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M Poidinger

Publications and source records attributed to M Poidinger.

15 recordsLinked to original sources
PubMed2001

TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases.

MOTIVATION: Sequence databases represent an enormous resource of phylogenetic information, but there is a lack of tools for accessing that information in order to assess the amount of evolutionary information in these databases that may be suitable for phylogenetic reconstruction and for identifying areas of the taxonomy that are under-represented for specific gene sequences. RESULTS: We have developed TreeGeneBrowser which allows inspection and evaluation of gene sequence data for phylogenetic reconstruction. This program improves the efficiency of identification of genes that may be useful for particular phylogenetic studies and identifies taxa and taxonomic branches that are under-represented in sequence databases.

Algorithms↗
PubMed2000

The molecular epidemiology of Kokobera virus.

We describe herein the molecular epidemiology and phylogeny of Kokobera (KOK) virus, a flavivirus found in Australia and Papua New Guinea. We sequenced a region encompassing the 200 nucleotides of the 3' terminus of the NS5 gene, and the first 300 nucleotides of the 3' untranslated region (UTR). The study included 25 isolates of the virus, including an isolate from PNG, and several recent isolates from the south-west of Western Australia (WA), where the virus had not previously been detected. We found that the KOK isolates clustered according to geographic location and time of isolation into three distinct topotypes: one covering Queensland and New South Wales; another represented by the single isolate from PNG; and a third covering the Northern Territory and WA. This latter group was further subdivided into northern and south-west isolates. This molecular epidemiology is significantly different from other Australian flaviviruses, such as Murray Valley encephalitis (MVE) and Kunjin (KUN) viruses, which exist as single genetic types across the entire Australian continent. However, it is similar to the molecular epidemiology of the alphavirus Ross River (RR) virus. This may be explained by the fact that MVE and KUN viruses are known to have birds as their main vertebrate hosts, whereas RR virus utilises macropods, which have also been implicated as the vertebrate host for KOK virus. In addition, the south-west isolates exhibited a degree of sequence heterogeneity, including one isolate that has a nine nucleotide deletion in the 3'UTR. This suggests that KOK virus has been in the south-west of WA for some time, and was not recently introduced.

3' Untranslated Regions↗
PubMed2000

Hepatitis G virus genotypes in Australia, Papua New Guinea and the Solomon Islands: a possible new Pacific type identified.

BACKGROUND: Hepatitis G Virus (HGV)/GB Virus-C (GBV-C) is a newly discovered RNA virus. Nucleotide sequence comparison and phylogenetic studies of the 5' untranslated region (5'UTR) within the viral genome have identified at least three different types which have provisionally been classified as type 1 (West African origin), type 2 (North American origin) and type 3 (Asian origin). METHODS AND RESULTS: The products of RT-PCR were sequenced by using blood donors and patients infected with HGV/GBV-C in Australia, Papua New Guinea and the Solomon Islands to investigate the genotype distribution in this area of the world. All the Australian isolates showed strong sequence homology with type 2, while the Papua New Guinea and Solomon Islands sequences were more closely related, but differ from type 3, which has previously been reported from isolates studied within Asia. CONCLUSIONS: Phylogenetic analysis suggests that these latter sequences are either a new HGV/GBV-C Pacific type or a subtype of the Asian type RNA virus. Isolates homologous with type 1 were not identified in these population groups.

Australia↗
PubMed1999

Isolation of homologous arbovirus cultures from heterologous mixtures using limit dilution and virus-specific enzyme immunoassays.

Viral cultures were identified recently that contained both Kunjin virus and the closely related flavivirus West Nile. The observation that the KUN virus population grew more efficiently in a mosquito cell line (C6/36) while the WN population replicated more effectively in mammalian cells (Vero) allowed enrichment for either virus by culturing the mixture in the appropriate cell line. Limit dilution of the enriched virus preparations was then performed by infecting microtitre cultures with serial ten fold dilutions. Culture wells that contained a pure population of virus were then identified by immunostaining fixed cell monolayers with virus-specific monoclonal antibodies. Subsequent passage of the 'cloned' viruses in either C6/36 or Vero cells and analysis of the infected cultures by specific monoclonal antibody staining, PCR and nucleotide sequencing confirmed the identity of the virus and that in each case an homogeneous virus population had been obtained. This procedure is particularly useful for isolating virus populations from heterogeneous mixtures that fail to develop discrete plaques in infected cell monolayers.

Animals↗
PubMed1999

Geographic distribution and evolution of Sindbis virus in Australia.

The molecular epidemiology and evolution of Sindbis (SIN) virus in Australia was examined. Several SIN virus strains isolated from other countries were also included in the analysis. Two regions of the virus genome were sequenced including a 418 bp region of the E2 gene and a 484 bp region containing part of the junction region and the 5' end of the C gene. Analysis of the nucleotide and deduced amino acid sequence data from 40 SIN virus isolates clearly separated the Paleoarctic/Ethiopian and Oriental/Australian genetic types of SIN virus. Examination of the Australian strains showed a temporal rather than geographic relationship. This is consistent with the virus having migratory birds as the major vertebrate host, as it allows for movement of virus over vast areas of the continent over a relatively short period of time. The results suggest that the virus is being periodically redistributed over the continent from an enzootic focus of evolving SIN virus. However, SIN virus strains isolated from mosquitoes collected in the south-west of Australia appear to represent a new SIN virus lineage, which is distinct from the Paleoarctic/Ethiopian and Oriental/Australian lineages. Given the widespread geographic dispersal of the Paleoarctic/Ethiopian and Oriental/Australian lineages, it is surprising that the South-west genetic type is so restricted in its area of circulation. Nucleotide sequence data from the C gene of the prototype strain of the alphavirus Whataroa were also determined. This virus was found to be genetically distinct from the SIN virus isolates included in the present study; however, it is clearly SIN-like and appears to have evolved from a SIN-like ancestral virus.

Africa↗
PubMed1998

Two contiguous outbreaks of dengue type 2 in north Queensland.

OBJECTIVES: To investigate two outbreaks of dengue type 2 in north Queensland, one in the Torres Strait beginning in late 1996, the other in a Cairns suburb in early 1997. DESIGN: Epidemiological investigation of all laboratory-confirmed cases of dengue, entomological investigation of the local environment, and laboratory analysis of the isolated dengue viruses. MAIN OUTCOME MEASURES: Numbers of confirmed and of locally acquired cases; virus serotype; comparison of nucleotide sequences between viruses isolated from the two outbreaks; and Breteau Index (BI = number of containers with larvae of the mosquito vector Aedes aegypti found per 100 houses investigated) on the affected islands and in the Cairns suburb. RESULTS: There were 201 confirmed cases of dengue in the Torres Strait outbreak, which lasted nearly seven months, and seven confirmed cases in the Cairns outbreak, which lasted about nearly 11 weeks. Most (190) were confirmed as dengue type 2. Nucleotide sequencing of viruses isolated from the two outbreaks showed they were identical. Ae. aegypti breeding sites were very common on the five Torres Strait islands surveyed (BIs, 73-219--high risk), but less so in the Cairns suburb (BI, 23). The most common breeding sites were water storage reservoirs, particularly rainwater tanks, on the outer Torres Strait islands, discarded containers (such as plastic containers, buckets and tyres) on Thursday Island, and garden items (such as flowerpot bases and jars) in Cairns. CONCLUSIONS: The virus responsible for the Cairns outbreak was most probably introduced from the Torres Strait, whereas the virus responsible for the Torres Strait outbreak was imported from Papua New Guinea. Preventive strategies tailored to specific locations are needed to reduce breeding of Ae. aegypti in north Queensland, and the consequent risk of future outbreaks of dengue.

Adolescent↗
PubMed1997

Isolation of Japanese encephalitis virus from Culex annulirostris in Australia.

Mosquitoes were collected using CO2 and octenol-baited light traps during an outbreak of Japanese encephalitis (JE) on Badu Island in the Torres Strait, Australia in April 1995. A total of 13,300 mosquitoes comprising 12 species were processed for virus isolation. Eight isolates of JE virus were obtained from Culex annulirostris, with a carriage rate of 2.97:1,000; this mosquito also yielded one Sindbis virus isolate. A reverse transcriptase-polymerase chain reaction was used to sequence the JE viruses, which were compared with published sequences. The eight isolates were 90% homologous with known JE strains but only 68% homologous with other flaviviruses. Among the isolates, 99% homology was obtained, suggesting a common point of origin.

Aedes↗
PubMed1997

Genetic stability among temporally and geographically diverse isolates of Barmah Forest virus.

An increase in the incidence of polyarthritis caused by Barmah Forest (BF) virus, and its recent emergence into Western Australia, prompted a study of the molecular epidemiology of this Australian mosquito-borne alphavirus. The nucleotide sequence of a 500-basepair region of the 3' end of the envelope (E2) gene of the prototype BF virus strain (BH2193) was compared with other members of the alphavirus genus, and to a panel of isolates of BF virus collected more for than 20 years from different geographic regions of Australia. The BF virus was shown to be genetically distinct from other members of the alphavirus genus. A high degree of sequence homology (98-100%) was found between the BF isolates, with no evidence of geographic or temporal divergence. This nucleotide homogeneity was similar to that observed with other Australian mosquito-borne viruses with avian vertebrate hosts, such as Sindbis, Murray Valley, and Kunjin viruses, but it contrasts to the heterogeneity reported for Ross River virus, an alphavirus with mammalian vertebrate hosts.

Alphavirus↗
PubMed1996

An outbreak of Japanese encephalitis in the Torres Strait, Australia, 1995.

OBJECTIVES: To determine the distribution of virus infection during an outbreak of Japanese encephalitis (JE) in the Torres Strait, and to describe the environmental factors facilitating the outbreak. DESIGN: Human and porcine serological surveys for JE virus activity throughout the Torres Strait, and mosquito and household surveys on the island of Badu. SETTING: The island of Badu (where the clinical cases occurred) and the other islands of the Torres Strait, Australia, during April-May 1995. RESULTS: The serological surveys identified recent JE virus infection among residents or domestic pigs on at least nine outer Torres Strait islands. A JE virus, confirmed by nucleotide sequencing, was isolated from two asymptomatic Badu residents. Virus isolations and mosquito surveys implicated Culex annulirostris as the major vector involved in the outbreak. There was prolific Cx. annulirostris breeding in a variety of water bodies close to and within the Badu community. Over half (53%) of the households kept pigs in pens, and many (63%) of the pigpens were situated near standing water; in 56% of these "wet" pigpens Cx. annulirostris was breeding. CONCLUSIONS: There was evidence of widespread JE virus activity throughout the outer islands of the Torres Strait. We suggest that migratory birds and/or wind-blown mosquitoes could have imported the virus into the Torres Strait from a focus of viral activity, possibly in Papua New Guinea, thereby initiating the outbreak. A combination of environmental factors, with large numbers of domestic pigs in close proximity to human dwellings and mosquito breeding sites, undoubtedly facilitated the outbreak on Badu.

Adult↗
PubMed1996

Molecular characterization of the Japanese encephalitis serocomplex of the flavivirus genus.

The Japanese encephalitis (JE) serocomplex of flaviviruses comprises 10 members, 9 of which: Alfuy (ALF); Koutango (KOU); Kokobera (KOK); Kunjin (KUN); Murray Valley encephalitis (MVE); JE; Stratford (STR); Usutu (USU); and West Nile (WN) have been isolated from Africa, southern Europe, Middle East, Asia, and Australia. The tenth member, St. Louis encephalitis (SLE) virus, is confined to North, Central, and South America. For ALF, KOK, KOU, STR, and USU, no sequence data have as yet been reported, and little molecular phylogeny has been determined for this complex as a whole. Using a rapid, one-step RT-PCR and universal primers, we have amplified and sequenced a 450-600 base pair region of the virus genome encompassing the N terminus of the nonstructural protein NS5 and the 5' end of the 3' noncoding region, for several strains of all of these viruses, except USU and SLE viruses. These data, as well as published sequence data for other flaviviruses, were analyzed with the ClustalW and Phylip computer packages. The resultant phylogenetic data were consistent with some of the current flavivirus serological classification, showing a close relationship between ALF and MVE viruses and between KOK and STR viruses, but suggested that KOK and STR are distantly related to the other viruses and should perhaps be reclassified in their own serocomplex. The data also confirmed the close relationship between KUN and WN viruses and showed that an isolate of KUN virus from Sarawak may represent a "link" between these two virus species. In addition, the primary sequence data revealed a polymorphic region just downstream of the stop codon in the 3' end of the viral genomes.

Amino Acid Sequence↗
PubMed1995

Molecular epidemiology and evolution of mosquito-borne flaviviruses and alphaviruses enzootic in Australia.

Three distinct patterns in the molecular epidemiology and evolution are evident among the alphaviruses and flaviviruses enzootic in Australia. One pattern, exemplified by MVE and KUN viruses, is of a single genetic type evolving slowly and uniformly in geographically widely separated regions of Australia with no evidence of independent divergence. The second pattern, exemplified by RR virus, is of separate genotypes evolving in different geographic regions with significant nucleotide divergence between genotypes. The third pattern, exemplified by SIN virus, is of a succession of temporally related genotypes that extend over most of the Australian continent, with relatively low levels of nucleotide divergence within a genotype, and which are each replaced by the subsequent genotype. These patterns are associated in part due to the nature and dispersal of their vertebrate hosts. Nucleotide divergence rates for Australian alphaviruses are similar to those reported elsewhere. Genomic relationships between Australian flavivirus members of the JE virus serological complex and between Australian alphaviruses are discussed, and evidence is presented for a possible new genomic lineage of SIN virus.

Alphavirus↗
PubMed1993

Sequence analysis of the PrP protein from two species of antelope susceptible to transmissible spongiform encephalopathy.

The sequence of the coding regions of the PrP genes of the Arabian oryx and greater kudu have been determined and compared with the related sheep and bovine PrP gene sequences. The oryx gene sequence was found to be very closely related to that of the sheep, encoding just one amino acid difference. The greater kudu gene sequence was found to be more closely related to the bovine, encoding four amino acid differences. The possible influence that the gene sequences have on the transmission of spongiform encephalopathy to these antelope species is discussed.

Animals↗
PubMed1991

Persistent infection of Vero cells by the flavivirus Murray Valley encephalitis virus.

Murray Valley encephalitis (MVE) virus strain OR2 was serially passaged on Vero cells to establish a persistent infection which was maintained for over 300 days. Supernatants from infected cells protected Vero cells from c.p.e. and caused up to a 95% reduction of wild-type virus yield. These protective and interfering effects suggest that defective interfering (DI) particles are responsible for the establishment and maintenance of the MVE virus persistent infection. The persistently infected cell supernatant preparations shared several features with DI particle preparations from other viral systems, such as their amplification to detectable levels after two to four passages of virus. However, results from this study suggest that DI particles of MVE virus differ from other studied systems in that they are able to affect only moderately the yield of infectious wild-type virus. The genetic drift of the parental virus during the course of a long term persistent infection in vitro appears to be minimal.

Animals↗
PubMedDate not supplied

The relationships between West Nile and Kunjin viruses.

Until recently, West Nile (WN) and Kunjin (KUN) viruses were classified as distinct types in the Flavivirus genus. However, genetic and antigenic studies on isolates of these two viruses indicate that the relationship between them is more complex. To better define this relationship, we performed sequence analyses on 32 isolates of KUN virus and 28 isolates of WN virus from different geographic areas, including a WN isolate from the recent outbreak in New York. Sequence comparisons showed that the KUN virus isolates from Australia were tightly grouped but that the WN virus isolates exhibited substantial divergence and could be differentiated into four distinct groups. KUN virus isolates from Australia were antigenically homologous and distinct from the WN isolates and a Malaysian KUN virus. Our results suggest that KUN and WN viruses comprise a group of closely related viruses that can be differentiated into subgroups on the basis of genetic and antigenic analyses.

Aedes↗