurately reproduces the normal transmission, acute viremia, lifelong persistence, and immune responses found in EBV-infected humans. This chapter will summarize the advances made over the last 50 years in our understanding of LCVs that naturally infect both Old and New World NHPs, the recent, groundbreaking developments in the use of rhesus macaques as an animal model for EBV infection, and how NHP LCVs and the rhLCV animal model can advance future EBV research and the development of an EBV vaccine.

Endemic Viruses of Squirrel Monkeys (Saimiri spp.)

Nonhuman primates are the experimental animals of choice for the study of many human diseases. As such, it is important to understand that endemic viruses of primates can potentially affect the design, methods, and results of biomedical studies designed to model human disease. Here we review the viruses known to be endemic in squirrel monkeys (Saimiri spp.). The pathogenic potential of these viruses in squirrel monkeys that undergo experimental manipulation remains largely unexplored but may have implications regarding the use of squirrel monkeys in biomedical research.

African great apes are naturally infected with roseoloviruses closely related to human herpesvirus 7

Primates are naturally infected with herpesviruses. During the last 15 years, the search for homologues of human herpesviruses in nonhuman primates allowed the identification of numerous viruses belonging to the different herpesvirus subfamilies and genera. No simian homologue of human herpesvirus 7 (HHV7) has been reported to date. To investigate the putative existence of HHV7-like viruses in African great apes, we applied the consensus-degenerate hybrid oligonucleotide primers (CODEHOP) program-mediated PCR strategy to blood DNA samples from the four common chimpanzee subspecies (Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii), pygmy chimpanzees (Pan paniscus), as well as lowland gorillas (Gorilla gorilla gorilla). This study led to the discovery of a novel roseolovirus close to HHV7 in each of these nonhuman primate species and subspecies. Generation of the partial glycoprotein B (1,111-bp) and full-length DNA polymerase (3,036/3,042-bp) gene sequences allowed the deciphering of their evolutionary relationships. Phylogenetic analyses revealed that HHV7 and its African great ape homologues formed well-supported monophyletic lineages whose topological resemblance to the host phylogeny is suggestive of virus-host codivergence. Notably, the evolutionary branching points that separate HHV7 from African great ape herpesvirus 7 are remarkably congruent with the dates of divergence of their hosts. Our study shows that African great apes are hosts of human herpesvirus homologues, including HHV7 homologues, and that the latter, like other DNA viruses that establish persistent infections, have cospeciated with their hosts.

IMPORTANCE

Human herpesviruses are known to possess simian homologues. However, surprisingly, none has been identified to date for human herpesvirus 7 (HHV7). This study is the first to describe simian homologues of HHV7. The extensive search performed on almost all African great ape species and subspecies, i.e., common chimpanzees of the four subspecies, bonobos, and lowland gorillas, has allowed characterization of a specific virus in each. Genetic characterization of the partial glycoprotein B and full-length DNA polymerase gene sequences, followed by their phylogenetic analysis and estimation of divergence times, has shed light on the evolutionary relationships of these viruses. In this respect, we conclusively demonstrate the cospeciation between these new viruses and their hosts and report cases of cross-species transmission between two common chimpanzee subspecies in both directions.

Partial molecular characterisation of New World non-human primate lymphocryptoviruses

The description of numerous viruses belonging to the Lymphocryptovirus genus from different Old and New World non-human primate species during the past 10 years has led to developing and supporting co-speciational evolution hypotheses for these viruses and their hosts. Among the different primate species tested, only a few were from the New World. This study attempted to achieve a better understanding of the evolutionary processes within the Platyrrhini branch. Molecular screening of 253 blood DNA samples from 20 New World non-human primate species from Central and South America was carried out using polymerase chain reaction amplification with degenerate consensus primers targeting highly conserved amino acid motifs of the herpesvirus DNA polymerase gene. In addition to the 33 samples from which we have already described three lymphocryptoviruses, amplification products were detected in 17 other samples originating from 11 species (13 sub-species). BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirm that they all belong to the Lymphocryptovirus genus. Fourteen distinct Lymphocryptovirus sequences were detected, of which nine have never been reported. Phylogenetic analyses showed that, as expected, the New World virus lineage formed a sister clade to that of the Old World viruses. The parallel determination of the host taxa has demonstrated a good correlation between the distinct monophyletic clades of viruses and the infected primates at the sub-family level. In addition, these results further suggest the existence of two distinct groups within the Cebidae for Saimirinae and Cebinae primates. Nevertheless, based on the current genetic data, this study fell short of achieving a tree that was completely resolved within the lineage of Platyrrhini viruses. Further studies will be needed to better assess the evolutionary relationships between these viruses.

Characterization of natural killer cells in tamarins: a technical basis for studies of innate immunity

Natural killer (NK) cells are capable of regulating viral infection without major histocompatibility complex restriction. Hepatitis C is caused by chronic infection with hepatitis C virus (HCV), and impaired activity of NK cells may contribute to the control of the disease progression, although the involvement of NK cells in vivo remains to be proven. GB virus B (GBV-B), which is genetically most closely related to HCV, induces acute and chronic hepatitis upon experimental infection of tamarins. This non-human primate model seems likely to be useful for unveiling the roles of NK cells in vivo. Here we characterized the biological phenotypes of NK cells in tamarins and found that depletion of the CD16+ subset in vivo by administration of a monoclonal antibody significantly reduced the number and activity of NK cells.

Genetic diversity and molecular evolution of human and non-human primate Gammaherpesvirinae

The Gammaherpesvirinae sub-family is divided into two genera: Lymphocryptovirus and Rhadinovirus. Until the middle of the 1990s, the Rhadinovirus genus was only represented by Herpesvirus saimiri and Herpesvirus ateles, which infect New World monkey species. Until the year 2000, Epstein-Barr virus (EBV), the human prototype of the Lymphocryptovirus, and simian homologues had only been detected in humans and Old World non-human primates. It was thought, therefore, that the separation of the continents had resulted in drastic changes in Gammaherpesvirinae evolution. The discovery of Kaposi's sarcoma-associated herpesvirus in humans, belonging to the Rhadinovirus, followed by the identification of CalHV3 (Callitrichine herpesvirus 3), a lymphocryptovirus of the marmoset, challenged this paradigm. The description of numerous viruses belonging to this sub-family from various Old and New World primate species enabled a cospeciation hypothesis for these viruses and their hosts to be developed. This review focuses on the current knowledge of primate Gammaherpesvirinae genetic diversity and molecular evolution. We discuss the various theories based on current genetic data regarding evolutionary relationships between lymphocryptoviruses of Old World primates, the use of these data as a tool to study evolutionary relationships between New World monkey species, and the possible existence of a ninth human herpesvirus belonging to the Rhadinovirus genus.

Novel mammalian herpesviruses and lineages within the Gammaherpesvirinae: cospeciation and interspecies transfer

Novel members of the subfamily Gammaherpesvirinae, hosted by eight mammalian species from six orders (Primates, Artiodactyla, Perissodactyla, Carnivora, Scandentia, and Eulipotyphla), were discovered using PCR with pan-herpesvirus DNA polymerase (DPOL) gene primers and genus-specific glycoprotein B (gB) gene primers. The gB and DPOL sequences of each virus species were connected by long-distance PCR, and contiguous sequences of approximately 3.4 kbp were compiled. Six additional gammaherpesviruses from four mammalian host orders (Artiodactyla, Perissodactyla, Primates, and Proboscidea), for which only short DPOL sequences were known, were analyzed in the same manner. Together with available corresponding sequences for 31 other gammaherpesviruses, alignments of encoded amino acid sequences were made and used for phylogenetic analyses by maximum-likelihood and Bayesian Monte Carlo Markov chain methods to derive a tree which contained two major loci of unresolved branching details. The tree was rooted by parallel analyses that included alpha- and betaherpesvirus sequences. This gammaherpesvirus tree contains 11 major lineages and presents the widest view to date of phylogenetic relationships in any subfamily of the Herpesviridae, as well as the most complex in the number of deep lineages. The tree's branching pattern can be interpreted only in part in terms of the cospeciation of virus and host lineages, and a substantial incidence of the interspecies transfer of viruses must also be invoked.

Prevalence and molecular characterization of the polymerase gene of gibbon lymphocryptovirus

BACKGROUND

Lymphocryptovirus (LCV) is found in various non-human primates. As a herpesvirus naturally infecting gibbons it is closely related to human Epstein-Barr virus (EBV) with which it shares considerable genetic, biological and epidemiologic features.

METHODS

We collected blood samples from 70 gibbons (51 Hylobates lar, 18 Hylobates pileatus and 1 Hylobates agilis) for further separation into serum and peripheral blood mononuclear cells (PBMC).

RESULTS

Only 13 of 70 (18.6%) sera were serologically positive for human EBV IgG but 64 of 70 (91.4%) PBMCs yielded the partial LCV DNA polymerase gene by semi-nested PCR, which we subjected to direct sequencing. All sequences showed 84% nucleic acid and 91% amino acid identity to human EBV. Phylogenetic tree analysis demonstrated gibbon LCVs clustered separately from other gammaherpesvirinae but closely related to LCV of other species.

CONCLUSIONS

Based on LCV DNA detection, we discovered a high prevalence of LCV infection among gibbons. Further characterization of non-human primate LCV might thus provide new insight into both evolution and pathogenicity of gammaherpesvirinae.

Development of a polymerase chain reaction for the detection of Anguillid herpesvirus DNA in eels based on the herpesvirus DNA polymerase gene

Anguillid herpesvirus (AnHV, also known as Herpesvirus anguillae or HVA) is found in both Japanese and European eels. Based on restriction enzyme analysis a small number of differences were found between AnHV isolated from Japanese eels and from European eels. The total genome size of both is about 245 kb, which is confirmed by alternating-field electrophoresis. Using a set of degenerate primers based on conserved regions within DNA-directed DNA polymerase coding regions, a 463 base pair fragment was isolated from both Japanese and European AnHV. Nucleotide sequence analysis showed that the cloned regions of both viruses have identical sequences. Based on this part of the DNA-polymerase sequence, primers were selected and used to develop a sensitive PCR to detect AnHV DNA in eel tissue samples. To avoid false negative results and to estimate the number of AnHV genome copies found in tissues, 100 copies of an internal control plasmid were added to the tissue samples. This semi-quantitative AnHV PCR can be used for both the European and Japanese isolates of AnHV, detects as few as 10 genome copies and is 100 times more sensitive than standard virus isolation.

The Effect of Paralogous Lineages on the Application of Reconciliation Analysis by Cophylogeny Mapping

Paralogy defines similarity caused by duplication rather than common descent and is well known in the case of paralogous gene copies within a single genome. The term is here extended to paralogous lineages of associates within a single host. The phylogenies of four genera within the Herpesviridae were reconciled with host phylogenies using cophylogenetic mapping. The observed correspondence for each pair of phylogenies was evaluated through randomization of the viral phylogeny and demonstrated to be greater than expected by chance. A simulation study was then carried out to assess the influence of paralogous lineages on the efficacy of reconciliation analysis. Combining viral taxa from different genera that infected common hosts introduced incongruence into the cophylogenies and reduced both the minimum and maximum observed number of codivergence events relative to the initial analysis of orthologous clades. However, at an average sample size this did not alter the fundamental significance of observed correspondence. With smaller sample sizes, the number of orthologous taxa selected at random from the pool of taxa was reduced. False-negative results then increased in proportion from 0.02 to 0.33. These results demonstrated that reconciliation analysis is robust under conditions of paralogy at "normal" sample sizes but is adversely affected by a combination of paralogy and low sample size. Consideration of phylogenies for Papillomavirus, Atadenovirus, and Mastadenovirus suggest that paralogous lineages may be a widespread phenomenon among DNA viruses and that duplication irrespective of host speciation is an important cause of viral diversification.