In silico microarray probe design for diagnosis of multiple pathogens

<p>Abstract</p> <p>Background</p> <p>With multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as well as fingerprints that are unique to each individual genome. We present algorithmic enhancements to an existing single-genome pipeline that allows for efficient design of microarray probes common to groups of target genomes. The enhanced pipeline takes advantage of the similarities in the input genomes to narrow the search to short, nonredundant regions of the target genomes and, thereby, significantly reduces the computation time. The pipeline also computes a three-state hybridization matrix, which gives the expected hybridization of each probe with each target.</p> <p>Results</p> <p>Design of microarray probes for eight pathogenic <it>Burkholderia </it>genomes shows that the multiple-genome pipeline is nearly four-times faster than the single-genome pipeline for this application. The probes designed for these eight genomes were experimentally tested with one non-target and three target genomes. Hybridization experiments show that less than 10% of the designed probes cross hybridize with non-targets. Also, more than 65% of the probes designed to identify all <it>Burkholderia mallei </it>and <it>B. pseudomallei </it>strains successfully hybridize with a <it>B. pseudomallei </it>strain not used for probe design.</p> <p>Conclusion</p> <p>The savings in runtime suggest that the enhanced pipeline can be used to design fingerprints for tens or even hundreds of related genomes in a single run. Hybridization results with an unsequenced <it>B. pseudomallei </it>strain indicate that the designed probes might be useful in identifying unsequenced strains of <it>B. mallei </it>and <it>B. pseudomallei</it>.</p

Cynomolgus Macaque as an Animal Model for Severe Acute Respiratory Syndrome

BACKGROUND: The emergence of severe acute respiratory syndrome (SARS) in 2002 and 2003 affected global health and caused major economic disruption. Adequate animal models are required to study the underlying pathogenesis of SARS-associated coronavirus (SARS-CoV) infection and to develop effective vaccines and therapeutics. We report the first findings of measurable clinical disease in nonhuman primates (NHPs) infected with SARS-CoV. METHODS AND FINDINGS: In order to characterize clinically relevant parameters of SARS-CoV infection in NHPs, we infected cynomolgus macaques with SARS-CoV in three groups: Group I was infected in the nares and bronchus, group II in the nares and conjunctiva, and group III intravenously. Nonhuman primates in groups I and II developed mild to moderate symptomatic illness. All NHPs demonstrated evidence of viral replication and developed neutralizing antibodies. Chest radiographs from several animals in groups I and II revealed unifocal or multifocal pneumonia that peaked between days 8 and 10 postinfection. Clinical laboratory tests were not significantly changed. Overall, inoculation by a mucosal route produced more prominent disease than did intravenous inoculation. Half of the group I animals were infected with a recombinant infectious clone SARS-CoV derived from the SARS-CoV Urbani strain. This infectious clone produced disease indistinguishable from wild-type Urbani strain. CONCLUSIONS: SARS-CoV infection of cynomolgus macaques did not reproduce the severe illness seen in the majority of adult human cases of SARS; however, our results suggest similarities to the milder syndrome of SARS-CoV infection characteristically seen in young children

Reverse transcription-PCR detection of LaCrosse virus in mosquitoes and comparison with enzyme immunoassay and virus isolation.

A reverse transcription-PCR (RT-PCR) assay was developed and compared with enzyme immunoassay (EIA) and virus isolation for detecting LaCrosse virus (LAC) in mosquito pools. All three techniques were able to detect a single LAC-infected mosquito in a pool of 99 negative mosquitoes. Virus isolation was the most sensitive of the three techniques; it was possible to isolate virus immediately following intrathoracic inoculation of mosquitoes. RT-PCR was second in sensitivity; LAC RNA was detected 1 day postinfection. EIA detected LAC antigen 2 days postinfection. Additionally, RT-PCR and EIA were able to detect LAC RNA and protein, respectively, from mosquito samples which were subjected to seven freeze-thaw cycles, and RT-PCR was able to detect LAC RNA from mosquito samples which remained at room temperature for up to 7 days

Isolation of Japanese encephalitis and getah viruses from mosquitoes (Diptera: Culicidae) collected near camp greaves, Gyonggi Province, Republic of Korea, 2000

As part of an evaluation of the ecology of arthropod-borne diseases in the Republic of Korea (ROK), we examined 8,765 mosquitoes captured in Paju County, Gyonggi Province, ROK, for the presence of viruses. Mosquitoes were captured in propane lantern/human-baited Shannon traps, Mosquito Magnet traps, or American Biophysics Corporation (East Greenwich, RI) miniature light traps with or without supplemental octenol bait and/or dry ice. Mosquitoes were identified to species, placed in pools of up to 40 mosquitoes each, and tested on Vero cells for the presence of virus. A total of 15 virus isolations were made from 293 pools of mosquitoes. Viruses were identified by reverse transcriptase- polymerase chain reaction and sequencing and consisted of 14 isolations of Japanese encephalitis (JE) virus and one isolation of Getah (GET) virus. All JE isolates were from Culex tritaeniorhynchus Giles, and the isolate of GET was from Aedes vexans (Meigen). The minimum field infection rate for JE in Cx. tritaeniorhynchus was 3.3 per 1,000, whereas the GET virus infection rate for Ae. vexans was 0.2 per 1,000. Isolation of JE and GET indicated that both viruses were actively circulating in northern Gyonggi Province, ROK. The lack of human cases of JE among the Korean population probably is because of an effective government-mandated vaccination program. The reason for no cases among \u3e 10,000 United States military and others that reside or train nearby is unknown, but may be related to personnel protection measures (permethrin-impregnated uniforms and use of deet repellent), adult mosquito control, mosquito selection of nonhuman hosts (unpublished data), and the low symptomatic to asymptomatic ratio of disease in adults