An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies

Martı́n, Verónica; Perales, Celia; Fernández-Algar, María; Santos, Helena; Garrido, Patricia; Pernas, María; Parro, Vı́ctor; Moreno, Miguel; García-Pérez, Javier; Alcamı́, José; Torán, José Luis; Abia, David; Domingo, Esteban; Briones, Carlos

doi:10.1371/journal.pone.0166902

Cited by 6 publications

(3 citation statements)

References 70 publications

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“…DNA microarray was also utilized for high-throughput multiplex detection of gastrointestinal viruses [ 105 ], viruses transmitted by small mammals and arthropods [ 106 ], herpesviruses, enteroviruses and flaviviruses [ 107 ], HIV-1, HIV-2, and hepatitis viruses [ 108 ] and dual infection with two dengue virus serotypes [ 109 ] in human specimens. DNA microarray was used to identify and genotype drug-resistant mutations of HIV [ 110 , 111 ] to detect and genotype drug-resistant hepatitis B virus (HBV) mutations [ 112 ], to detect and genotype SARS coronavirus [ 113 ], and to detect and determine lineage of influenza B viruses [ 114 ]. During an outbreak of SARS in China in 2002, DNA microarray also served for the discovery of a new member of the coronavirus family [ 115 ].…”

Section: Molecular Diagnostic Techniques Of Medical Virusesmentioning

confidence: 99%

Molecular and Immunological Diagnostic Techniques of Medical Viruses

Reta

Tessema

Ashenef

et al. 2020

International Journal of Microbiology

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Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.

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Section: Molecular Diagnostic Techniques Of Medical Virusesmentioning

confidence: 99%

Molecular and Immunological Diagnostic Techniques of Medical Viruses

Reta

Tessema

Ashenef

et al. 2020

International Journal of Microbiology

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show abstract

“…We have also used some of our protein-specific ssDNA aptamers as bioaffinity probes to develop graphenebased aptasensors (Bueno et al, 2019). In parallel, we have accumulated experience in the use of nucleic acid-based microarrays for the characterization of fluorescence-labeled, structured RNAs (Fernández et al, 2011;Romero-López et al, 2014) as well as for mutation screening in bacteria (Garrido et al, 2006) and viruses (Martín et al, 2016).…”

Section: The Molecular-affinity-based Detection Principlementioning

confidence: 99%

The Complex Molecules Detector (CMOLD): A Fluidic-Based Instrument Suite to Search for (Bio)chemical Complexity on Mars and Icy Moons

et al. 2020

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Organic chemistry is ubiquitous in the Solar System, and both Mars and a number of icy satellites of the outer Solar System show substantial promise for having hosted or hosting life. Here, we propose a novel astrobiologically focused instrument suite that could be included as scientific payload in future missions to Mars or the icy moons: the Complex Molecules Detector, or CMOLD. CMOLD is devoted to determining different levels of prebiotic/biotic chemical and structural targets following a chemically general approach (i.e., valid for both terrestrial and nonterrestrial life), as well as their compatibility with terrestrial life. CMOLD is based on a microfluidic block that distributes a liquid suspension sample to three instruments by using complementary technologies: (1) novel microscopic techniques for identifying ultrastructures and cell-like morphologies, (2) Raman spectroscopy for detecting universal intramolecular complexity that leads to biochemical functionality, and (3) bioaffinity-based systems (including antibodies and aptamers as capture probes) for finding life-related and nonlife-related molecular structures. We highlight our current developments to make this type of instruments flight-ready for upcoming Mars missions: the Raman spectrometer included in the science payload of the ESAs Rosalind Franklin rover (Raman Laser Spectrometer instrument) to be launched in 2022, and the biomarker detector that was included as payload in the NASA Icebreaker lander mission proposal (SOLID instrument). CMOLD is a robust solution that builds on the combination of three complementary, existing techniques to cover a wide spectrum of targets in the search for (bio)chemical complexity in the Solar System.

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“…In addition, the loss of some unique patterns such as potential N-linked glycosylation site (PNGs) and coreceptor recognition motifs exhibit failure to establish infection or cause slower disease progression. 10 It is important to examine minor genetic variations that occur within the population to characterize the host adaptation of the viral quasispecies and its evolution toward drug resistance and immune evasion. 11 It is often difficult to distinguish minor mutations that exist in the viral population through Sanger sequencing.…”

Section: Introductionmentioning

confidence: 99%

Deep Profiling Identifies Selection of Nonsynonymous Amino Acid Substitutions in HIV-1 Envelope During Early Infection

Ashokkumar

Sathyamurthi

Tripathy

et al. 2020

AIDS Research and Human Retroviruses

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Understanding the evolutionary dynamics of the viruses within an individual at or near the moment of transmission can provide critical inputs for the design of an effective vaccine for HIV infection. In this study, highthroughput sequencing technology was employed to analyze the evolutionary rate in viruses obtained at a single time point from drug-naive recently infected infants and adults in the chronic stage of disease. Gene-wise nonsynonymous (pN) and synonymous (pS) mutation rates were estimated and compared between the two groups. Significant differences were observed in the evolutionary rates between viruses in the early and late stages of infection. Higher rates of adaptive mutations in the HIV-1 envelope gene (env) were found in the chronic viruses as compared with those in the early stages of HIV infection. Conversely, percentage of nonsynonymous substitutions in env was found to be higher in recently transmitted viruses. In addition, a positive correlation was found between mutation and the evolutionary rate, and infectivity titer in recent infection. Despite the small sample size, the study identified useful information about viral evolution on transmission-associated bottlenecks. The effect of intraindividual HIV-1 evolution at the population level was highly contemporary, and the higher percentage of nonsynonymous substitutions seen in env during recent HIV-1 infection has suggested a pattern of convergent evolution leading to a positive selection for survival fitness and disease progression.

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An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies

Cited by 6 publications

References 70 publications

Molecular and Immunological Diagnostic Techniques of Medical Viruses

Molecular and Immunological Diagnostic Techniques of Medical Viruses

The Complex Molecules Detector (CMOLD): A Fluidic-Based Instrument Suite to Search for (Bio)chemical Complexity on Mars and Icy Moons

Deep Profiling Identifies Selection of Nonsynonymous Amino Acid Substitutions in HIV-1 Envelope During Early Infection

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