Genetic evolution of influenza viruses among selected countries in Latin America, 2017-2018.

OBJECTIVE: Since the 2009 influenza pandemic, Latin American (LA) countries have strengthened their influenza surveillance systems. We analyzed influenza genetic sequence data from the 2017 through 2018 Southern Hemisphere (SH) influenza season from selected LA countries, to map the availability of influenza genetic sequence data from, and to describe, the 2017 through 2018 SH influenza seasons in LA. METHODS: We analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers (NICs) in ten countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Ecuador, Mexico, Paraguay, Peru and Uruguay) with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018. These sequences were generated by the NIC or the WHO Collaborating Center (CC) at the U.S Centers for Disease Control and Prevention, uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform, and used for phylogenetic reconstruction. FINDINGS: Influenza hemagglutinin sequences from the participating countries (A/H1pdm09 n = 326, A/H3 n = 636, B n = 433) were highly concordant with the genetic groups of the influenza vaccine-recommended viruses for influenza A/H1pdm09 and influenza B. For influenza A/H3, the concordance was variable. CONCLUSIONS: Considering the constant evolution of influenza viruses, high-quality surveillance data-specifically genetic sequence data, are important to allow public health decision makers to make informed decisions about prevention and control strategies, such as influenza vaccine composition. Countries that conduct influenza genetic sequencing for surveillance in LA should continue to work with the WHO CCs to produce high-quality genetic sequence data and upload those sequences to open-access databases.

First New World Primate Papillomavirus Identification in the Atlantic Forest, Brazil: Alouatta guariba papillomavirus 1.

We report here the complete genome sequence of the first papillomavirus detected in a New World primate, howler monkey, Alouatta guariba clamitans papillomavirus 1 (AgPV1), from the Atlantic Forest in São Paulo State, Brazil.

The His131Arg substitution in the FCGR2A gene (rs1801274) is not associated with the severity of influenza A(H1N1)pdm09 infection.

BACKGROUND: The virulence and pathogenicity of different influenza strains are responsible for a more or less severe disease. Recent studies have attempted to understand how host genetic factors may influence the clinical presentation of the disease. In the present study, the His131Arg (rs1801274) polymorphism was investigated in individuals from a Brazilian admixed population with a diagnosis of influenza A(H1N1)pdm09 infection. METHODS: In the present study, the influence of the His131Arg (rs1801274) polymorphism, a variant of the FCGR2A gene, was investigated in 436 patients with a diagnosis of influenza A(H1N1)pdm09, evaluated at health services in the northern and northeastern regions of Brazil between June 2009 and August 2010. Patients were divided into a group of non-hospitalized patients (n = 192) and a group of hospitalized patients (n = 244; 100 of them died). RESULTS: No significant difference in the allele or genotype frequencies of the rs1801274 polymorphism was observed between groups (p = 0.952 and p = 0.388). Multinomial logistic regression showed no effect of the rs1801274 polymorphism on severity or death of patients from the Brazilian admixed population (p = 0.368 and p = 0.469). CONCLUSIONS: The rs1801274 polymorphism is not associated with severe disease in patients infected with influenza A(H1N1)pdm09.

The CCR5Δ32 (rs333) polymorphism is not a predisposing factor for severe pandemic influenza in the Brazilian admixed population.

BACKGROUND: Recent studies have tried to identify host genetic variants that could explain severe cases and deaths in infection with Influenza A(H1N1)pdm09, especially among children and young adults. CCR5 is a chemokine receptor expressed on T cells, macrophages and dendritic cells, which is an important mediator of leukocyte chemotaxis during the immune response. A deletion mutation (Δ32) in this gene interferes with the response of immune cells, impairing viral clearance. We evaluated the CCR5Δ32 polymorphism (rs333) in individuals of the Brazilian admixed population with a diagnosis of Influenza A(H1N1)pdm09 infection. METHODS: A total of 330 subjects with a diagnosis of Influenza A(H1N1)pdm09, evaluated at health services in the northern and northeastern regions of Brazil between June 2009 and August 2010, were genotyped for the Δ32 deletion (rs333). The cases were classified according to the progression of infection into a group of hospitalized patients (n = 156) and a group of non-hospitalized patients (n = 174). RESULTS: No significant differences in the allele or genotype frequencies of the CCR5Δ32 polymorphism were observed between non-hospitalized and hospitalized patients (p = 0.289 and p = 0.431, respectively). CONCLUSION: The Δ32 deletion in the CCR5 gene is not associated with an unfavorable outcome in patients infected with Influenza A(H1N1)pdm09 in the Brazilian admixed population.

Molecular findings from influenza A(H1N1)pdm09 detected in patients from a Brazilian equatorial region during the pandemic period.

After the World Health Organization officially declared the end of the first pandemic of the XXI century in August 2010, the influenza A(H1N1)pdm09 virus has been disseminated in the human population. In spite of its sustained circulation, very little on phylogenetic data or oseltamivir (OST) resistance is available for the virus in equatorial regions of South America. In order to shed more light on this topic, we analysed the haemagglutinin (HA) and neuraminidase (NA) genes of influenza A(H1N1)pdm09 positive samples collected during the pandemic period in the Pernambuco (PE), a northeastern Brazilian state. Complete HA sequences were compared and amino acid changes were related to clinical outcome. In addition, the H275Y substitution in NA, associated with OST resistance, was investigated by pyrosequencing. Samples from PE were grouped in phylogenetic clades 6 and 7, being clustered together with sequences from South and Southeast Brazil. The D222N/G HA gene mutation, associated with severity, was found in one deceased patient that was pregnant. Additionally, the HA mutation K308E, which appeared in Brazil in 2010 and was only detected worldwide the following year, was identified in samples from hospitalised cases. The resistance marker H275Y was not identified in samples tested. However, broader studies are needed to establish the real frequency of resistance in this Brazilian region.

Molecular findings from influenza A(H1N1)pdm09 detected in patients from a Brazilian equatorial region during the pandemic period

After the World Health Organization officially declared the end of the first pandemic of the XXI century in August 2010, the influenza A(H1N1)pdm09 virus has been disseminated in the human population. In spite of its sustained circulation, very little on phylogenetic data or oseltamivir (OST) resistance is available for the virus in equatorial regions of South America. In order to shed more light on this topic, we analysed the haemagglutinin (HA) and neuraminidase (NA) genes of influenza A(H1N1)pdm09 positive samples collected during the pandemic period in the Pernambuco (PE), a northeastern Brazilian state. Complete HA sequences were compared and amino acid changes were related to clinical outcome. In addition, the H275Y substitution in NA, associated with OST resistance, was investigated by pyrosequencing. Samples from PE were grouped in phylogenetic clades 6 and 7, being clustered together with sequences from South and Southeast Brazil. The D222N/G HA gene mutation, associated with severity, was found in one deceased patient that was pregnant. Additionally, the HA mutation K308E, which appeared in Brazil in 2010 and was only detected worldwide the following year, was identified in samples from hospitalised cases. The resistance marker H275Y was not identified in samples tested. However, broader studies are needed to establish the real frequency of resistance in this Brazilian region.

Prevalence of human papillomavirus infection and phylogenetic analysis of HPV-16 E6 variants among infected women from Northern Brazil.

BACKGROUND: The main cause of cervical cancer in the world is high risks human papillomavirus infection (mainly represented by HPV-16 and HPV-18), that are associated to the development of malign transformation of the epithelium. HPV prevalence exhibits a wide geographical variability and HPV-16 variants have been related to an increased risk of developing cervical intraepithelial lesion. The aim of this study was to describe DNA-HPV prevalence and HPV-16 variants among a women population from Northern Brazil. METHODS: One hundred and forty three women, during routine cervical cancer screening, at Juruti Project, fulfilled an epidemiological inquiry and were screened through a molecular HPV test. HPV-16 variants were determined by sequencing the HPV-16 E6 open reading frame. RESULTS: Forty two samples were considered HPV positive (29.4%). None of those had abnormal cytology results. HPV prevalence varied between different age groups (Z(U) = 14.62; p = <0.0001) and high-risk HPVs were more frequent among younger ages. The most prevalent type was HPV-16 (14%) and it variants were classified, predominantly, as European (87.5%). CONCLUSIONS: HPV prevalence in our population was higher than described by others and the most prevalent HPV types were high-risk HPVs. The European HPV-16 variant was the most prevalent among HPV-16 positive samples. Our study reinforces the fact that women with normal cytology and a positive molecular test for high-risk HPVs should be submitted to continuous follow up, in order to verify persistence of infection, promoting an early diagnosis of cervical cancer and/or its precursors.

Prevalence and clinical features of respiratory syncytial virus in children hospitalized for community-acquired pneumonia in northern Brazil.

BACKGROUND: Childhood pneumonia and bronchiolitis is a leading cause of illness and death in young children worldwide with Respiratory Syncytial Virus (RSV) as the main viral cause. RSV has been associated with annual respiratory disease outbreaks and bacterial co-infection has also been reported. This study is the first RSV epidemiological study in young children hospitalized with community-acquired pneumonia (CAP) in Belém city, Pará (Northern Brazil). METHODS: With the objective of determining the prevalence of RSV infection and evaluating the patients' clinical and epidemiological features, we conducted a prospective study across eight hospitals from November 2006 to October 2007. In this study, 1,050 nasopharyngeal aspirate samples were obtained from hospitalized children up to the age of three years with CAP, and tested for RSV antigen by direct immunofluorescence assay and by Reverse Transcription Polymerase Chain Reaction (RT-PCR) for RSV Group identification. RESULTS: RSV infection was detected in 243 (23.1%) children. The mean age of the RSV-positive group was lower than the RSV-negative group (12.1 months vs 15.5 months, p<0.001) whereas gender distribution was similar. The RSV-positive group showed lower means of C-reactive protein (CRP) in comparison to the RSV-negative group (15.3 vs 24.0 mg/dL, p<0.05). Radiological findings showed that 54.2% of RSV-positive group and 50.3% of RSV-negative group had interstitial infiltrate. Bacterial infection was identified predominantly in the RSV-positive group (10% vs 4.5%, p<0.05). Rhinorrhea and nasal obstruction were predominantly observed in the RSV-positive group. A co-circulation of RSV Groups A and B was identified, with a predominance of Group B (209/227). Multivariate analysis revealed that age under 1 year (p<0.015), CRP levels under 48 mg/dL (p<0.001) and bacterial co-infection (p<0.032) were independently associated with the presence of RSV and, in the analyze of symptoms, nasal obstruction were independently associated with RSV-positive group (p<0.001). CONCLUSION: The present study highlights the relevance of RSV infection in hospitalized cases of CAP in our region; our findings warrant the conduct of further investigations which can help design strategies for controlling the disease.

The role of laboratory diagnosis of influenza

INTRODUCTIONSince 1948 the World Health Organization (WHO) has established an international network of laboratories for the surveillance of influenza viruses. Currently, the Global Influenza Surveillance Network (GISN) includes 128 National Influenza Centers (NICs) distributed in 89 countries. Among their attributions the NICs are responsible for collecting and receiving specimens and virus isolates from patients suspected of being infected with influenza viruses and conducting preliminary laboratory analysis. Representative virus isolates are then selected and shipped to one of four specialized WHO Collaborating Centers (WHOCCs) for reference purposes and for advanced antigenic and genetic influenza analysis. Based on the results of this, the WHO makes an annual recommendation on influenza vaccine composition. NICs also alert the WHO to unusual outbreaks of influenza or influenza-like illness, and they detect non-subtypable and low-reacting virus isolates using the WHO diagnostic reagents provided through the GISN. Under the agreed terms of reference (www.who.int/csr/disease/influenza/TORNICs.pdf), NICs must disseminate the generated data in FluNet (www.who.int/flunet), a webbased tool for the support and coordination of national and global influenza surveillance and reporting. Laboratory diagnosis of influenza is an important public health tool that has become a cornerstone of the prevention, containment, surveillance and therapeutic management of patients. In this context, there are a variety of laboratory methods that allow the identification of influenza viruses circulating in the community. Diagnostic approaches for the identification of the virus include viral culture, detection of viral antigens (e.g., immunofluorescence tests), and nucleic acid testing methods. A presumptive diagnosis can be made by a validated rapid antigen test. Antibody detection is usually accomplished by virus neutralization (NT) and hemagglutination inhibition (HI) tests, which

Ocorrência de Bocavírus Humano associado às infecções respiratórias agudas em crianças de 0 a 2 anos de idade na Cidade de Belém, Pará, Brasil / Ocurrence of Human Bocavirus associated with acute respiratory infections in children up to 2 years old in the City of Belém, Pará State, Brazil

INTRODUÇÃO: As Infecções Respiratórias Agudas (IRA) permanecem como um dos principais problemas de saúde pública em todo o mundo. Essas infecções são associadas a diversos patógenos sendo os vírus os prevalentes. Recentemente, foi descrito na literatura um novo parvovírus denominado Bocavírus Humano (HBoV). Investigações ainda são escassas na associação deste novo agente a casos de IRA na população em geral. Neste contexto, o presente artigo relata a pesquisa do HBoV em um segmento populacional da Amazônia. MATERIAIS E MÉTODOS: Neste estudo, foram analisadas amostras de aspirado nasofaríngeo de pacientes com diagnóstico de IRA atendidos ambulatorialmente na Cidade de Belém, Pará, Brasil. A pesquisa, com a identificação laboratorial do vírus, foi realizada mediante o emprego da técnica de reação em cadeia mediada pela polimerase, utilizando pares de oligonucleotídeos específicos, seguida da análise filogenética das sequências nucleotídicas encontradas. RESULTADOS: Das 397 amostras clínicas analisadas, encontrou-se positividade em amostras de três pacientes, sendo um destes em coinfecção com o vírus respiratório sincicial. DISCUSSÃO: O percentual de positividade obtido na investigação se revelou inferior ao descrito na literatura. Entretanto, vale ressaltar que os estudos já publicados envolveram pacientes hospitalizados, diferentemente do grupo populacional presentemente abordado. As análises filogenéticas realizadas evidenciaram expressiva similaridade dos vírus encontrados com as cepas virais já descritas. CONCLUSÃO: A presente pesquisa se caracteriza como o primeiro relato associando o HBoV à IRA na Região Amazônica.

INTRODUCTION: Acute Respiratory Infections (ARI) are one of the main public health problems in the world. Most of these infections are associated with several pathogens, and viruses are the most prevalent agents. Recently, a new parvovirus named Human Bocavirus (HBoV) has been described. Investigations on the relationship between this new agent and cases of ARI in individuals are still scarce. Herein, we review a study of HBoV in a population segment in the Amazon. MATERIALS AND METHODS: In this study, samples of nasopharyngeal aspirates from patients with ARI treated in Health Care Units in Belém, Brazil, were analyzed. Identification of the virus was carried out by polymerase chain reaction using pairs of specific oligonucleotides, followed by phylogenetic analysis of the nucleotide sequences obtained. RESULTS: Of the 397 samples studied, three specimens were HBoV-positive, and one presented as a co-infection with the respiratory syncytial virus.DISCUSSION: The positivity rate obtained in this investigation was lower than that described in other studies; however, previous studies involved hospitalized patients, which constitute a different population group. The phylogenetic analyses revealed a significant similarity between the virus strains found and those previously described. CONCLUSION: This is the first report associating HBoV with ARI in the Amazon.

Low frequency of human papillomavirus detection in prostate tissue from individuals from Northern Brazil.

The presence of human papillomavirus (HPV) was evaluated in 65 samples of prostate tumours and six samples of prostates with benign prostatic hyperplasia from individuals from Northern Brazil. We used a highly sensitive test, the Linear Array HPV Genotyping Test, to detect 37 high and low-risk HPV types. In this study, only 3% of tumour samples showed HPV infection. Our findings support the conclusion that, despite the high incidence of HPV infection in the geographic regions studied, HPV was not associated with a higher risk of prostate cancer. To our knowledge, this is the first study evaluating the frequency of HPV detection in prostatic tissue of individuals from Brazil.

Low frequency of human papillomavirus detection in prostate tissue from individuals from Northern Brazil

The presence of human papillomavirus (HPV) was evaluated in 65 samples of prostate tumours and six samples of prostates with benign prostatic hyperplasia from individuals from Northern Brazil. We used a highly sensitive test, the Linear Array HPV Genotyping Test, to detect 37 high and low-risk HPV types. In this study, only 3 percent of tumour samples showed HPV infection. Our findings support the conclusion that, despite the high incidence of HPV infection in the geographic regions studied, HPV was not associated with a higher risk of prostate cancer. To our knowledge, this is the first study evaluating the frequency of HPV detection in prostatic tissue of individuals from Brazil.

The dilemma of influenza vaccine recommendations when applied to the tropics: the Brazilian case examined under alternative scenarios.

Since 1999 the World Health Organization issues annually an additional influenza vaccine composition recommendation. This initiative aimed to extend to the Southern Hemisphere (SH) the benefits-previously enjoyed only by the Northern Hemisphere (NH)--of a vaccine recommendation issued as close as possible to the moment just before the onset of the influenza epidemic season. A short time between the issue of the recommendation and vaccine delivery is needed to maximize the chances of correct matching between putative circulating strains and one of the three strains present in the vaccine composition. Here we compare the effectiveness of the SH influenza vaccination adopted in Brazil with hypothetical alternative scenarios defined by different timings of vaccine delivery and/or composition. Scores were based on the temporal overlap between vaccine-induced protection and circulating strains. Viral data were obtained between 1999 and 2007 from constant surveillance and strain characterization in two Brazilian cities: Belém, located at the Equatorial region, and São Paulo, at the limit between the tropical and subtropical regions. Our results show that, among currently feasible options, the best strategy for Brazil would be to adopt the NH composition and timing, as in such case protection would increase from 30% to 65% (p<.01) if past data can be used as a prediction of the future. The influenza season starts in Brazil (and in the equator virtually ends) well before the SH winter, making the current delivery of the SH vaccination in April too late to be effective. Since Brazil encompasses a large area of the Southern Hemisphere, our results point to the possibility of these conclusions being similarly valid for other tropical regions.

Inquérito soroepidemiológico para os vírus influenza em Belém, Pará, Brasil, 1992-1993 / Seroepidemiological survey for influenza virus in Belém, Pará, Brasil, 1992-1993

Um estudo soroepidemiológico foi realizado para determinar a prevalência de anticorpos IH para os sorotipos de influenza circulantes entre pacientes atendidos no Laboratório de Virologia do IEC, em Belém, Pa, Brasil, em 1992 e 1993. Um total de 179 (11 por cento) amostras de sangue foi coletado durante período pós-epidêmico e processado pelo teste da Inibiçäo da Hemaglutinaçäo para os vírus da influenza A/Taiwan/1/86 (HINI), A/Beijing/353/89 (H3N2) e B/Yamagatal/16/88. Os resultados indicaram a circulaçäo de vírus antigenicamente relacionados aos três sorotipos pesquisados. Em 1992, altas taxas de soropositividade foram observadas para as cepas HINI (84 por cento) e H3N2 (56 por cento), bem como anticorpos IH foram detectados em todas as faixas de idade, sugerindo intensa circulaçäo desses vírus. No mesmo ano, a atividade da influenza B revelou-se em níveis moderados. A prevalência de anticorpos IH para os vírus H1N1, em 1993, foi similar à observada em 1992, indicando a circulaçäo desses vírus em ambos os anos. Um aumento na prevalência dos vírus H3N2, em 1993, sugere que a cepa A/Beijing/353/89 (ou uma antigenicamente relacionada) também circulou intensamente naquele ano. Do mesmo modo, a atividade dos vírus da influenza B aumentou em 1993, como apontam as infecçöes em todas as idades, particularmente entre os adultos jovens.