Animal Viruses Probe Dataset (AVPDS) for Microarray-Based Diagnosis and Identification of Viruses

Abstract

AVPDS (Animal Viruses Probe dataset) is a dataset of virus-specific and conserve oligonucleotides for identification and diagnosis of viruses infecting animals. The current dataset contain 20,619 virus specific probes for 833 viruses and their subtypes and 3,988 conserved probes for 146 viral genera. Dataset of virus specific probe has been divided into two fields namely virus name and probe sequence. Similarly conserved probes for virus genera table have genus, and subgroup within genus name and probe sequence. The subgroup within genus is artificially divided subgroups with no taxonomic significance and contains probes which identifies viruses in that specific subgroup of the genus. Using this dataset we have successfully diagnosed the first case of Newcastle disease virus in sheep and reported a mixed infection of Bovine viral diarrhea and Bovine herpesvirus in cattle. These dataset also contains probes which cross reacts across species experimentally though computationally they meet specifications. These probes have been marked. We hope that this dataset will be useful in microarray-based detection of viruses. The dataset can be accessed through the link https://dl.dropboxusercontent.com/u/94060831/avpds/HOME.html.

Virological and Immunological Outcomes of Coinfections

“…Despite the availability of a wide range of sensitive and specific diagnostic assays, profiling of microbial species has not been possible. Microarray-based methods, such as ViroChip (96)(97)(98)(99)(100) and PathChip (101,102), that allowed detection of multiple agents but did not support detection of a divergent virus were developed. Sequenceindependent amplification techniques (next-generation sequencing [NGS] platforms) have been successfully employed for rapid detection of novel (16)(17)(18)(19) and multiple (103) viruses in clinical settings (104)(105)(106) and have allowed whole-virus genome organization (107) and analyses of minority variants (108,109).…”

Viral diagnosis in Indian livestock using customized microarray chips

“…The microarray chip used contained 4079 viruses specific probes for 124 viruses and their subtypes and 3,988 conserved probes for 146 viral genera and 3000 random probes. A database of microarray probes was also created and made available online for developing custom designed microarray probes [ 11 ]. The length of probes (60 mer) was similar to Palacios et al .…”

“…We have earlier reported the identification of Newcastle disease virus in sheep [ 15 ] and mixed infection of bovine viral diarrhea virus subtype 2 and bovine herpes virus 1 [ 17 ] in cattle. We have also created an oligo-nucleotide probe catalogue for making customized microarray chip for virus diagnosis [ 11 ]. One of the biggest disadvantages of this technique is cost and this is prohibitive in Indian circumstance [ 10 ].…”

Detection of Peste Des Petits Ruminants Virus (PPRV) Genome from Nasal Swabs of Dogs

“…The difference between this and the previous version of the microarray is inclusion of new probes for many new viruses (206 viruses as compared to 175 viruses for the previous version). The probes used in the microarray are available online (https://dl.dropbox usercontent.com/u/94060831/avpds/HOME.html) and have been described earlier [29]. The swab samples were collected in PBS.…”