Picobirnavirus (PBV) pertencem à família Picobirnaviridae, divididos em duas espécies Human Picobirnavirus e Rabbit Picobirnavirus. São pequenos vírus constituídos de genoma bissegmentado de cadeia dupla de RNA (dsRNA), não envelopados, com capsídeo de simetria icosaédrica, sendo divididos em dois genogrupos, GI e GII. Já foram detectados em fezes humanas e de uma ampla gama de espécies animais, com ou sem sinais diarreicos, sendo considerados agentes emergentes e oportunistas, e seu potencial zoonótico foi sugerido. Entretanto, os estudos epidemiológicos e moleculares de PBV em bovinos são raros na literatura nacional e internacional. Devido à carência de dados a respeito de PBV em bovinos, o presente estudo foi realizado objetivando-se a detecção e caracterização moleculares de cepas de PVB bovinos dos genogrupos GI e GII em amostras fecais de bovinos com ou sem sintomatologia diarreica de diferentes idades e regiões do Brasil. O estudo foi conduzido a partir de 77 animais, obtendo-se 18 (23,3%) amostras positivas para GI, compreendendo animais provenientes dos estados de São Paulo, Minas Gerais e Goiás. Não foram detectadas amostras positivas para GII. A identidade nucleotídica das amostras obtidas apresentou média de 67,4% quando comparadas uma com as outras e de até 83,77% quando comparadas com amostras de PBV de referência. Na reconstrução filogenética, três amostras agruparam-se em clado de PVB humano e somente uma agrupou-se em clado de PVB bovino. Em síntese, os resultados obtidos indicam, de maneira inédita, a circulação de PVB bovino pertencente ao genogrupo GI em diferentes estados brasileiros, com perfis filogenéticos heterogêneos. / Picobirnavirus (PBV) belong to the Picobirnaviridae family, divides into two species Human Picobirnavirus and Rabbit Picobirnavirus. They are small, non-enveloped, bisegmented double-stranded RNA (dsRNA) virus with an icosahedral capsid, being divided into two genogroups, GI and GII. They have been detected in feces of humans and many animal species, with or without diarrheal signs and are considered emerging and opportunistic agents, and its zoonotic potential has been suggested. However, epidemiological and molecular studies of bovine PBV are rare in the national and international literature. Due to lack of data on PBV in cattle, this study was conducted aiming to detect and molecularly characterize bovine PBV strains of GI and GII genogroups in feces from animals with or without diarrheal signs of different ages and regions of Brazil. Seventy-seven animals were sampled, resulting in 18 (23.3%) positive samples for GI, including animals from the states of São Paulo, Minas Gerais and Goiás. There were no positive samples for GII. The nucleotide identity of the samples obtained showed a mean of 67.4% compared to each other and up to 83.77% compared to PBV reference samples. In phylogenetic reconstruction, three samples were grouped in the human PBV clade and only one sample was clustered in the bovine PVB clade. In summary, the results indicate in an unprecedented way the circulation of the bovine PBV belong to GI genogroup in different Brazilian states, with heterogeneous phylogenetic profiles.

Tuberculosis is a major public health problem in Ethiopia. The aims of this study were (i) to investigate the recovery rate of M. tuberculosis from smear positive single morning sputum specimens subjected to long-term storage at -20°C, (ii) to assess the level and risk factors for first- and second-line anti-TB drug resistance, (iii) to evaluate the performance of the GenoType®MTBDRplus and GenoType®MTBDRsl assays for drug susceptibility testing compared to the BacT/ALERT 3D system as reference method, (iv) to analyze the frequency of gene mutations associated with resistance to isoniazid (INH), rifampicin (RMP) and ethambutol (EMB) among M. tuberculosis isolates, and (v) to study the population structure and transmission dynamics of M. tuberculosis isolates from patients in Amhara region, Northwest Ethiopia. The median specimen storage time was 132 days. Of 319 specimens, 90.0% were culture positive. The length of time of sputum storage had no significant effect on the recovery rate of M. tuberculosis. Of 260 M. tuberculosis isolates, 15.8% were resistant to at least one first-line drug, 5.0% were multidrug resistant (MDR) and 3.5% were resistant to all first-line drugs. Any resistance to INH, RMP, streptomycin (STM), EMB and pyrazinamide (PZA) was 13.8%, 5.8%, 10.0%, 7.3% and 4.6%, respectively. All isolates were susceptible to second-line drugs. The GenoType®MTBDRplus assay had a sensitivity of 92% and specificity of 99% to detect INH resistance, and 100% sensitivity and specificity to detect RMP resistance and MDR. The GenoType®MTBDRsl assay had a sensitivity of 42% and specificity of 100% to detect EMB resistance. According to the molecular methods, mutations conferring resistance to INH, RMP, or EMB were detected in 13.5%, 5.8%, and 3.1% of the isolates, respectively, while mutation conferring MDR was present in 5.0% of the isolates. Of 244 M. tuberculosis isolates, 59.0% were classified as known lineages; Dehli/CAS (38.9%), Haarlem (8.6%), Ural (3.3%), LAM (3.3%), TUR (2.0%), X-type (1.2%), S-type (0.8%), Beijing (0.4%) and Uganda II (0.4%) lineage. Interestingly, 31.6% of the isolates were grouped in to four previously undefined phylogenetic lineages and were named as Ethiopia_3 (13.1%), Ethiopia_1 (7.8%), Ethiopia_H37Rv like (7.0%) and Ethiopia_2 (3.7%) lineages. The remaining 9.4% of the isolates could not be assigned to the known or new lineages. Overall, 45.1% of the isolates were grouped in clusters, indicating high rate of recent transmission. Similarly, 66.7% of MDR strains were grouped in clusters.

Abstract Parkinson’s disease and Huntington’s disease are progressive neurodegenerative movement disorders that typically manifest in adulthood. In this study, genetic risk factors contributing to these two movement disorders were investigated in Finnish patients. Patients with early-onset or late-onset Parkinson’s disease as well as population controls were examined. The p.L444P mutation in GBA was found to contribute to the risk of Parkinson’s disease. POLG1 compound heterozygous mutations were detected in two patients with Parkinson’s disease and rare length variants in POLG1 were associated with Parkinson’s disease. Variants in SMPD1, LRRK2 or CHCHD10, previously detected in other populations, were not detected, suggesting that they are rare or even absent in the Finnish population. Patients with Huntington’s disease were investigated for HTT gene haplotypes as well as whether these haplotypes alter the stability of the elongated CAG repeat. Haplogroup A was less common in Finns than in other European populations, whereas it was significantly more common in patients with Huntington’s disease than in the general population. Certain HTT haplotypes as well as the parental gender were found to affect the repeat instability. We found that compound heterozygous mutations in POLG1 were causative of Parkinson’s disease, rare length variants in POLG1 were associated with Parkinson’s disease and GBA p.L444P was significantly more frequent in patients than in the controls, which suggests that these mutations are associated with the development of Parkinson’s disease. The low prevalence of Huntington’s disease in Finland correlates with the low frequency of the disease-associated HTT haplogroup A. Paternal inheritance combined with haplotype A1 increased the risk of repeat expansion. Movement disorders in Finland were found to share some of the same genetic risk factors found in other European populations, but some other recognized genetic variants could not be detected. / Tiivistelmä Parkinsonin tauti ja Huntingtonin tauti ovat hermostoa rappeuttavia eteneviä liikehäiriösairauksia, jotka tyypillisesti ilmenevät aikuisiällä. Tässä tutkimuksessa selvitettiin näiden kahden liikehäiriösairauden geneettisiä riskitekijöitä suomalaisilla potilailla. Tutkimme potilaita, joilla oli varhain alkava Parkinsonin tauti tai myöhään alkava Parkinsonin tauti sekä väestökontrolleja. GBA-geenin p.L444P mutaation havaittiin lisäävän Parkinsonin taudin riskiä. Kaksi Parkinsonin tautia sairastavaa potilasta oli yhdistelmäheterotsygootteja haitallisten POLG1-geenin varianttien suhteen ja harvinaiset POLG1 CAG toistojaksovariantit assosioituivat Parkinsonin tautiin. Tutkittuja variantteja SMPD1-, LRRK2- ja CHCHD10-geeneissä ei löydetty tästä aineistosta lainkaan, mikä viittaa siihen, että ne puuttuvat suomalaisesta väestöstä tai ovat harvinaisia. Huntingtonin tautia sairastavilta potilailta tutkittiin HTT-geenin haploryhmiä ja niiden vaikutusta Huntingtonin tautia aiheuttavan pidentyneen toistojakson epästabiiliuteen. Haploryhmä A oli suomalaisessa väestössä harvinainen verrattuna eurooppalaiseen väestöön ja se oli huomattavasti yleisempi Huntingtonin tautipotilailla kuin väestössä. Toistojakson epästabiiliuteen vaikuttivat tietyt HTT-geenin haplotyypit samoin kuin sen vanhemman sukupuoli, jolta pidentynyt toistojakso periytyy. POLG1 yhdistelmäheterotsygoottien katsottiin aiheuttavat Parkinsonin tautia ja harvinaisten POLG1 CAG toistojaksovarianttien todettiin assosioituvan Parkinsonin tautiin Suomessa. GBA p.L444P mutaatio merkittävästi yleisempi Parkinsonin tautipotilailla kuin kontrolleilla, mikä viittaa siihen, että se on Parkinsonin taudin riskitekijä. Huntingtonin tautiin assosioituvan haploryhmä A:n matala frekvenssi selittää taudin vähäistä esiintyvyyttä Suomessa. Paternaalinen periytyminen ja haplotyyppi A1 lisäsivät HTT-geenin toistojakson pidentymisen riskiä. Liikehäiriösairauksilla todettiin Suomessa osittain samanlaisia riskitekijöitä kuin muualla Euroopassa, mutta kaikkia tutkittuja variantteja emme havainneet.

Tesis por compendio / [EN] Legionella pneumophila is a strictly environmental and opportunistic pathogen that can cause severe pneumonia after inhalation of aerosols with enough bacterial load. Outbreaks and sporadic cases are usually localized in temperate environments, and the reservoirs are often water-related sources where biofilms are created. The existence of non-cultivable forms of the bacteria increases the risk for public health, as culture-based methods may miss them, thus complicating the environmental investigations of the sources. Genetic classification through the Sequence-Based Typing (SBT) technique allowed an increased discrimination among L. pneumophila strains compared to previous methods. SBT data can also be used for genetic variability and population structure studies, but a more exhaustive analysis can be performed using high-throughput genome sequencing strategies. This thesis describes the use of both SBT and genomic sequencing to evaluate and provide solutions to different public health needs in L. pneumophila epidemiology. We have focused in the Comunidad Valenciana (CV), the second region in Spain with the highest incidence of Legionellosis, with special interest in the city of Alcoy, where recurrent outbreaks have occurred since 1998. Firstly, SBT data were used to gain a deeper insight into the genetic variability and distribution of the most abundant Sequence Types (ST) in the CV area. We have shown that the level of variability in this region is comparable to that from other countries, revealing the existence of both locally and broadly extended profiles. Approximately half of the observed genetic diversity was found to result from geographical and temporal structure. Secondly, L. pneumophila detection from environmental sources remains a challenge for public health. A comparison between water and biofilm samples using a sensitive touchdown PCR (TD-PCR) strategy revealed that the use of biofilms increased by ten-fold the detection rate. This method allowed evaluating the hidden uncultivable L. pneumophila diversity in the locality of Alcoy and the real-time investigation of a Legionellosis outbreak affecting a hotel in Calpe (Southeast of Spain) in 2012. Thirdly, genomic sequencing was applied to a set of 69 strains isolated during 13 outbreaks occurred in Alcoy in the period 1999-2010, mainly the recurrent ST578. Higher intra-outbreak variability than expected was observed, pointing to the potential existence of multiple sources in this endemic area or high environmental diversity. Interestingly, above 98% of the genomic variability in this ST was found as being incorporated through recombination processes rather than through point mutations. Finally, a metagenomic analysis of environmental biofilms from Alcoy revealed a microbial community dominated by Proteobacteria, Cyanobacteria, Actinobacteria and Bacteroidetes. Despite the known endemism of Legionella in this area, the genus was only found in a relative abundance ranging 0.01-0.07%, which explains the low recovery from environmental sources. In summary, the results from this thesis can benefit public health efforts to control this pathogen in the environment, as we provide new insight into its molecular epidemiology, with immediate applications to surveillance and outbreak investigations. / [ES] Legionella pneumophila es un patógeno oportunista estrictamente ambiental capaz de causar neumonía debido a la inhalación de aerosoles con suficiente carga bacteriana. Los brotes y casos esporádicos suelen producirse en ambientes templados y los reservorios encontrarse en zonas con agua donde pueden crearse biopelículas microbianas. La existencia de formas no cultivables de la bacteria aumenta el riesgo para la salud pública, ya que los métodos estándar basados en cultivo microbiológico no pueden detectarlas, complicando las investigaciones ambientales. La clasificación genética basada en el método Sequence-Based Typing (SBT) permite un mayor poder de discriminación entre cepas de L. pneumophila en comparación con métodos previos. Los datos derivados del SBT pueden utilizarse para estudios de variabilidad genética y estructura poblacional. Sin embargo, puede llevarse a cabo un análisis más exhaustivo mediante técnicas de secuenciación genómica de alto rendimiento. Esta tesis describe la utilización tanto de SBT como de secuenciación genómica para evaluar e incluso proponer soluciones a diferentes necesidades en salud pública relacionadas con la epidemiología de L. pneumophila. Nos centramos en la Comunidad Valenciana (CV), la segunda región en España con mayor incidencia de Legionelosis, con especial interés en la localidad de Alcoy, donde ocurren brotes de forma recurrente. En primer lugar, utilizamos datos derivados de SBT para conocer mejor la variabilidad y la distribución de los perfiles genéticos (Sequence Types, ST) en el área de la CV. Mostramos que el nivel de variabilidad en sólo esta región es comparable a la de otros países, con perfiles extendidos local y globalmente. Aproximadamente la mitad de la diversidad genética observada se estima que procede de estructuración geográfica y temporal. En segundo lugar, la detección de L. pneumophila a partir de fuentes ambientales sigue suponiendo un reto para la salud pública. En esta tesis realizamos una comparación entre la detección mediante touchdown PCR (TD-PCR) a partir de muestras de agua y biopelículas microbianas y mostramos que estas últimas proporcionan un aumento de 10 veces en la tasa de detección de la bacteria. Este método permitió evaluar la diversidad no cultivable de L. pneumophila en la localidad de Alcoy y la investigación a tiempo real de un brote en un hotel en Calpe (Sudeste de España) en 2012. A continuación, aplicamos la secuenciación genómica a 69 cepas aisladas durante 13 brotes ocurridos en Alcoy en el período 1999-2010, principalmente el recurrente ST578. Se observó mayor variabilidad entre cepas de un mismo brote que la esperada, lo cual apunta a la existencia potencial de múltiples fuentes en este área, o alta diversidad ambiental. Además, se observó que más del 98% de la variabilidad genómica fue introducida por procesos de recombinación y no de mutación puntual. Finalmente, se realizó un análisis metagenómico de biopelículas ambientales recogidas en Alcoy. Se encontró que la comunidad está dominada por Proteobacteria, Cyanobacteria, Actinobacteria y Bacteroidetes. A pesar del conocido endemismo de Legionella en el área, este género sólo se encontró en una abundancia relativa entre 0.01-0.07%, lo cual explica su baja tasa de recuperación a partir de muestras ambientales. En resumen, los resultados de esta tesis pueden ser de utilidad para los programas de control de este patógeno llevados a cabo por las autoridades de salud pública, ya que proporcionan una nueva percepción de su epidemiología molecular, con aplicación inmediata a la vigilancia e investigación de brotes. / [CA] Legionella pneumophila és un patogen oportunista estrictament ambiental capaç d'ocasionar pneumònia degut a la inhalació d'aerosols amb la suficient carga bacteriana. Els brots i casos esporàdics solen ocórrer en ambients temperats, i els reservoris solen trobar-se en zones amb aigua on poden crear-se biopel·lícules microbianes. La existència de formes no cultivables del bacteri augmenten el risc per a la salut pública, ja que els mètodes estàndard basats en el cultiu microbiològic no poden detectar-les, complicant les investigacions ambientals. La classificació genètica basada en el mètode Sequence-Based Typing (SBT) permet un major poder de discriminació entre soques de L. pneumophila en comparació amb previs mètodes. Les dades derivades del SBT poden utilitzar-se per a estudis de variabilitat genètica i estructura poblacional, però un anàlisis més exhaustiu pot dur-se a terme a través de tècniques de seqüenciació genòmica d'alt rendiment. Esta tesis descriu la utilització tant del SBT com de la seqüenciació genòmica per a avaluar i proposar solucions a diferents necessitats en salut pública relacionades amb l'epidemiologia de L. pneumophila. Ens centrem en la Comunitat Valenciana (CV), la segona regió d'Espanya amb la major incidència de Legionel·losi, amb especial interès en la localitat d'Alcoi, on els brots ocorren de forma recurrent des de 1998. Primer, hem utilitzat dades derivades del SBT per a conèixer millor la variabilitat i la distribució dels perfils genètics (Sequence Types, ST) en l'àrea de la CV. Mostrem que el nivell de variabilitat en només aquesta regió és comparable a la d'altres països, amb perfils estesos tant de forma local com més amplia. Aproximadament la meitat de la diversitat genètica observada s'estima que procedeix d'estructuració geogràfica i temporal. Segon, la detecció de L. pneumophila a partir de fonts ambientals continua suposant un repte per a la salut pública. En aquesta tesis realitzem una comparació entre la detecció mitjançant touchdown PCR (TD-PCR) a partir de mostres d'aigua i biopel·lícules microbianes i mostrem que aquestes últimes proporcionen un augment de deu vegades en la tassa de detecció. A més, aquest mètode ens va permetre avaluar la diversitat no cultivable de L. pneumophila a la localitat d'Alcoi i la investigació a temps real d'un brot de Legionelosis que va afectar a un hotel en Calp (Sud-est d'Espanya) a l'any 2012. Tercer, vam aplicar la seqüenciació genòmica a 69 soques aïllades durant 13 brots ocorreguts a Alcoi en el període 1999-2010, principalment el recurrent ST578. Es va observar una major variabilitat entre soques d'un mateix brot de l'esperada, apuntant a l'existència potencial de múltiples fonts en aquesta àrea, considerada endèmica, o alta diversitat ambiental. A més, es va observar que més del 98% de la variabilitat genòmica havia sigut introduïda a partir de processos de recombinació i no de mutació puntual. Finalment, es va realitzar una anàlisi metagenòmica de biopel·lícules ambientals recollides a Alcoi. Varem trobar que la comunitat està dominada per Proteobacteria, Cyanobacteria, Actinobacteria i Bacteroidetes. A pesar del conegut endemisme de Legionella en l'àrea, aquest gènere només es va trobar en una abundància relativa entre 0.01-0.07%, el qual explica la seua baixa tassa de recuperació a partir de mostres ambientals. En resum, els resultats d'aquesta tesi poden ser d'utilitat per als programes de control d'aquest patogen duts a terme per les autoritats de salut pública, ja que proporcionen una nova percepció de la seua epidemiologia molecular, amb aplicació immediata a la vigilància i la investigació de brots. / Sánchez Busó, L. (2015). Genetic and genomic variability of Legionella pneumophila: applications to molecular epidemiology and public health [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/52854 / TESIS / Premios Extraordinarios de tesis doctorales / Compendio

IV. ABSTRACT The human metapneumovirus is a novel paramyxovirus associated with acute respiratory infections in children, adults, elderly and immunocompromised individuals. It has a worldwide distribution and the prevalence range between 1.5% to 25% in individuals with respiratory infections. Based on phylogenetic analysis 2 distinct genetic groups (A and B) that are sub-divided into four subgroups (A1, A2, B1 and B2) have been shown to circulate. Until recently, there was no information on the molecular epidemiology and the clinical characteristics of the hMPV in Africa, including South Africa, a region with a high prevalence of paediatric human immunodeficiency virus type-1 (HIV) infection. The molecular epidemiology and clinical characteristics of the hMPV in South Africa was investigated over a three period (2000-2002) in children hospitalized with lower respiratory tract infection. The children were part of a cohort participating in a phase 3 clinical trial investigating the efficacy of a 9-valent-pneumocococcal protein-polysaccharide conjugate vaccine (PCV). The objectives of the study were: i. to investigate the molecular epidemiology of hMPV in South Africa; ii. characterize the burden of hMPV disease and determine the clinical features of hMPV-LRTI in children infected and not infected by HIV; iii. probe the role of Streptococcus pneumoniae in the pathogenesis of hMPV-LRTI. The overall prevalence of hMPV in children hospitalized with lower respiratory tract infections (LRTI) was 7.4%. The mean age of children with hMPV associated LRTI (hMPV-LRTI) in South Africa was 13.3 months (range 1.4-49.2 months), with HIV infected children being older than children not infected with HIV (mean [range] 17.6 [4.5-44.3] vs. 12.3 [1.4-49.2] months; P=0.007). The incidence of hMPV-LRTI was 5.0 (95%C.I.3.3-7.5) fold greater in HIV infected children (incidence rate: 2 504 [95%C.I. 1 683-3 577] per 100 000) than in HIV uninfected children (incidence rate: 505 [95%C.I. 409-618] per 100 000, P<0.0001). Human metapneumovirus was identified less frequently than RSV but more commonly than other studied respiratory viruses. The double-blind PCV-9 vs. placebo controlled trial was used to probe the role of pneumococcal co-infections contributing to the pathogenesis of severe hMPV-LRTI. The incidence of hospitalization for hMPV-LRTI was reduced by 46% (95%, CI, 25-63; P=0.0002) in PCV-9 vaccinees compared to placebo recipients. This inferred that coinfection with Streptococcus pneumoniae was integral to the pathogenesis of hMPV-LRTI requiring hospitalization. Both groups of the hMPV circulated during the three year period including concurrent circulation of multiple subtypes of the virus. There was a transition from group B to group A subtype virus as the dominant circulating virus over sequential years. Sequence analysis of the two attachment glycoproteins (F and G), showed the F gene protein to be highly conserved, in contrast the attachment protein gene (G protein) was highly variable particularly in the extracellular domain between lineages. Repeat hMPV-LRTI by either homologous or heterologous strains within 3 months of each other suggested that natural infection did not confer complete immunity to hMPV. The present study demonstrated that hMPV is a leading pathogen associated with LRTI among children in Africa and indicated that occult pneumococcal co-infections’ were integral in the pathogenesis of hMPV-LRTI requiring hospitalization. Additionally, this is the first study to have characterized the molecular epidemiology of hMPV in Africa and provides insight as to issues that may exist regarding the design of an hMPV vaccine.

Rhinoviruses (RVs) constitute a substantial public health burden. To evaluate their abundance and genetic diversity in adult patients, RV RNA in respiratory samples was assessed using real-time RT-PCR and the partial nucleic acid sequencing of viral genomes. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of adult RV infections. In total, the respiratory specimens of 284 adult patients (18–90 years), collected from 2013 to 2017, were analyzed. Infections occurred throughout the entire year, with peaks occurring in fall and winter, and showed a remarkably high intra- and interseasonal diversity of RV genotypes. RV species were detected in the following ratios: 60.9% RV-A 173, 12.7% RV-B, and 26.4% RV-C. No correlations between RV species and underlying comorbidities such as asthma (p = 0.167), COPD (p = 0.312) or immunosuppression (p = 0.824) were found. However, 21.1% of the patients had co-infections with other pathogens, which were associated with a longer hospital stay (p = 0.024), LRTI (p < 0.001), and pneumonia (p = 0.01). Taken together, this study shows a pronounced genetic diversity of RV in adults and underlines the important role of co-infections. No correlation of specific RV species with a particular clinical presentation could be deduced.

No description available.

No description available.

Rhinoviruses (RVs) constitute a substantial public health burden. To evaluate their abundance and genetic diversity in pediatric patients, RV RNA in respiratory samples was assessed using real-time RT-PCR and partial nucleic acid sequencing of viral genomes. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of pediatric RV infections. In total, the respiratory specimens of 776 patients (<18 years), collected from 2013 to 2017, were analyzed. Infections occurred throughout the entire year, with peaks occurring in fall and winter, and showed remarkably high intra- and interseasonal diversity for RV genotypes. RV species were detected in the following frequencies: 49.1% RV-A, 5.9% RV-B, and 43.6% RV-C. RV-C was found to be more frequently associated with asthma (p = 0.04) and bronchiolitis (p < 0.001), while RV-A was more frequently associated with fever (p = 0.001) and pneumonia (p = 0.002). Additionally, 35.3% of the patients had co-infections with other pathogens, which were associated with a longer hospital stay (p < 0.001), need for ventilation (p < 0.001), and pneumonia (p < 0.001). Taken together, this study shows pronounced RV genetic diversity in pediatric patients and indicates differences in RV-associated pathologies, as well as an important role for co-infections.

No / In this study, we assessed if the superimposition of incident sexually transmitted infections (STIs) on HIV phylogenetic analyses could reveal possible sexual behaviour misclassifications in our HIV-infected population. HIV-1 sequences collected between 1997 and 2014 from 1169 individuals attending a HIV clinic in Antwerp, Belgium were analysed to infer a partial HIV transmission network. Individual demographic, clinical and laboratory data collected during routine HIV follow-up were used to compare clustered and non-clustered individuals using logistic regression analyses. In total, 438 (37.5%) individuals were identified in 136 clusters, including 76 transmission pairs and 60 clusters consisting of three or more individuals. Individuals in a cluster were more likely to have a history of syphilis, Chlamydia and/or gonorrhoea (P < 0.05); however, when analyses were stratified by HIV transmission risk groups (heterosexual and men who have sex with men [MSM]), this association only remained significant for heterosexuals with syphilis (P = 0.001). Under closer scrutiny, this association was driven by six heterosexual men who were located in six almost exclusively MSM clusters. A parsimonious conclusion is that these six individuals were potentially misclassified as heterosexual. Improving the accuracy of sexual behaviour reporting could improve care.