Viral diversity in oral cavity from Sapajus nigritus by metagenomic analyses

Abstract

Sapajus nigritus are non-human primates which are widespread in South America. They are omnivores and live in troops of up to 40 individuals. The oral cavity is one of the main entry routes for microorganisms, including viruses. Our study proposed the identification of viral sequences from oral swabs collected in a group of capuchin monkeys (n = 5) living in a public park in a fragment of Mata Atlantica in South Brazil. Samples were submitted to nucleic acid extraction and enrichment, which was followed by the construction of libraries. After high-throughput sequencing and contig assembly, we used a pipeline to identify 11 viral families, which are Herpesviridae, Parvoviridae, Papillomaviridae, Polyomaviridae, Caulimoviridae, Iridoviridae, Astroviridae, Poxviridae, and Baculoviridae, in addition to two complete viral genomes of Anelloviridae and Genomoviridae. Some of these viruses were closely related to known viruses, while other fragments are more distantly related, with 50% of identity or less to the currently available virus sequences in databases. In addition to host-related viruses, insect and small vertebrate-related viruses were also found, as well as plant-related viruses, bringing insights about their diet. In conclusion, this viral metagenomic analysis reveals, for the first time, the profile of viruses in the oral cavity of wild, free ranging capuchin monkeys.

Metagenomic Analysis of Saliva Reveals Disease-Associated Microbiotas in Patients With Periodontitis and Crohn’s Disease-Associated Periodontitis

“…The limited number of patients (only six samples each group) was the major limiation of this study. Although there were also studies performed based on samll sample size (Zeng et al, 2019;Dos Santos et al, 2020), we advocate that convincing conclusions can be proposed based on only large number of samples. In addition, potential influencing factors such as diet, lifestyle factors (such as socio-economic status and the attention to oral hygiene) that may influence oral microbiota composition were not considered, which may be confounding factors to the results.…”

Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics

“…As it is the sister group to Old World primates (OWP) (infraorder Catarrhini), including humans, the comprehension of their evolution, immunology and susceptibility to infectious diseases is central to the characterization of the scope of etiological agents that may impact global health 18 . In this sense, previous investigations have shown that multiple viral families might be found in the virome of NP: novel papillomaviruses were found infecting Callithrix penicillata 16 and Alouatta guariba 15 , anellovirus and genomovirus in Sapajus nigritus 10 , smacovirus in Alouatta caraya 12 and foamy virus in Brachyteles arachnoides 14 and Sapajus xanthosternos The Anelloviridae family is one of the most frequently found in metagenomic surveys of NP. This family is composed of non-enveloped virions with circular single-stranded negative sense DNA (ssDNA), whose genomes range from 1.6 to 3.9kb.…”

“…In this regard, Neotropical primates (NP) (infraorder Platyrrhini) stand out as a group with great ecological importance, whose viral diversity hasn't been fully explored. Only 18% (4/22) and 3.4% (6/178) of NP genera and species, respectively, have been previously assessed through viral metagenomics 10,[12][13][14][15][16] .…”

“…A high prevalence in healthy populations and the lack of clinical signs have also been shown in free-living and captive populations of chimpanzees and gorillas [24][25][26] . Although new anelloviruses species have been discovered in NP -such as in Saguinus oedipus, Aotus trivirgatus 27 and Sapajus nigritus 10 -an extensive knowledge gap for anelloviruses infecting NP still remains.…”

“…Once a matter of contention, the establishment of novel viral species and higher taxonomic groups based solely on sequencing data became commonplace. Prospective studies describing multiple previously unknown viral groups are increasingly common [3][4][5][6] , as are studies expanding the diversity of well-established viral families [7][8][9][10] . While these efforts have broad implications on the comprehension of virus diversity, ecology, evolution and epidemiology, large fractions of the viruses infecting non-model organisms remain to be discovered 11 .…”