Genome announcement : complete genome sequence of a novel Mupapillomavirus, HPV204

Human papillomaviruses (HPVs) are small, non-enveloped viruses with a circular double-stranded DNA genome, etiologically associated with various benign and malignant neoplasms of the skin and mucosa. As of May 30, 2015, 201 different HPV types had been completely sequenced and officially recognized and divided into five PV-genera: Alpha-, Beta-, Gamma-, Mu-, and Nupapillomavirus. The Mupapillomavirus genus currently consists of only two HPV types: HPV1 and HPV63, identified in 1980 and 1993, respectively, both associated with sporadic cases of cutaneous warts. In this preliminary study, we announce the complete genome sequence of a novel HPV type, now officially recognized as HPV204. Based on preliminary data, the genome of HPV204 comprises a total of 7,227 bp and contains five early open reading frames (E1, E2, E4, E6, and E7) and two late ORFs (L1 and L2). No E5 ORF could be identified. Preliminary HPV204 clusters to the Mu-PV genus, species Mu-3.Fil: Kocjan, Boštjan J. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; SloveniaFil: Šterbenc, Anja. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; SloveniaFil: Hošnjak, Lea. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; SloveniaFil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área de Virología; ArgentinaFil: Bolatti, Elisa María. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área de Virología; ArgentinaFil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área de Virología; ArgentinaFil: Poljak, Mario. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; Sloveni

Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.Fil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Area Virología; ArgentinaFil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); ArgentinaFil: Bolatti, Elisa María. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); ArgentinaFil: Germán R. Pérez. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Area Virología; ArgentinaFil: Germán R. Pérez. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); ArgentinaFil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Area Virología; ArgentinaFil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); Argentin

Identification of human papillomavirus in benign and malignant nonmelanoma skin lesions by molecular methods

Los virus papiloma humano (PVH) están presentes en la piel como flora normal, donde permanecen en forma latente, pudiendo desarrollar en ciertas oportunidades, lesiones cutáneas. Objetivo: Identificar los tipos de PVH con tropismo por epitelios cutáneos y analizar su posible asociación con lesiones cutáneas benignas y carcinomas cutáneos no melanoma. Materiales y métodos: Estudio prospectivo realizado en el servicio de dermatología del Hospital provincial del Centenario, desde Junio de 2007 a Noviembre de 2008. Se obtuvieron muestras mediante hisopados de regiones: fotoexpuesta (FE), no fotoexpuesta (NFE), perilesional (PL), superficie de lesión (SL) y biopsias de lesiones para estudio histopatológico. Se incluyeron pacientes derivados para estudio histopatológico de las lesiones antes referidas. Detección de PVH mediante PCR. Resultados: Participaron 67 pacientes, 41 hombres y 26 mujeres, edad promedio de 51 años (rango: 19-89 años). 300 muestras resultaron idóneas para la amplificación por PCR. La frecuencia de ADN de PVH hallado fue del 58% (176/300) (Figura 1), encontrándose 75% en FE, 39% en NFE, 75% en PL, 66% en SL y 35% en las biopsias. Se identificaron 69 tipos diferentes de HPV, siendo más frecuentes el 2, 21, 20 y 6. Se detectó un nuevo PVH, el 115. No se identificó PVH en muestras de carcinomas. En queratosis seborreicas se detectó en un 27%. Conclusiones: Se obtuvieron datos acerca de los PVH circulantes en los pacientes de nuestra región. Corroboramos la influencia de la radiación ultravioleta sobre la infección por este virus, así como su presencia en queratosis seborreicas. Identificamos un nuevo HPV en Sudamérica.The human papillomavirus (HPV) establish a latent infection of the skin as normal flora and can develop skin lesions on some situations. Objectives: Identify the HPV types which exhibit tropism for cutaneous epithelium and analyse its possible association with benign skin lesions and nonmelanoma skin cancer. Materials and methods: Prospective study was carried out in the Department of Dermatology at the Centenario Provincial Hospital from June 2007 to November 2008. Samples were collected by swabs from the following areas: sun-exposed (FE), non-sun-exposed (NFE), perilesional (PL), lesion area (SL) and biopsy of lesions for histopathological study. We included patients referred to surgical removal of a skin lesion for histopathological study. Detection of HPV by PCR. Results: 67 patients were recruited, 41 men and 26 women, median age of 51 years (range, 19-89 years). 300 samples were suitable for amplification by PCR. HPV DNA was present in 58% of the analyzed samples (176/300), and 75% in FE, 39% in NFE, 75% in PL, 66% in SL and 35% in biopsies. 69 different types of HPV were identified, being more frequent 2, 21, 20, and 6. We detected a new HPV, 115. HPV were not identified in samples of carcinomas. In seborrhoeic keratosis were present in 27% of the samples. Conclusions: We collected data about the HPV circulating in patients of our region. We affirmed the influence of ultraviolet radiation on this viral infection, as well as their presence in seborrhoeic keratosis. We identified a new HPV in South America.Fil: Piccirilli, Gustavo. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Squeff, Mario. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Quattrocchi, Cristian. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Fernández Bussy, Ramón Alfredo. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); ArgentinaFil: Gorosito, Mario. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Sanchez, Adriana. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Bergero, Adriana. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; ArgentinaFil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); ArgentinaFil: Fernández Bussy, Ramón Alfredo. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; Argentin

Prevalence of human papillomavirus infection in Argentinean women attending two different hospitals prior to the implementation of the National vaccination program.

Cervarix vaccine was included in the National Immunization Program of Argentina in 2011 but data about the local distribution of human papillomavirus (HPV) infection in women exposed to the virus are scarce. This cross-sectional study determined the prevalence and type distribution of HPV infection in unvaccinated women attending routine gynaecological screening in two public hospitals located in Buenos Aires and Santa Fe, Argentina. Socio-demographic, sexual behaviour and co-factors information was obtained from all participants (Buenos Aires, n=429; Santa Fe, n=433). Cervicovaginal swabs were tested with an MY11/09 primer-based assay and with the CUT primer system targeting mucosal/cutaneous HPVs. Participants from Buenos Aires showed significantly higher rates of HPV infection (52.4% vs. 40.6%), of multiple infections (24.2% vs. 16.4%), and of low-risk (20.3% vs. 13.9%) and highrisk types (44.1% vs. 33.3%) than those from Santa Fe. HPV-66 (Buenos Aires: 17%) and HPV-16 (Santa Fe: 8.5%) were the most prevalent types. Novel HPV-66 putative subtype and variants were identified. Vaccine types 16 and 18 were frequent (Buenos Aires: 13.5%; Santa Fe F: 10.2%) but few participants had co-infections with both (Buenos Aires: 1.4%; Santa Fe: 0.2%). A common risk factor for HPV infection was having a new sexual partner in the last year (Buenos Aires: OR 2.53, p<0.001; Santa Fe: OR 1.85, p=0.04). This study provides valuable baseline data for future assessment of the impact of massive vaccination in Argentina and it underlines the use of additional HPV testing strategies, such as the CUT system, for surveillance and vaccinology.Fil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área de Virología; ArgentinaFil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); ArgentinaFil: Mamprín D´Andrea, Rubén. Santa Fe. Ministerio de Salud. Hospital-Escuela “Eva Perón”. División de Ginecología; ArgentinaFil: Iglesias, Mercedes. Ciudad Autónoma de Buenos Aires. Hospital General de Agudos “Dr. Teodoro Alvarez”. Laboratorio Central; ArgentinaFil: Messina, Analía. Ciudad Autónoma de Buenos Aires. Hospital General de Agudos “Dr. Teodoro Alvarez”. Departamento de Obstetricia y Pediatría; ArgentinaFil: Ivancovich, Juan José. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Estadística y Procesamiento de Datos; ArgentinaFil: Cerda, Belén. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área de Virología; ArgentinaFil: Galimberti, Diana. Ciudad Autónoma de Buenos Aires. Hospital General de Agudos “Dr. Teodoro Alvarez”. Departamento de Obstetricia y Pediatría; ArgentinaFil: Bottai, Hebe. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Estadística y Procesamiento de Datos; ArgentinaFil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área de Virología; ArgentinaFil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (UNR-CONICET); Argentin

Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses

Bats are natural reservoirs of a variety of zoonotic viruses, many of which cause severe human diseases. Characterizing viruses of bats inhabiting different geographical regions is important for understanding their viral diversity and for detecting viral spillovers between animal species. Herein, the diversity of DNA viruses of five arthropodophagous bat species from Argentina was investigated using metagenomics. Fecal samples of 29 individuals from five species (Tadarida brasiliensis, Molossus molossus, Eumops bonariensis, Eumops patagonicus, and Eptesicus diminutus) living at two different geographical locations, were investigated. Enriched viral DNA was sequenced using Illumina MiSeq, and the reads were trimmed and filtered using several bioinformatic approaches. The resulting nucleotide sequences were subjected to viral taxonomic classification. In total, 4,520,370 read pairs were sequestered by sequencing, and 21.1% of them mapped to viral taxa. Circoviridae and Genomoviridae were the most prevalent among vertebrate viral families in all bat species included in this study. Samples from the T. brasiliensis colony exhibited lower viral diversity than samples from other species of New World bats. We characterized 35 complete genome sequences of novel viruses. These findings provide new insights into the global diversity of bat viruses in poorly studied species, contributing to prevention of emerging zoonotic diseases and to conservation policies for endangered species.Fil: Bolatti, Elisa María. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET). Grupo Virología Humana; Argentina.Fil: Bolatti, Elisa María. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Virología; Argentina.Fil: Viarengo, Gastón. Centro Científico Tecnológico CONICET Rosario. DETx MOL S.A; Argentina.Fil: Zorec, Tomaž M. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; Slovenia.Fil: Cerri, Agustina. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET). Grupo Virología Humana; Argentina.Fil: Montani, María E. Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”; Argentina.Fil: Montani, María E. Miguel Lillo 251; Argentina.Fil: Montani, María E. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Programa de Investigaciones de Biodiversidad Argentina (PIDBA); Argentina.Fil: Hošnjak, Lea. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; Slovenia.Fil: Casal, Pablo E. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Virología; Argentina.Fil: Bortolotto, Eugenia. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Estadística y Procesamiento de Datos; Argentina.Fil: Di Domenica, Violeta. Miguel Lillo 251; Argentina.Fil: Chouhy, Diego. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET). Grupo Virología Humana; Argentina.Fil: Chouhy, Diego. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Virología; Argentina.Fil: Chouhy, Diego. Centro Científico Tecnológico CONICET Rosario. DETx MOL S.A; Argentina.Fil: Allasia, María Belén. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Estadística y Procesamiento de Datos; Argentina.Fil: Barquez, Rubén M. Miguel Lillo 251; Argentina.Fil: Barquez, Rubén M. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Programa de Investigaciones de Biodiversidad Argentina (PIDBA); Argentina.Fil: Poljak, Mario. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; Slovenia.Fil: Giri, Adriana Angélica. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET). Grupo Virología Humana; Argentina.Fil: Giri, Adriana Angélica. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Virología; Argentina

Omicron Waves in Argentina: Dynamics of SARS-CoV-2 Lineages BA.1, BA.2 and the Emerging BA.2.12.1 and BA.4/BA.5

The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.Fil: Villanova, Gabriela Vanina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología Acuática. Centro Científico Tecnológico y Educativo Acuario del río Paraná; Argentina