Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population.

Koala populations are in serious decline across many areas of mainland Australia, with infectious disease a contributing factor. Koala retrovirus (KoRV) is a gammaretrovirus present in most wild koala populations and captive colonies. Five subtypes of KoRV (A to E) have been identified based on amino acid sequence divergence in a hypervariable region of the receptor binding domain of the envelope protein. However, analysis of viral genetic diversity has been conducted primarily on KoRV in captive koalas housed in zoos in Japan, the United States, and Germany. Wild koalas within Australia have not been comparably assessed. Here we report a detailed analysis of KoRV genetic diversity in samples collected from 18 wild koalas from southeast Queensland. By employing deep sequencing we identified 108 novel KoRV envelope sequences and determined their phylogenetic diversity. Genetic diversity in KoRV was abundant and fell into three major groups; two comprised the previously identified subtypes A and B, while the third contained the remaining hypervariable region subtypes (C, D, and E) as well as four hypervariable region subtypes that we newly define here (F, G, H, and I). In addition to the ubiquitous presence of KoRV-A, which may represent an exclusively endogenous variant, subtypes B, D, and F were found to be at high prevalence, while subtypes G, H, and I were present in a smaller number of animals. IMPORTANCE: Koala retrovirus (KoRV) is thought to be a significant contributor to koala disease and population decline across mainland Australia. This study is the first to determine KoRV subtype prevalence among a wild koala population, and it significantly expands the total number of KoRV sequences available, providing a more precise picture of genetic diversity. This understanding of KoRV subtype prevalence and genetic diversity will be important for conservation efforts attempting to limit the spread of KoRV. Furthermore, KoRV is one of the only retroviruses shown to exist in both endogenous (transmitted vertically to offspring in the germ line DNA) and exogenous (horizontally transmitted between infected individuals) forms, a division of fundamental evolutionary importance.

Phylogeography and evolutionary history of rodent-borne hantaviruses.

Hantavirus (Family Bunyaviridae) are mostly associated to rodents and transmitted to man by inhalation of aerosolized infected excreta of these animals. The human infection by hantaviruses can lead to severe diseases such as hemorrhagic fever with renal syndrome (HFRS) in Asia and Europe, and pulmonary syndrome (HPS) in the Americas. To determine the origin, spreading and evolutionary dynamics of rodent-borne hantaviruses, 190 sequences of nucleoprotein (N) of hantaviruses identified in 30 countries, from 1985 to 2010, were retrieved from the GenBank and analyzed using the BEAST program. Our evolutionary analysis indicates that current genetic diversity of N gene of rodent-borne hantaviruses probably was originated around 2000 years ago. Hantavirus harbored by Murinae and Arvicolinae subfamilies, probably, were originated in Asia 500-700 years ago and later spread toward Siberia, Europe, Africa and North America. Hantavirus carried by Neotominae subfamily, probably, emerged 500-600 years ago in Central America and spread toward North America. Finally, hantaviruses associated to Sigmodontinae occurred in Brazil 400 years ago and were, probably, originated from Neotominae-associated virus from northern South America. These data offer subsidies to understand the time-scale and worldwide dissemination dynamics of rodent-borne hantaviruses.

Viral load of human bocavirus-1 in stools from children with viral diarrhoea in Paraguay.

Since their discovery, four species of human bocavirus (HBoV) have been described in patients with respiratory and gastrointestinal diseases. However, a clear causal association between HBoV-1 and gastroenteritis has not been demonstrated. In this study, we describe the detection and quantification of HBoV-1 in stools from children with acute non-bacterial gastroenteritis using quantitative polymerase chain reaction. HBoV-1 genome was detected in 10.6% of stools with frequent association with rotavirus and norovirus. The median of HBoV-1 viral load was 1.88 × 104 genome/ml, lower than previously shown in secretions of patients with respiratory infections, without any obvious association between high viral load and presence of HBoV as single agent. Thus, although HBoV-1 was frequently detected in these patients, there is no clear causal association of this agent with diarrhoea. Indeed, HBoV-1 DNA in stools of patients with gastroenteritis without respiratory symptoms may be a remnant of previous infections or associated with prolonged shedding of virus in the respiratory or digestive tracts.

Detección del virus influenza pandémica A (H1N1) en Paraguay 2009, y amplificación de genes hemaglutinina y neuraminidasa / Detection of pandemic influenza A (H1N1) virus in Paraguay in 2009, and amplification of the hemagglutinin and neuraminidase genes

Introducción: El virus de influenza pandémica A (H1N1), cuya circulación se inició en abril del año 2009 en México y Estados Unidos, se constituyó en el último virus pandémico desde los casos detectados en Hong Kong en 1968. El genoma del virus de influenza A está formado por 8 segmentos ARN de cadena simple (polaridad negativa), que codifican para 10 proteínas. Los genes hemaglutinina y neuraminidasa codifican para dos proteínas de superficie y son los utilizados en los análisis de variabilidad genética. Objetivos: a) Detectar la circulación del virus pandémico en pacientes con sospecha clínica de infección por influenza, y b) Diseñar una estrategia para amplificar de forma completa los genes hemaglutinina y neuraminidasa. Materiales y Métodos: Fueron analizados por Real-Time RT-PCR (transcripción reversa y reacción en cadena de la polimerasa en tiempo real) un total de 181 muestras de hisopado faríngeo, colectadas o remitidas al Hospital de Clínicas, del 6 de agosto al 11 de octubre de 2009. Para el diseño de amplificación de los genes hemaglutinina y neuraminidasa, se han utilizado herramientas bioinformáticas y reacción en cadena de la polimerasa. Resultados: Del total de muestras analizadas, 27 (14.9 %) dieron resultado positivo para el nuevo virus pandémico. Por otra parte, la amplificación completa de ambos genes proporcionó los resultados esperados: 1678-pares de bases (pb) para la hemaglutinina, y 1427-pb para la neuraminidasa. Conclusiones: La implementación de esta tecnología de amplificación permitirá posteriormente la secuenciación de estos genes a fin de determinar las variaciones genéticas del virus que podrían tener un impacto en la salud humana.

Introduction: The pandemic influenza A (H1N1) virus, whose circulation was detected in April 2009 in Mexico and the United States, is the latest pandemic virus since the cases reported in Hong Kong in 1968. The genome of the influenza A virus consists of 8 segments of single-stranded RNA of negative polarity, coding for 10 proteins. The hemagglutinin and neuraminidase genes encode for two surface proteins and are used in the analysis of genetic variability. Objectives: a) to detect circulation of the pandemic virus in patients with clinical suspicion of influenza infection and b) design a strategy to fully amplify the hemagglutinin and neuraminidase genes.Materials and Methods: A total of 181 pharyngeal swabs were collected and sent to the Hospital de Clínicas for analysis using Real-Time RT-PCR (reverse transcription and polymerase chain reaction in real time) between 6 August and 11 October 2009. To design the amplification of hemagglutinin and neuraminidase genes, we used bioinformatic tools and polimerase chain reaction. Results: Of the samples analyzed, 27 (14.9%) were positive for the new pandemic virus. Moreover, the complete amplification of both genes provided the expected results: 1678-base pairs (bp) for the hemagglutinin, and 1427-bp for neuraminidase. Conclusions: The use of this technology for amplification will eventually allow sequencing to identify genetic variations of the virus that could have an impact on human health.