Abstract A complete genome of the first anellovirus infecting the wild felid Leopardus pardalis (ocelot) and a partial genome were assembled and annotated through high-throughput sequencing protocols followed by Sanger sequencing validation. The full-length virus obtained comprises 2,003 bp, while the partial genome comprises 1,224 bp. Phylogenetic analysis grouped these two sequences in two distinct clusters related to previously described Felidae anelloviruses. The ORF1 of the partial genome was identified as a new species provisionally called Torque teno ocelot virus, with 53.6% identity with its sister lineage. The complete genome was inferred as a new representative of the Torque teno felid virus 3 species, with 73.28% identity to the closest reference. This study expands known virus diversity and the host span of anelloviruses.

RESUMO Introdução: As infecções sexualmente transmissíveis (ISTs) ainda são um importante problema de saúde pública, e a vigilância é essencial para sua prevenção e seu controle. Objetivo: Avaliar a prevalência das ISTs em uma unidade de referência ginecológica no Rio de Janeiro, Brasil. Materiais e métodos: Trata-se de um estudo transversal realizado entre agosto de 2016 e junho de 2017. Foram coletados sangue total e células cervicais de 62 mulheres e realizados testes para detecção de papiloma vírus humano (HPV), vírus da imunodeficiência humana (HIV), sífilis, clamídia, gonorreia e vírus do herpes simples 1 e 2 (HSV-1/2). As lesões cervicais foram diagnosticadas por citopatologia, e em algumas pacientes, por colposcopia (79%). Outras ISTs foram avaliadas durante o exame clínico. Resultados: Foram encontradas lesões cervicais pelo exame citopatológico em 46,8% das pacientes; aquelas com história de quatro parceiros sexuais tiveram mais risco de desenvolvê-las. Houve concordância moderada entre os resultados da citopatologia e colposcopia (Kappa = 0,69). A prevalência de HSV (96,7%), sífilis (6,4%) e HIV (3,2%) foi maior que a descrita na literatura, enquanto a prevalência de clamídia (6,4%) e gonorreia (1,6%) foi similar. O HPV foi detectado em 53,2% das mulheres, sendo 32,3% delas infectadas pelo HPV 16. No contexto das coinfecções, 38 mulheres (61,3%) tinham mais de uma IST. Conclusão: Visto que a maioria das mulheres analisadas era acometida por mais de uma IST, nossos resultados sugerem que uma triagem rotineira dessas infecções nas unidades de saúde poderia auxiliar na detecção precoce, bem como no tratamento e na prevenção. Essas medidas também impactariam no controle do câncer cervical das pacientes.

ABSTRACT Introduction: Sexually transmitted infections (STI) remain a major public health problem and surveillance is crucial for prevention and control strategies. Objective: Our aim was to assess the prevalence of STI in a reference center for gynecology in Rio de Janeiro, Brazil. Materials and methods: It is a cross-sectional study conducted between August 2016 and June 2017. Whole blood and cervical cells were collected from 62 women and tested for human papillomavirus (HPV), human immunodeficiency virus (HIV), syphilis, chlamydia, gonorrhea and herpes simples virus 1 and 2 (HSV-1/2). Cervical lesions were diagnosed by cytopathology and in some patients by colposcopy (79%). Other STI were evaluated during clinical examination. Results: Cervical lesions were detected by cytopathology examinations in 46.8% of patients; those with a history of four sexual partners were at higher risk of developing them. There was moderate agreement between the cytopathology e colposcopy results (Kappa = 0.69). The prevalence of HSV (96.7%), syphilis (6.4%) and HIV (3.2%) were higher than that described in the literature, while the prevalence of chlamydia (6.4%) and gonorrhea (1.6%) were similar. HPV was detected in 53.2% of women, 32.3% of which were infected by HPV 16. In the context of co-infections, 38 women (61.3%) presented more than one STI. Conclusion: Since most of the women analyzed were affected by more than one STI, our results suggest that routine screening for these infections at health centers would help in early detection, treatment and prevention of these infections. These measures would also impact on patients’ cervical cancer control.

The classification of human papillomavirus (HPV) intratypic lineages by complete genome sequencing is a determinant in understanding biological differences in association with this disease. In this work, we have characterised complete HPV genomes from southern Brazil. Fifteen cervicovaginal Pap smear negative samples previously categorised as HPV-positive were sequenced using ultradeep sequencing, and 18 complete genomes from 13 different HPV types were assembled. Phylogenetic and genetic distance analyses were performed to classify the HPV genomes into lineages and sublineages. This is the first report describing the distribution of HPV intratype lineages of high and low oncogenic risk in asymptomatic women from southern Brazil.

BACKGROUND Increasing evidence suggests that human papillomavirus (HPV) intratype variants (specific lineages and sublineages) are associated with pathogenesis and progression from HPV infection to persistence and the development of cervical cancer. OBJECTIVES This study aimed to verify the prevalence of HPV infection and distribution of HPV types and HPV16 variants in southern Brazil in women with normal cytology or intraepithelial lesions. METHODS HPV typing was determined by L1 gene sequencing. To identify HPV16 variants, the LCR and E6 regions were sequenced, and characteristic single nucleotide variants were identified. FINDINGS A total of 445 samples were studied, with 355 from cervical scrapes and 90 from cervical biopsies. HPV was detected in 24% and 91% of these samples, respectively. The most prevalent HPV types observed were 16 (cervical, 24%; biopsies, 57%) and 58 (cervical, 12%; biopsies, 12%). Seventy-five percent of the HPV16-positive samples were classified into lineages, with 88% defined as lineage A, 10% as lineage D, and 2% as lineage B. MAIN CONCLUSIONS This study identified a high frequency of European and North American HPV16 lineages, consistent with the genetic background of the human population in southern Brazil.

This study investigated the rate of human papillomavirus (HPV) persistence, associated risk factors, and predictors of cytological alteration outcomes in a cohort of human immunodeficiency virus-infected pregnant women over an 18-month period. HPV was typed through L1 gene sequencing in cervical smears collected during gestation and at 12 months after delivery. Outcomes were defined as nonpersistence (clearance of the HPV in the 2nd sample), re-infection (detection of different types of HPV in the 2 samples), and type-specific HPV persistence (the same HPV type found in both samples). An unfavourable cytological outcome was considered when the second exam showed progression to squamous intraepithelial lesion or high squamous intraepithelial lesion. Ninety patients were studied. HPV DNA persistence occurred in 50% of the cases composed of type-specific persistence (30%) or re-infection (20%). A low CD4+T-cell count at entry was a risk factor for type-specific, re-infection, or HPV DNA persistence. The odds ratio (OR) was almost three times higher in the type-specific group when compared with the re-infection group (OR = 2.8; 95% confidence interval: 0.43-22.79). Our findings show that bonafide (type-specific) HPV persistence is a stronger predictor for the development of cytological abnormalities, highlighting the need for HPV typing as opposed to HPV DNA testing in the clinical setting.

The human immunodeficiency virus type 1 (HIV-1) protease mutation D30N is exclusively selected by the protease inhibitor (PI) nelfinavir and confers resistance to this drug. We demonstrate that D30N increases the susceptibility to saquinavir (SQV) and amprenavir in HIV-1 subtype B isolates and that the N88D mutation in a D30N background neutralizes this effect. D30N also suppresses indinavir (IDV) resistance caused by the M46I mutation. Interestingly, in patients with viruses originally containing the D30N mutation who were treated with IDV or SQV, the virus either reversed this mutation or acquired N88D, suggesting an antagonistic effect of D30N upon exposure to these PIs. These findings can improve direct salvage drug treatment in resource limited countries where subtype B is epidemiologically important and extend the value of first and second line PIs in these populations.

Diferentes subtipos do virus da imunodeficiência humana do tipo 1 (HIV-1) podem ter propriedades biológicas, imunológicas e patogênicas distintas. A eficiência da transmissão materno-infantil (TMI) pode estar entre estas propriedades, porém resultados escassos e controversos foram descritos até o momento. Neste estudo, 102 crianças nascidas de mães infectadas pelo HIV-1 entre 1998 e 2004 na cidade do Rio Grande, Brasil, foram analisadas para fatores de risco potenciais associados à TMI. Aquela região geográfica é caracterizada por uma alta proporção de indivíduos infectados pelo subtipo C do HIV-1, permitindo a comparação entre os subtipos B e C e sua influência na transmissão vertical do vírus. A análise também incluiu parâmetros clínicos, obstétricos e imunológicos. Análises de regressão multivariada foram conduzidas para avaliar a influência daqueles parâmetros na TMI, e as razões de prevalência (RP) e intervalos de confiança de 95% (IC95) foram também calculados. Um prevalência surpreendentemente alta do subtipo C acima dos 70% foi encontrada. Somente a carga viral do HIV e o uso de protocolo ACGT 076 maternos forma preditivos de TMI. O subtipo do HIV-1 e a contagem de células T CD4+ não foram associados a um risco aumentado de transmissão. Embora uma clara expansão do subtipo C seja evidente no sul do Brasil, esta não parece estar correlacionada com risco aumentado de transmissão vertical.

Different human immunodeficiency virus type 1 (HIV-1) subtypes may have distinct biological, immunological and pathogenic properties. Efficiency of mother-to-child transmission (MTCT) may be among those properties, but few and controversial results have been described so far. In this study, 102 children born from HIV-1-infected mothers between 1998 and 2004 in the city of Rio Grande, Brazil were analyzed for potential risk factors associated with MTCT. That geographic region is characterized by a high proportion of subtype C-infected subjects, and it allowed comparison between subtypes B and C and their influence on MTCT. The analysis also included clinical, obstetric and immunological parameters. Multivariate regression analyses were conducted to evaluate the influence of the parameters on MTCT, and prevalence ratios (PR) and 95% confidence intervals (CI95) were also calculated. A surprisingly high prevalence of subtype C of over 70% was found. Only the HIV viral load and the use of ACTG 076 protocol were predictive of MTCT. HIV subtype and CD4 T-cell counts were not associated with increased risk of transmission. Although a clear expansion of subtype C is evident in southern Brazil, it does not seem to correlate with increased risk of vertical transmission.

Embora os protocolos de prevenção da transmissão materno-infantil do HIV tenham diminuído a infecção pediátrica pelo HIV nos países desenvolvidos, um grande número de crianças ainda se infectam nas nações em desenvolvimento. Dados disponíveis de infecção pediátrica são entretanto ainda escassos. Neste trabalho, nós conduzimos um levantamento clínico, laboratorial e genotípico de um grande coorte de crianças infectadas pelo HIV em acompanhamento em dois grandes centros de atendimento de HIV/AIDS pediátrica do Rio de Janeiro. Crianças em tratamento anti-retroviral, bem como crianças recentemente diagnosticadas e ainda virgens de tratamento foram analisadas. A prevalência de mutações de resistência às drogas, beem como as respostas imunológicas e virológicas ao tratamento foram avaliadas. Além disso, as frequências dos subtipos do HIV-1 e a sua distrbuição ao longo da epidemia de HIV/AIDS no Brasil foram estudadas. Nós observamos uma alta prevalência de mutações de resistência em vírus de crianças em tratamento, ao passo que o grupo virgem de tratamento não possuía mutações. Apesar dos altos níveis de mutações nas crianças tratadas, uma significativa melhora de sua condição imunológica foi observada. A distribuição de subtipos do HIV-1 seguiu as tendências da população adulta, com o aparecimento de subtipos não-B e de formas recombinantes após 1990. Dentro do nosso conhecimento, este é o maior coorte pediátrico de HIV/AIDS já analisado no Brasil, e os resultados obtidos são de suma importância para um melhor entendimento da evolução do HIV/AIDS em um contexto pediátrico.

Although mother-to-child HIV transmission prevention has slowed down pediatric HIV infection in developed countries, large numbers of infants still become infected in developing nations. Data on pediatric HIV infection is however largely scarce. In this study, we have overviewed clinical, laboratory and genotypic data from a large cohort of HIV-infected infants regularly followed at two pediatric HIV outpatient clinics in Rio de Janeiro, Brazil. Children on antiretroviral therapy, as well as drug-naïve, newly diagnosed infants were analyzed. Prevalence of drug resistance mutations, as well as immunological and virological responses to therapy were evaluated. Additionally, HIV-1 subtype frequencies and their distribution over the course of the epidemic were studied. We have found a high prevalence of mutations among ARV-experienced children, whereas mutations were absent in the drug-naïve group. Despite the high levels of resistance among treated infants, an important improvement of their immunological status was observed. HIV-1 subtype distribution followed the trends of the adult population, with the appearance of non-B subtypes and recombinant forms after 1990. To our knowledge, this is the largest pediatric cohort ever analyzed in Brazil, and the data provided is of paramount importance to a better understanding of HIV/AIDS evolution in pediatric settings.