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Sanchez-Fernandez C, Bolatti EM, Culasso ACA, Chouhy D, Kowalewski MM, Stella EJ, Schurr TG, Rinas MA, Liotta DJ, Campos RH, Giri AA, Badano I. Identification and evolutionary analysis of papillomavirus sequences in New World monkeys (genera Sapajus and Alouatta) from Argentina. Arch Virol 2022; 167:1257-1268. [PMID: 35353206 DOI: 10.1007/s00705-022-05420-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/03/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE In this study, we investigated the occurrence of papillomavirus (PV) infection in non-human primates (NHPs) in northeastern Argentina. We also explored their evolutionary history and evaluated the co-speciation hypothesis in the context of primate evolution. METHODS We obtained DNA samples from 57 individuals belonging to wild and captive populations of Alouatta caraya, Sapajus nigritus, and Sapajus cay. We assessed PV infection by PCR amplification with the CUT primer system and sequencing of 337 bp (112 amino acids) of the L1 gene. The viral sequences were analyzed by phylogenetic and Bayesian coalescence methods to estimate the time to the most common recent ancestor (tMRCA) using BEAST, v1.4.8 software. We evaluated viral/host tree congruence with TreeMap v3.0. RESULTS We identified two novel putative PV sequences of the genus Gammapapillomavirus in Sapajus spp. and Alouatta caraya (SPV1 and AcPV1, respectively). The tMRCA of SPV1 was estimated to be 11,941,682 years before present (ybp), and that of AcPV1 was 46,638,071 ybp, both before the coalescence times of their hosts (6.4 million years ago [MYA] and 6.8 MYA, respectively). Based on the comparison of primate and viral phylogenies, we found that the PV tree was no more congruent with the host tree than a random tree would be (P > 0.05), thus allowing us to reject the model of virus-host coevolution. CONCLUSION This study presents the first evidence of PV infection in platyrrhine species from Argentina, expands the range of described hosts for these viruses, and suggests new scenarios for their origin and dispersal.
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Affiliation(s)
- C Sanchez-Fernandez
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - E M Bolatti
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - A C A Culasso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - D Chouhy
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - M M Kowalewski
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Estación Biológica Corrientes (EBCo-MACN-CONICET), Corrientes, Argentina
| | - E J Stella
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina
| | - T G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - M A Rinas
- Ministerio de Ecología y Recursos Naturales Renovables, Posadas, Misiones, Argentina
| | - D J Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.,Instituto Nacional de Medicina Tropical, ANLIS, Pto. Iguazú, Misiones, Argentina
| | - R H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - A A Giri
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - I Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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D'arc M, Moreira FRR, Dias CA, Souza AR, Seuánez HN, Soares MA, Tavares MCH, Santos AFA. The characterization of two novel neotropical primate papillomaviruses supports the ancient within-species diversity model. Virus Evol 2020; 6:veaa036. [PMID: 32665860 PMCID: PMC7326299 DOI: 10.1093/ve/veaa036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Papillomaviruses (PVs) are non-enveloped icosahedral viruses with a circular double-stranded DNA genome of ∼8,000 base pairs (bp). More than 200 different PV types have been identified to date in humans, which are distributed in five genera, with several strains associated with cancer development. Although widely distributed in vertebrates, Neotropical Primates (NP) PV infection was described for the first time only in 2016. Currently, four complete genomes of NP PVs have been characterized, three from Saimiri sciureus (SscPV1 to SscPV3) and one from Alouatta guariba (AgPV1). In this work, we describe two novel PV strains infecting Callithrix penicillata (provisionally named CpenPV1 and CpenPV2), using anal swab samples from animals residing at the Brasilia Primatology Center and next generation sequencing. The genomes of CpenPV1 (7,288 bp; 41.5% guanine-cytosine content - GC) and CpenPV2 (7,250 bp; 40.7% GC) contain the characteristic open reading frames (ORFs) for the early (E6, E7, E1, E2, and E4) and late (L2 and L1) PV genes. The L1 ORFs, commonly used for phylogenetic identification, share 76 per cent similarity with each other and differ 32 per cent from any other known PV, indicating that these new strains meet the criteria for defining novel species. PV genes phylogenetic variance was analyzed and different degrees of saturation revealed similar levels of topological heterogeneity, ruling out saturation as primary etiological factor for this phenomenon. Interestingly, the two CpenPV strains form a monophyletic clade within the Gammapapillomavirus genus (provisionally named gammapapillomavirus 32). Unlike for other NP PV strains, which grouped into a new sister genus of Alphapapillomavirus, this is the first report of NP PV strains grouping into a genus previously considered to exclusively comprise Old World Primates (OWP) PVs, including human PVs. These findings confirm the existence of a common ancestor for Gammapapillomavirus already infecting primates before the split of OWP and NP at ∼40 million years ago. Finally, our findings are consistent with an ancient within-species diversity model and emphasize the importance of increasing sampling to help understanding the PV-primate codivergence dynamics and pathogenic potential.
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Affiliation(s)
- Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Filipe R R Moreira
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Cecilia A Dias
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Antonizete R Souza
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, Postal Code 20231-050, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, Postal Code 20231-050, Rio de Janeiro, Brazil
| | - Maria C H Tavares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - André F A Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
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Complete Genome Sequences of Papillomavirus Isolates from the Oral Cavity, Skin, and Feces of Wild Rats. Microbiol Resour Announc 2018; 7:MRA01258-18. [PMID: 30533755 PMCID: PMC6256490 DOI: 10.1128/mra.01258-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/06/2018] [Indexed: 11/20/2022] Open
Abstract
Six genome sequences of papillomavirus were determined from oral and skin swabs and fecal samples collected from wild rats. Three genomes were 7,722 bp, two genomes were 7,716 bp, and one was 7,730 bp, displaying typical papillomavirus genome organizations. Phylogenetic analysis revealed that these six genomes belonged to two different clusters.
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Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 2018; 14:e1007352. [PMID: 30383862 PMCID: PMC6211759 DOI: 10.1371/journal.ppat.1007352] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.
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Affiliation(s)
- Zigui Chen
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States of America
| | - Rolando Herrero
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Charles E. Wood
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Julio C. Ruiz
- Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Gary M. Clifford
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul K. S. Chan
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology; Epidemiology and Population Health; Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
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