Academic literature on the topic 'Influenza viruses. Influenza'

En el primer estudi de la present tesi, es van estudiar brots de malaltia respiratòria compatible amb virus de la influença de tipus A (IAV) així com granges que no mostraven simptomatologia clínica. Per a l'estudi dels brots, es van recollir mostres de hisops nasals d'animals amb signes respiratoris i febre (&#8805;40 ° C), mentre que a les granges sense simptomatologia clínica, es van recollir hisops nasals de garrins de maternitat, transició i porcs d'engreix (20 per grup). Es va estudiar un total de 211 brots i 19 granges aparentment subclíniques. La presència i llinatge es van determinar per RT-qPCR, i es va fer l'aïllament de mostres seleccionades usant cèl·lules MDCK. Els aïllats van ser seqüenciats (genoma complet) mitjançant la tecnologia Illumina Miseq. Es va confirmar la presència de IAV en 145 casos de brots (68.7%), i en 15 granges aparentment subclíniques (78.9%). Els llinatges majorment detectats van ser H1avN2hu (33.6%), H1avN1av (24.3%) i H1huN2hu (18.7%). Es va obtenir un total de 60 aïllats, i els seus genomes van ser completament seqüenciats. Els genotips majoritàriament detectats van ser el tipus D i l'A, que es corresponen als llinatges H1avN2hu i H1avN1av, respectivament. Es van detectar un total de 14 genotips diferents, dels quals, 7 d'ells no havien estat prèviament reportados.En el segon estudi de la present tesi, es va estudiar la dinàmica de transmissió de IAV en les transicions d'una granja endèmica abans i després de l'aplicació de diferents esquemes de vacunació a les truges. Es van realitzar un total de tres estudis longitudinals: abans de la vacunació, després de la vacunació amb una vacuna comercial polivalent inactivada H1N1-H1N2-H3N2 i després de la vacunació amb una vacuna comercial monovalent pandèmica H1N1. Es van recollir mostres setmanals de hisops nasals dels garrins des de les 3-9 setmanes de vida, i mostres de sang a les 3, 6 i 9 setmanes de vida. En el primer longitudinal abans de la vacunació, es va avaluar la circulació vírica basal en 50 garrins de 4 lots consecutius. En el segon longitudinal, es va realitzar vacunació en llençol de truges usant la vacuna comercial polivalent (grup control) i la meitat d'aquestes van ser revacunades 3 setmanes abans de el part (grup tractament). Es va seleccionar un grup aleatori de 10 truges de cada grup i es va fer el seguiment setmanal de 5 garrins per truja. L'estudi va ser repetit en 4 lots consecutius. En el tercer estudi longitudinal, el procediment va ser el mateix que en l'anterior, però fent servir la vacuna inactivada pandèmica H1N1. Hisops nasals van ser examinats per RT-qPCR i els sèrums van ser analitzats utilitzant un ELISA comercial (CIVTEST ©-Suis Influenza). En el segon longitudinal després de l'aplicació de la primera vacuna, l'inici de la infecció es va retardar en dues setmanes, però no es van observar diferències significatives entre els dos grups; i en el tercer, l'inici de la infecció es va moure cap a l'esquerra en tots els grups, sense diferències significatives entre ells. En els tres estudis, es van detectar animals que excretaron virus en dos o fins a en tres mostrejos consecutius, així com alguns casos de re-infeccions. El llinatge present a la granja durant els dos primers estudis longitudinals es correspon a un H1avN1av. No obstant això, durant el tercer estudi, es va detectar circulant en tots els grups d'animals 1 H3huN2hu que portava un nou llinatge H3 humà derivat d'un virus de la grip estacional humana.<br>En el primer estudio de la presente tesis, se estudiaron brotes de enfermedad respiratoria compatible con virus de la influenza de tipo A (IAV) así como granjas que no mostraban sintomatología clínica. Para el estudio de los brotes, se recogieron muestras de hisopos nasales de animales con signos respiratorios y fiebre (&#8805;40°C), mientras que en las granjas sin sintomatología clínica, se recogieron hisopos nasales de lechones de maternidad, transición y cerdos de engorde (20 por grupo). Se estudió un total de 211 brotes y 19 granjas aparentemente subclínicas. La presencia y linaje se determinaron por RT-qPCR, y se hizo el aislamiento de muestras seleccionadas usando células MDCK. Los aislados fueron secuenciados (genoma completo) mediante la tecnología Illumina Miseq. Se confirmó la presencia de IAV en 145 casos de brotes (68.7%), y en 15 granjas aparentemente subclínicas (78.9%). Los linajes mayormente detectados fueron H1avN2hu (33.6%), H1avN1av (24.3%) y H1huN2hu (18.7%). Se obtuvo un total de 60 aislados, y sus genomas fueron completamente secuenciados. Los genotipos mayoritariamente detectados fueron el tipo D y el A, que se corresponden a los linajes H1avN2hu y H1avN1av, respectivamente. Se detectaron un total de 14 genotipos diferentes, de los cuales, 7 de ellos no habían sido previamente reportados.En el segundo estudio de la presente tesis, se estudió la dinámica de transmisión de IAV en las transiciones de una granja endémica antes y después de la aplicación de diferentes esquemas de vacunación en las cerdas. Se realizaron un total de tres estudios longitudinales: antes de la vacunación, después de la vacunación con una vacuna comercial polivalente inactivada H1N1-H1N2-H3N2 y después de la vacunación con una vacuna comercial monovalente pandémica H1N1. Se recogieron muestras semanales de hisopos nasales de los lechones desde las 3-9 semanas de vida, y muestras de sangre a las 3, 6 y 9 semanas de vida. En el primer longitudinal antes de la vacunación, se evaluó la circulación vírica basal en 50 lechones de 4 lotes consecutivos. En el segundo longitudinal, se realizó vacunación en sábana de cerdas usando la vacuna comercial polivalente (grupo control) y la mitad de estas fueron revacunadas 3 semanas antes del parto (grupo tratamiento). Se seleccionó un grupo aleatorio de 10 cerdas de cada grupo y se hizo el seguimiento semanal de 5 lechones por cerda. El estudio fue repetido en 4 lotes consecutivos. En el tercer estudio longitudinal, el procedimiento fue el mismo que en el anterior, pero usando la vacuna inactivada pandémica H1N1. Hisopos nasales fueron examinados por RT-qPCR y los sueros fueron analizados usando un ELISA comercial (Civtest-Suis Influenza). En el segundo longitudinal después de la aplicación de la primera vacuna, el inicio de la infección se retrasó en dos semanas, pero no se observaron diferencias significativas entre ambos grupos; y en el tercero, el inicio de la infección se movió hacia la izquierda en todos los grupos, sin diferencias significativas entre ellos. En los tres estudios, se detectaron animales que excretaron virus en dos o hasta en tres muestreos consecutivos, así como algunos casos de re-infecciones. El linaje presente en la granja durante los dos primeros estudios longitudinales se corresponde a un H1avN1av. Sin embargo, durante el tercer estudio, se detectó circulando en todos los grupos de animales un H3huN2hu que llevaba un nuevo linaje de H3 humano derivado de un virus de la gripe estacional humana.<br>In the first study of the present thesis, we investigated outbreaks of respiratory disease (n=211) compatible with influenza A virus (IAV) as well as farms without overt respiratory disease (n=19) for the presence of IAV. In the outbreak investigations, nasal swabs were taken from animals with respiratory signs and fever (&#8805;40°C) while in the farms with no evident respiratory disease, nasal swabs were randomly taken from suckling piglets, weaners and fatteners (20 animals per phase). Presence of IAV and lineage determination were assessed by RT-qPCR and isolation was attempted in selected samples using MDCK cells. Isolates were sequenced (full genome) by using Illumina Miseq technology. IAV participation was confirmed in 145 (68.7%) of the outbreaks, and in 15 (78.9%) of the farms without overt disease. The most commonly detected lineages were H1avN2hu (33.6%), H1avN1av (24.3%) and H1huN2hu (18.7%). Sixty IAV isolates were obtained and the genomes were fully sequenced. Genotypes D and A, H1avN2hu and H1avN1av, respectively, were predominant but up to 14 genotypes were identified, of which seven had not been previously reported. Four isolates containing a new H3hu lineage derived from a human seasonal virus were detected, and isolates containing genes from the pandemic virus represented a 31.7 % of the total. In the second study of the present thesis, the transmission dynamics of IAV in the nurseries from an endemic farm were assessed before and after the application of different vaccination schemes for sows. Three follow-up periods were examined: before vaccination, after vaccination with a commercial inactivated polyvalent H1N1-H1N2-H3N2 and after vaccination with a monovalent pandemic H1N1. Nasal swabs of piglets were taken weekly from 3-9 weeks of age and blood samples were taken at three, six and nine weeks of age. In the first follow-up before vaccination, the basal IAV circulation was assessed by sampling 50 piglets in 4 batches. In the second longitudinal study, sows were blanket vaccinated with the polyvalent vaccine (control group) and half of them received an extra dose 3 weeks pre-farrowing (treatment group). A random cohort of 10 sows in each group was selected and 5 piglets per sow were weekly followed. The trial was replicated in 4 consecutive batches. In the third follow-up period, the procedure was the same as in the second, but using a pandemic H1N1 inactivated vaccine. Nasal swabs were examined by RT-qPCR and serum samples were analysed using a commercial ELISA (Civtest-Suis Influenza). Incidences and beta values per week and pen were calculated after the RT-qPCR results. Before applying any vaccination scheme, the patterns of incidence were diverse in the examined pens but often viral circulation was detected as early as 4 weeks of age. At three weeks of age, most of the analysed animals were positive with high S/P ratios. In the second follow-up period after the application of the first vaccination scheme, the onset of infection was delayed by two weeks but there were no other significant differences between both groups, and in the third, the onset of infection shifted to the left for all groups, without significant differences among them. In all of the three studies, animals that shed virus in two and even three consecutive sampling times were detected, as well as some cases of re-infection. Interestingly, an H1avN1av virus was initially detected in the farm, but during the third study, a H3huN2hu was found circulating in the batches, carrying a new H3 human-like derived from human seasonal virus.<br>Universitat Autònoma de Barcelona. Programa de Doctorat en Medicina i Sanitat Animals

A number of different cell cultures were examined for their susceptibility to the influenza virus A/swine/Weybridge/86(H1N1) and A/swine/Weybridge/87(H3N2). PK1 (porcine kidney) was found to be the most susceptible to the viruses, and MDCK (canine kidney), the best cell line for primary isolation. A method of infectivity assay by immunoperoxidase in microplate cultures of MDCK cells was developed which was simple enough for routine use and practically as sensitive as the egg infectivity test. The potential risks of accidental importation of influenza infection in pig was assessed by determining the survival time of the porcine influenza virus H1N1 in pig tissues. It was found that the virus may keep its infectivity in frozen (-20&deg;C) pig tissues for up to 15 days. The interspecies transmission of porcine influenza viruses was studied using turkeys infected with porcine influenza isolates. Although both A/swine/Weybridge/86 and A/swine/Weybridge/87 were transmitted from infected turkeys to pigs, only A/swine/Weybridge/86(H1N1) infected turkeys presented clinical signs of disease. More than 50% of the pigs presented the virus in the nostrils and/or faeces, at some time during the experiment, and all seroconverted. Transmission from these pigs to newly introduced turkeys was not observed, nor was seroconversion detected. Influenza epidemiology in Brazil was investigated by serological studies using pig sera collected in different areas of that country, using human, porcine and avian isolates of influenza viruses. Highest antibody titres were found against A/Leningrad/86(H3N2) (19%) and A/Port Chalmers/73(H3N2) (17%), but not against specific porcine isolates. Only serological evidence was found to suggest that reassortant influenza viruses occur in English pig herds. However, interspecies transmission of influenza viruses between man and pigs, and the maintenance of human strains in English pig herds was demonstrated by the isolation of two H3N2 influenza viruses very similar to A/Port Chalmers/73, present in the human population in the 1970s.

Human populations are constantly exposed to emerging pathogens such as influenza A viruses that result from cross-species transmissions. Generally these sporadic events are evolutionary dead-ends, but occasionally, viruses establish themselves in a new host that offers a novel genomic context to which the virus must adjust to avoid attenuation. However, the dynamics of this process are unknown. Here we present a novel method to characterize the time it takes to G+C composition at third codon positions (GC3 content) of influenza viruses to adjust to that of a new host. We compare the inferred dynamics in two subtypes, H1N1 and H3N2, based on complete genomes of viruses circulating in humans, swine and birds between 1900-2009. Our results suggest that both subtypes have the same fast-adjusting genes, which are not necessarily those with the highest absolute rates of evolution, but those with the most relaxed selective pressures. Our analyses reveal that NA and NS2 genes adjust the fastest to a new host and that selective pressures of H3N2 viruses are relaxed faster than for H1N1. The asymmetric nature of these processes suggests that viruses with the greatest adjustment potential to humans are coming from both birds and swine for H3N2, but only from birds for H1N1.