Australia as a global sink for the genetic diversity of avian influenza A virus.

Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.

Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia.

The current panzootic of high pathogenicity avian influenza virus H5N1 demonstrates how viral incursions can have major ramifications for wildlife and domestic animals. Herein, we describe the recent incursion into Australia of two low pathogenicity avian influenza virus subtypes, H4 and H10, that exhibited contrasting evolutionary dynamics. Viruses detected from national surveillance and disease investigations between 2020 and 2022 revealed 27 genomes, 24 of which have at least one segment more closely related to Eurasian or North American avian influenza lineages than those already circulating in Australia. Phylogenetic analysis revealed that H4 viruses circulating in shorebirds represent a recent incursion from Asia that is distinct from those circulating concurrently in Australian waterfowl. Analysis of the internal segments further demonstrates exclusive, persistent circulation in shorebirds. This contrasts with H10, where a novel lineage has emerged in wild waterfowl, poultry, and captive birds across Australia and has likely replaced previously circulating H10 lineages through competitive exclusion. Elucidating different dynamics for avian influenza incursions supports effective disease risk identification and communication that better informs disease preparedness and response.

Genetics of mating and sex determination in the parasitic nematode Haemonchus contortus.

Genetic analysis of parasitic nematodes has been a neglected area of research and the basic genetics of this important group of pathogens are poorly understood. Haemonchus contortus is one of the most economically significant livestock parasites worldwide and is a key experimental model for the strongylid nematode group that includes many important human and animal pathogens. We have undertaken a study of the genetics and the mode of mating of this parasite using microsatellite markers. Inheritance studies with autosomal markers demonstrated obligate dioecious sexual reproduction and polyandrous mating that are reported here for the first time in a parasitic helminth and provide the parasite with a mechanism of increasing genetic diversity. The karyotype of the H. contortus, MHco3(ISE) isolate was determined as 2n = 11 or 12. We have developed a panel of microsatellite markers that are tightly linked on the X chromosome and have used them to determine the sex chromosomal karyotype as XO male and XX female. Haplotype analysis using the X-chromosomal markers also demonstrated polyandry, independent of the autosomal marker analysis, and enabled a more direct estimate of the number of male parental genotypes contributing to each brood. This work provides a basis for future forward genetic analysis on H. contortus and related parasitic nematodes.

Microsatellite genotyping supports the hypothesis that Teladorsagia davtiani and Teladorsagia trifurcata are morphotypes of Teladorsagia circumcincta.

Traditionally nematode species designations have been based on morphological criteria. However, it is has long been recognised that valid species designations are critical for basic biological and epidemiological studies. The ever increasing use of molecular and genetic techniques has allowed traditional classifications to be more closely examined. The sub-family Ostertagiinae is of particular interest as many of the species within this group are of economic importance worldwide, with unresolved classification complicating epidemiology, management, control and genetic studies. This study examines genetic differences between three morphological variants (morphotypes) within the genus Teladorsagia (sub-family: Ostertagiinae) using a multi-locus population genetic analysis approach. Five microsatellites were used to genotype a total of 31 T. davtiani (ScKiTD), 30 T. trifurcata (ScKiTT), and 31 T. circumcincta (ScKiTC). Population genetic analysis detected no genetic differentiation between T. davtiani, T. trifurcata, and T. circumcincta supporting the hypothesis that these are morphotypes of the same species.

Microsatellite analysis reveals marked genetic differentiation between Haemonchus contortus laboratory isolates and provides a rapid system of genetic fingerprinting.

Many of the Haemonchus contortus isolates currently used for experimental work were originally derived from different regions of the world and are commonly exchanged between laboratories. In most cases, these are largely genetically uncharacterised other than the analyses conducted on specific genes of interest. We have used a panel of eight microsatellite markers to genetically characterise five different commonly used H. contortus isolates including MHco3 (ISE), the isolate chosen for full genome sequencing as part of the H. contortus genome project. There is an extremely high level of genetic differentiation between each of the isolates except the two which have a common origin, MHco1 (MOSI) and MHco3 (ISE). We have investigated the amplification of microsatellite markers from pooled DNA as a potential method for fingerprinting different isolates. Good estimates of the true allele frequencies can be made by amplification from either pooled adult DNA or bulk L3 DNA for seven out of the eight markers tested. Both single worm genotyping and bulk DNA fingerprinting revealed no genetic differentiation between adult worms in the host and larvae derived from faecal culture. Furthermore, none of the eight markers showed genetic changes when isolates were passaged through different individual hosts. Hence the microsatellite genotyping of bulk larval DNA samples provides a simple and rapid method to genetically define and monitor laboratory isolates, and to determine their relationship with particular field populations.

Population genetic analysis of the ovine parasitic nematode Teladorsagia circumcincta and evidence for a cryptic species.

An understanding of genetic variation in parasite populations, and how it is partitioned, is required to underpin many areas of basic and applied research. Population genetic studies on parasitic nematode populations are still in their infancy and have been dominated by the use of single locus markers. We have used a panel of five microsatellite markers to undertake a genetic study of a number of field and laboratory populations of Teladorsagia circumcincta. High levels of polymorphism were seen in all the populations examined with the majority of diversity being within rather than between populations. There was no detectable genetic differentiation between the UK populations examined although they included both laboratory passaged and field isolates derived from different geographical regions and host species. This broadly supports previous mtDNA sequence diversity studies of this parasite in the UK and USA. However, some between-population genetic differentiation was apparent when several populations from French goats and a laboratory population from New Zealand were examined. Most notably, a population from a French goat farm, which has previously been suggested to contain a cryptic species, showed very high levels of genetic differentiation from all the other populations. Analysis of multi-locus genotypes suggested the presence of two sympatric parasite populations on this farm with little or no gene flow between them. This supports the hypothesis that parasites currently defined as T. circumcincta by routine morphological criteria comprise more than a single species.

PREVALENCE OF COLUMBID HERPESVIRUS INFECTION IN FERAL PIGEONS FROM NEW SOUTH WALES AND VICTORIA, AUSTRALIA, WITH SPILLOVER INTO A WILD POWERFUL OWL (NINOX STRUENA).

Columbid herpesvirus-1 (CoHV-1) is widespread in feral pigeons in North America and Europe. We used a PCR assay to detect CoHV-1 DNA in oral and cloacal tissues and oral swabs from naturally infected pigeons. Fifty-three feral pigeons from five flocks in Australia (n=3 from south-central Victoria and n=2 from Sydney) were examined for CoHV-1 DNA. We detected CoHV-1 DNA in oral mucosa and cloacal mucosa, with higher concentrations in the oral mucosa. The sensitivity of testing oral swabs was the same as testing the tissue, indicating that testing of oral swabs from live birds is an effective means of screening flocks for CoHV-1 infection. Infection was found in all five of the flocks examined and the prevalence of infection ranged from 70% to100%. Most positive birds could be detected with a single-amplification PCR, but a nested amplification was required to detect others. Oral swabs from Australian native doves and pigeons (n=18) and the introduced Collared Dove (Streptopelia chinensis; n=2) were also tested by the nested PCR and all were negative for CoHV-1 DNA. We describe a fatal infection of CoHV-1 in a wild Powerful Owl (Ninox strenua) that was observed feeding on feral pigeons. This is the first known case of CoHV-1 causing death in a wild bird of prey in Australia. Our data suggest that CoHV-1 is widespread in feral pigeon flocks in Australia but we did not find it in native doves and pigeons. Spillover into native avian predator species may be occurring.

Characterisation of Teladorsagia circumcincta microsatellites and their development as population genetic markers.

There is a need to develop tools to study the genetics of parasitic nematodes. This is particularly urgent for those species in which anthelmintic resistance is common such as the sheep parasite Teladorsagia (Ostertagia) circumcincta. The lack of information on the population genetics of such parasites severely limits our ability to study the genetic basis of anthelmintic resistance. This paper presents the results of three approaches used to isolate microsatellite markers from T. circumcincta and the development of a panel of markers suitable for population genetic analysis. Hybridisation screening of small insert genomic libraries and interspecies PCR amplification of Haemonchus contortus microsatellites were used to identify CA/GT microsatellites. Many of these loci were associated with a 146bp tandem repeat, named TecRep, that is related to a repetitive element previously identified in other trichostrongylid nematode genomes but apparently absent from other nematode groups. A large proportion of the loci isolated were problematic for use as population genetic markers, predominantly due to a high frequency of null alleles or the association with the TecRep repeat. Bioinformatic screening of a T. circumcincta EST database identified both di- and tri-nucleotide microsatellite repeats and a greater proportion of these turned out to be more robust markers than those derived from genomic sequence. A panel of seven markers has been selected and characterised which are sufficiently robust and polymorphic to be valuable population genetic markers for this parasite.

Emerging infectious diseases in free-ranging wildlife-Australian zoo based wildlife hospitals contribute to national surveillance.

Emerging infectious diseases are increasingly originating from wildlife. Many of these diseases have significant impacts on human health, domestic animal health, and biodiversity. Surveillance is the key to early detection of emerging diseases. A zoo based wildlife disease surveillance program developed in Australia incorporates disease information from free-ranging wildlife into the existing national wildlife health information system. This program uses a collaborative approach and provides a strong model for a disease surveillance program for free-ranging wildlife that enhances the national capacity for early detection of emerging diseases.

Gerencia de calidad del Instituto Nacional de Higiene Rafael Rangel: avances y logros / Quality management of the National Institute of Higiene Rafael Rangel

La reestructuración institucional, desarrollada durante el año 1990, impulsa la creación de la Gerencia de Calidad con el objeto de diseñar y establecer los procesos para mejorar la calidad de los bienes y servicios que presta el Instituto Nacional de Higiene Rafael Rangel. A partir del año 2002, se le asignan a esta Gerencia los re cursos para que desarrolle e implante el Sistema de Gestión de la Calidad (SGC), en los procesos que se ejecutan en la Institución. En el año 2004, se establece la Política de la Calidad de la Institución. Entre el año 2004 y 2008, se ha desarrollado un programa de formación para el personal de la Institución, que incluye cursos Internos y Externos, con el fin de sensibilizar, capacitar y comprometer al talento humano en el desarrollo e implantación del SGC. Del mismo modo, el equipo de trabajo realizó la normalización de la documentación, lo que se logra con el diseño e implantación de un Sistema de Control para la elaboración, revisión y aprobación de la documentación de los procesos administrativos y técnicos de la Institución, a través del establecimiento de Procedimientos y Documentos Normalizados. La Gerencia de Calidad brinda apoyo a los laboratorios de ensayo de la División de Alimentos, con el propósito de optar a la Acreditación de Métodos de ensayo y reconocimiento formal de su competencia. En el año 2006, se lleva a cabo un programa documentado y permanente de auditorías técnicas para verificar el cumplimiento de las normas nacionales e internacionales. Estas auditorías internas se ejecutan en todas las unidades operativas y de apoyo administrativo, así como a proveedores de bienes y servicios, para garantizar la calidad de las auditorias programadas. Los principales impactos y beneficios, al implementarel SGC, para los procesos que desarrolla el Instituto Nacional de Higiene Rafael Rangel, emprendiendo la certificación y acreditación de los mismos con la finalidad de producir mejores productos y servicios...

The institutional restructuring, developed in 1990, has impulsed the creation of the Quality Management with the pur pose of designing and establishing the procedures for improving the supplies and services of “The National Institute of Hygiene (Instituto Nacional de Higiene) Rafael Rangel. Since 2002, the resources have been assigned, to this Management, to develop and implement a Quality Control System (Q.C.S.), in the procedures undertaken in the Institution. In the year of 2004, the Institution Policy of Quality was established for. Between 2004 and 2008, a training program For the institutional personnel, including Internal and External courses, has been applied with the purpose of sensitizing, preparing, and committing the human talent in the development of Q.C.S. In the same way, the quality team developed the standardization of the document with the design and implementation of a Control System for the elaboration, revision and approving of the documentation of administrative and technical procedures of the Institution, by means of creating the Standardized Procedures and Documents. The Quality Control Management gives support to Food Division Laboratories with the purpose of selecting certification methods for validating their competition. In 2006, the institution began a permanent program oftechnical audits to verify the fulfillment of the national and international rules.This internal audits are applied to all of the functioning supporting units, as administrative back-up, as well as to suppliers of goods and services as guarantee of quality on behalf of the programmed audits. The main benefits and impacts, in implementing Q.C.S., to the process developed in The National Institute of Hygiene (Instituto Nacional de Higiene) Rafael Rangel, are described as follows produce better supplies and services be efficient and reduce production costs obtain satisfied Internal and External Users-Clients...