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Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral gen...
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... Thus, there is a need for simpler molecular diagnostic methodologies with similar specificity. DNA microarray platforms have been developed to identify a diversity of microorganisms such as viruses (14), bacteria (15), and fungi (16,17), simultaneously or individually, with good sensitivity and specificity. Due to the low stability of most fluorescent dyes and the expensive scanning equipment used in this technique to visualize the result, our research group developed a more accessible DNA microarray system for identification of fungi at the genus and species level, the result of which is visualized with the naked eye (18). ...
Cryptococcal meningitis affects normal hosts and immunocompromised patients exhibiting high mortality rates. The objective of this study was to design two molecular assays, visible microarray platforms and loop-mediated isothermal amplification (LAMP), to identify Cryptococcus spp. and the species neoformans and gattii from the cerebral spinal fluid (CSF). To identify Cryptococcus and the two species, we designed two microarrays DNA platforms based on the internal transcribed spacer (ITS) region and CAP59 gene and LAMP assays specific for Cryptococcus species. The assays were tested using CSF from patients with cryptococcal meningitis. CSF from patients with cryptococcal meningitis was cultured in Sabouraud culture medium, and the Cryptococcus spp. grown in the culture medium were also tested for LAMP and microarray platforms. The results were compared to DNA sequencing of the same genetic regions. A total of 133 CSF samples were studied. Eleven CSFs were positive for Cryptococcus (9 C. neoformans and 2 C. gattii), 15 were positive for bacteria, and 107 were negative. The CAP59 platform correctly identified 73% of the CSF samples, while the ITS platform identified 45.5%. CAP59 platform correctly identified 100% of the Cryptococcus isolates, and ITS platform identified 70%. The two sets of LAMP primers correctly identified 100% of the Cryptococcus isolates. However, for CSF samples, the amplification occurred only in 55.5% of C. neoformans. The methodologies were reliable in the identification of Cryptococcus species, mainly for isolates from culture medium, and they might be applied as adjunctive tests to identify Cryptococcus species.
... Microarray tests allow for simultaneous detection and subtyping of thousands of genes or target sequences within a short period of time [181]. Moreover, the rapid detection and differentiation of viruses is possible by determining the identity of the viruses directly from the detection signals [182]. As an example, a long oligonucleotide (70-mer) DNA microarray developed by Wang et al. [183] was able to detect hundreds of viruses at one time. ...
As the leading cause of acute gastroenteritis worldwide, human noroviruses (HuNoVs) have caused around 685 million cases of infection and nearly $60 billion in losses every year. Despite their highly contagious nature, an effective vaccine for HuNoVs has yet to become commercially available. Therefore, rapid detection and subtyping of noroviruses is crucial for preventing viral spread. Over the past half century, there has been monumental progress in the development of techniques for the detection and analysis of noroviruses. However, currently no rapid, portable assays are available to detect and subtype infectious HuNoVs. The purpose of this review is to survey and present different analytical techniques for the detection and characterization of noroviruses.
... Combined D2 arrays (detection and discovery) consist of a combination of probes, some of them targeting species-specific regions and able to detect and identify known pathogens (Table 7.1 and Fig. 7.2); other probes target conserved/generic regions to enable binding of novel organisms with a degree of homology to known ones. 69,70,74 On the contrary, truly novel, naturally occurring or engineered microbiomes are unlikely to bind to probes designed to target known genomes 69 and this is a strong argument in favor of next-generation sequencing (NGS) and other agnostic-oriented methods 18,77 (Table 7.1), further extended by the need to regularly recapitalize array design to include new sequence data as it becomes available. 69 On the other hand, tiled arrays able to actually (re)sequence fragments of interest can be even more descriptive 67 but, at the same time, of lower overall scope or, alternatively, extremely massive, and thus requiring more sample or elaborate incubation protocols. ...
The current challenge in public-health monitoring is the extended spectrum of agents that become pathogenic and virulent due to a number of diverse reasons: the climate change altering the ambient temperature and humidity; the deterioration of health and health care, for any and all applicable reason(s), allowing aggressive communicable patterns; advances in synthetic biology increasing the danger of custom-engineered microbiota for legitimate and nefarious purposes; and massive migration/travel and transportation movements dispersing microbiota and reshuffling local microbiomes in receiving countries. Thus new microbiota has to be processed on a regular basis so as to be included in monitoring and surveillance practice. The latter is challenged with an unprecedented range of pathogens and more aggressive outbreaks. A fast turnover is at a premium of a specification list, which also contains, without being limited to, operational flexibility, technical adaptability, reasonable cost, and straightforward applications, preferably decentralized and transdisciplinary application in the monitoring of plant, animal, and human pathogen, as a result of pathogens breaking through the species’ or kingdoms’ barriers much easier than thought. Common but adaptable platforms using genomic and postgenomic technological breakthroughs, such as portable instrumentation and very long–read sequencing, pave the way for adaptive, massive testing with limited up-front costs.
... The microarray-based virus diagnosis started at the beginning of this century (Schena et al. 1995). Microarrays based on oligonucleotide probes representing nucleic acid sequences conserved between members of a taxonomic group were first used for detection of the then unknown SARS coronavirus (Wang et al. 2002 and since then has been used for detection of many viruses (Chiu et al. 2007;Chou et al. 2006;Quan et al. 2007;Martín et al. 2006, Chen et al. 2010. The detection of multiple rhinovirus serotypes in cell culture and clinical specimen (Wang et al. 2002), papillomavirus in cervical lesions , parainfluenza virus 4 in nasopharyngeal aspirates (Chiu et al. 2006), influenza virus from nasal wash and throat swabs (Lin et al. 2006), gammaretrovirus in prostate tumors (Urisman et al. 2006), foot and mouth disease virus from animal tissue (Martín et al. 2006), coronaviruses and rhinoviruses from nasal lavage (Kistler et al. 2007), metapneumovirus from bronchoalveolar lavage (Chiu et al. 2007), different respiratory pathogens including influenza virus and non-influenza agents in nasal swabs and lung tissue (Quan et al. 2007), and common food born viruses such as coxsackievirus, hepatitis A virus, norovirus, and rotavirus identified using tiling microarray (Chen et al. 2010). ...
... Microarrays based on oligonucleotide probes representing nucleic acid sequences conserved between members of a taxonomic group were first used for detection of the then unknown SARS coronavirus (Wang et al. 2002 and since then has been used for detection of many viruses (Chiu et al. 2007;Chou et al. 2006;Quan et al. 2007;Martín et al. 2006, Chen et al. 2010. The detection of multiple rhinovirus serotypes in cell culture and clinical specimen (Wang et al. 2002), papillomavirus in cervical lesions , parainfluenza virus 4 in nasopharyngeal aspirates (Chiu et al. 2006), influenza virus from nasal wash and throat swabs (Lin et al. 2006), gammaretrovirus in prostate tumors (Urisman et al. 2006), foot and mouth disease virus from animal tissue (Martín et al. 2006), coronaviruses and rhinoviruses from nasal lavage (Kistler et al. 2007), metapneumovirus from bronchoalveolar lavage (Chiu et al. 2007), different respiratory pathogens including influenza virus and non-influenza agents in nasal swabs and lung tissue (Quan et al. 2007), and common food born viruses such as coxsackievirus, hepatitis A virus, norovirus, and rotavirus identified using tiling microarray (Chen et al. 2010). Grubaugh et al. (2013) identified 13 of 14 flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses) using microarray platform. ...
... The chip based on this conserved sequence was used to identify a coronavirus from the then unknown SARS-coronavirus samples. Chou et al. (2006) developed a comprehensive algorithm for designing conserved probes. They assumed that a virus genus (G) is a collection of n viruses, in which each virus v i (i ¼ 1, . . ...
The role of microbiome in agroecosystems has evolved due to improvements in microbial diversity analysis methods. The journey of microbial diversity estimation progressed from culture-dependent to culture-independent methods. The culture-dependent methods are important in finding the microbial diversity of different environments; however, they are immensely biased toward the dominant microorganisms present in a community. With the advancement in sequencing techniques and genomics, the community exploration using culture-independent methods has commenced a new understanding of microbial interactions with their surroundings. Molecular studies of different environmental communities have uncovered <1% of the total number of prokaryotic species representing the cultivable fraction. This chapter summarizes the different methods to acquire a microbial diversity that may eventually enhance plant growth in sustainable agriculture and may often play a role in the management of environmental problems. The merits and demerits of the commonly used molecular methods to investigate microbial communities are discussed. The potential applications of next-generation sequencing techniques for a comprehensive assessment of microbial diversity have been illustrated.
... Thus, there is a need for simpler, less expensive, and reliable molecular technologies, with an accuracy similar to that of DNA sequencing, for use in clinical practice. Several DNA microarray platforms have been developed to identify a diversity of microorganisms, such as viruses, bacteria, and fungi, simultaneously or individually, with good sensitivity and specificity (20)(21)(22)(23). Due to the low stability of most fluorescent dyes and the expensive scanning equipment used in this technique, our research group developed a more affordable DNA microarray system for fungal identification at the genus and species levels. ...
A DNA microarray platform, based on the nucleotide sequences of the internal transcribed spacer regions (ITS1, ITS2) of the rRNA gene, was developed to identify 32 fungal pathogens at the species level. The probe sequences were spotted onto polycarbonate slides with a mini-microarray printer, and after the hybridization, the results were visible with the naked eye. The performance of the microarray platform was evaluated against the commercial automated systems (Vitek
®
2 and BD Phoenix™ systems) and DNA sequencing (gold standard). A total of 461 blood culture bottles were tested: 127 positive for fungi, 302 positive for bacteria, and 32 tested negative. Once the microorganisms were identified by automated systems, fungal DNA was extracted directly from the blood culture bottles. The DNA products were tested using the microarray platform, and DNA sequencing was performed. The results of the microarray and DNA sequencing were concordant in 96.7% of cases, and the results from the automated systems and DNA sequencing were concordant in 98.4%. Of all the nucleotide sequences contained in the microarray platform, the microarray failed to identify four fungal isolates (one Candida parapsilosis, two Candida tropicalis, and one Cryptococcus neoformans). Of note, the microarray detected Candida krusei DNA in two blood cultures from the same patient, whereas the automated system was only positive for Enterococcus faecium. Our microarray system provided reliable and fast fungal identification compared to DNA sequencing and the automated systems. The simplicity of reading the results by the naked eye made this DNA platform a suitable method for fungal molecular diagnosis.
... It is presumed that this strategy may also be used for the genetic diversification of other viruses pathogenic for the respiratory tract [22]. Other authors [23] developed microarray probes for the identification and detection of viruses causing SARS (severe acute respiratory syndrome) at the gene level. Hasib et al. [24] developed a flow microarray based on multiplex amplification using ligation-dependent probes involving reverse transcriptase for the detection of European bunyaviruses. ...
Both the known biological agents that cause infectious diseases, as well as modified (ABF-Advanced Biological Factors) or new, emerging agents pose a significant diagnostic problem using previously applied methods, both classical, as well as based on molecular biology methods. The latter, such as PCR and real-time PCR, have significant limitations, both quantitative (low capacity), and qualitative (limited number of targets). The article discusses the results of studies on using the microarray method for the identification of viruses (e.g. Orthopoxvirus group, noroviruses, influenza A and B viruses, rhino- and enteroviruses responsible for the FRI (Febrile Respiratory Illness), European bunyaviruses, and SARS-causing viruses), and bacteria (Mycobacterium spp., Yersinia spp., Campylobacter spp., Streptococcus pneumoniae, Salmonella typhi, Salmonella enterica, Staphylococcus aureus, Neisseria meningitidis, Clostridium difficile , Helicobacter pylori), including multiple antibiotic-resistant strains. The method allows for the serotyping and genotyping of bacteria, and is useful in the diagnosis of genetically modified agents. It allows the testing of thousands of genes in one experiment. In addition to diagnosis, it is applicable for gene expression studies, analysis of the function of genes, microorganisms virulence, and allows the detection of even single mutations. The possibility of its operational application in epidemiological surveillance, and in the detection of disease outbreak agents is demonstrated.
... This and previous reports [45][46][47] have demonstrated the great potential of microarray technology for viral detection and identification. These studies pave the way to designing a universal viral signature chip that can be used to determine the presence of DENV, as well as the specific serotype, in a given sample. ...
... Robotic microarray techniques and laser-based image analysis have been applied to the design and development of DNA microarrays to analyse transcriptional responses of cells and microorganisms [33,43]. The use of defined oligonucleotide probes is especially attractive for the synthesis of specific microarrays for viral pathogens circulating in large human populations [47]. The first reported chip assay for a human pathogen (human herpes virus) was highly effective in a global assessment of human cytomegalovirus [48] and for more recent evaluations of genetic variability in West Nile virus [32]. ...
Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.
... Using genus level probes, microarrays are able to detect multiple viroid genera in a single chip and are capable of detecting new viroids at the genus level. Several microarrays have been reported that detect a wide range of viruses [51][52][53][54]. However, no microarray with a similar capability of detecting plant viroids has been reported before. ...
A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.
... The virochip discovery array was one of the first to target a broad range of pathogens; it is best known for its role in characterizing SARS as a coronavirus [10]. Chou et al. [1] designed conserved genus probes and species-specific probes covering 53 viral families and 214 genera. Palacios et al. [3] built the Greenechippm, an array targeting vertebrate viruses and rRNA sequences of fungi, bacteria and protozoa, containing approximately 30,000 probes. ...
... Chou et al. have computationally designed virus-specific and conserved probes for microarray-based diagnosis of viruses using a specifically designed algorithm. We had used conserved probes designed by them and found that some of them do not work experimentally and felt that there is need for a new dataset [1]. ...
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 .
... Several viruses, such as human immunodeficiency virus [26], simian retroviruses [27][28][29], and hepatitis E virus [30], have been identified using consensus sequences of known viruses; however, these methods have little or no value for characterizing completely novel viruses. Microarrays use probes that can hybridize to known viral sequences and potentially novel viruses with sufficient sequence similarity [31]. Microarrays have been applied in the detection of swine res-piratory viruses in clinical samples [32] and for dengue virus [33]. ...
Emerging and re-emerging viruses continue to surface all over the world. Some of these viruses have the potential for rapid and global spread with high morbidity and mortality, such as the SARS coronavirus outbreak. It is extremely urgent and important to identify a novel virus near-instantaneously to develop an active preventive and/or control strategy. As a culture-independent approach, viral metagenomics has been widely used to investigate highly divergent and completely new viruses in humans, animals, and even environmental samples in the past decade. A new model of Koch's postulates, named the metagenomic Koch's postulates, has provided guidance for the study of the pathogenicity of novel viruses. This review explains the viral metagenomics strategy for virus discovery and describes viruses discovered in human feces in the past 10 years using this approach. This review also addresses issues related to the metagenomic Koch's postulates and the challenges for virus discovery in the future.
