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ACS Appl Mater Interfaces ; 12(50): 55614-55623, 2020 Dec 16.
Article in English | MEDLINE | ID: covidwho-1387129


Multiplexed detection of viral nucleic acids is important for rapid screening of viral infection. In this study, we present a molybdenum disulfide (MoS2) nanosheet-modified dendrimer droplet microarray (DMA) for rapid and sensitive detection of retroviral nucleic acids of human immunodeficiency virus-1 (HIV-1) and human immunodeficiency virus-2 (HIV-2) simultaneously. The DMA platform was fabricated by omniphobic-omniphilic patterning on a surface-grafted dendrimer substrate. Functionalized MoS2 nanosheets modified with fluorescent dye-labeled oligomer probes were prepatterned on positively charged amino-modified omniphilic spots to form a fluorescence resonance energy transfer (FRET) sensing microarray. With the formation of separated microdroplets of sample on the hydrophobic-hydrophilic micropattern, prepatterned oligomer probes specifically hybridized with the target HIV genes and detached from the MoS2 nanosheet surface due to weakening of the adsorption force, leading to fluorescence signal recovery. As a proof of concept, we used this microarray with a small sample size (<150 nL) for simultaneous detection of HIV-1 and HIV-2 nucleic acids with a limit of detection (LOD) of 50 pM. The multiplex detection capability was further demonstrated for simultaneous detection of five viral genes (HIV-1, HIV-2, ORFlab, and N genes of SARS-COV-2 and M gene of Influenza A). This work demonstrated the potential of this novel MoS2-DMA FRET sensing platform for high-throughput multiplexed viral nucleic acid screening.

Biosensing Techniques , COVID-19/diagnosis , HIV Infections/diagnosis , HIV/isolation & purification , COVID-19/genetics , COVID-19/virology , Disulfides/chemistry , Fluorescence , Fluorescence Resonance Energy Transfer , HIV/pathogenicity , HIV Infections/genetics , HIV Infections/virology , Humans , Molybdenum/chemistry , Nanostructures/chemistry , Nucleic Acids/genetics , Nucleic Acids/isolation & purification , SARS-CoV-2/isolation & purification , SARS-CoV-2/pathogenicity
PLoS One ; 16(6): e0251727, 2021.
Article in English | MEDLINE | ID: covidwho-1282294


BACKGROUND: The emergence of vancomycin resistant Enterococci (VRE) has alarmed the global community due to its tendency for colonization of the gastrointestinal tract. Human Immunodeficiency Virus (HIV) patients are colonized by vancomycin resistant Enterococci than other groups. The aim of this study was to determine the incidence of vancomycin resistant Enterococci and its associated factors among HIV infected patients on Anti-Retroviral Therapy (ART). METHODS: Institution based cross sectional study was conducted among HIV infected patients on ART at from June 1 to August 30, 2020. Socio-demographic and clinical data were collected by pre-tested structured questionnaire. Stool sample was collected and processed by standard microbiological techniques. Kirby Bauer Disc diffusion method was used to perform antimicrobial susceptibility testing. Data were entered by Epi data version and analyzed by SPSS version 25. Bivariable and multivariable logistic regression model was used to analyze the association between dependent and independent variables. P-values in the multivariable analysis, adjusted odds ratio (AOR) and 95% confidence interval (CI) were used to determine the strength of association. P-value ≤0.05 was considered as significant. RESULTS: Enterococci spp was isolated on 123/200 (61.50%) patients. Among these isolates, the incidence of vancomycin resistant Enterococci was 11.4% [95% CI: (6.0-17.0)]. Antimicrobial susceptibility patterns against Enterococci showed highest rate of resistance to ampicillin (69.9%). Multidrug resistances were observed in 49.59% of Enterococci isolates. Study participants who had prior antibioticexposurer more than two weeks [AOR = 7.35; 95% CI: (1.2144.64)] and hospitalization for the last six months [AOR = 5.68; 95% CI: (1.09 29.74)] were significantly associated with vancomycin resistant Enterococci. CONCLUSIONS: In our study high incidence of vancomycin resistant Enterococci was found. Previous exposure to antibiotics for more than two weeks and hospitalization for more than six months were significantly associated with vancomycin resistant Enterococci. The isolated Enterococci had variable degrees of resistance to commonly prescribed antibiotics. Therefore, periodic surveillance on antimicrobial resistance pattern, adhering to rational use of antibiotics and implementing infection prevention protocols may reduce colonization by VRE.

Anti-Retroviral Agents/therapeutic use , Gastrointestinal Tract/microbiology , Gram-Positive Bacterial Infections/epidemiology , HIV Infections/complications , HIV/isolation & purification , Vancomycin-Resistant Enterococci/isolation & purification , Vancomycin/pharmacology , Adolescent , Adult , Aged , Anti-Bacterial Agents/pharmacology , Cross-Sectional Studies , Ethiopia/epidemiology , Female , Gram-Positive Bacterial Infections/microbiology , HIV Infections/drug therapy , HIV Infections/microbiology , HIV Infections/virology , Hospitalization/statistics & numerical data , Humans , Male , Middle Aged , Young Adult
Nature ; 582(7811): 277-282, 2020 06.
Article in English | MEDLINE | ID: covidwho-980299


The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.

CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems/genetics , Microfluidic Analytical Techniques/methods , Virus Diseases/diagnosis , Virus Diseases/virology , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Drug Resistance, Viral/genetics , Genome, Viral/genetics , HIV/classification , HIV/genetics , HIV/isolation & purification , Humans , Influenza A virus/classification , Influenza A virus/genetics , Influenza A virus/isolation & purification , Microfluidic Analytical Techniques/instrumentation , RNA, Guide/genetics , SARS-CoV-2 , Sensitivity and Specificity
Curr Opin HIV AIDS ; 16(1): 11-24, 2021 01.
Article in English | MEDLINE | ID: covidwho-927147


PURPOSE OF REVIEW: The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics. RECENT FINDINGS: Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges. SUMMARY: Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.

COVID-19/virology , HIV Infections/virology , HIV/genetics , SARS-CoV-2/genetics , COVID-19/epidemiology , HIV/classification , HIV/isolation & purification , HIV Infections/epidemiology , Humans , Molecular Epidemiology , Pandemics , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification
Medwave ; 20(9): e8049, 2020 Oct 27.
Article in Spanish, English | MEDLINE | ID: covidwho-902878


In December 2019, a new species of pneumonia-causing betacoronavirus was identified in Wuhan, China, which was later identified as SARS-CoV-2. This RNA virus presents certain similarities with other viruses of the same genetic material. It has been seen that infection by human immunodeficiency virus resembles the infection by SARS-CoV-2 in various aspects. In this comment, we present some of the virological, immunological, clinical, and pharmacological similarities between HIV and SARS-CoV-2, which could allow us to understand the immunopathogenesis of COVID-19 better, as well as make some decisions in regarding antiviral management.

En diciembre de 2019 una nueva especie de ß-coronavirus causante de neumonía fue identificada en la ciudad China de Wuhan, el cual posteriormente fue denominado SARS-CoV-2. Este virus de ácido ribonucleico presenta ciertas similitudes con otros virus del mismo material genético, dentro de ellos se ha visto que la infección por virus de la inmunodeficiencia humana se asemeja en diversos aspectos a la infección por SARS-CoV-2. En este comentario presentamos algunas de las similitudes virológicas, inmunológicas, clínicas y farmacológicas entre estos dos virus, las cuales podrían permitirnos entender de mejor manera la inmunopatogenia de COVID-19, así como también tomar algunas decisiones en cuanto al manejo antiviral.

Betacoronavirus/isolation & purification , Coronavirus Infections/virology , HIV Infections/virology , HIV/isolation & purification , Pneumonia, Viral/virology , Antiviral Agents/pharmacology , Betacoronavirus/immunology , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/immunology , HIV/immunology , HIV Infections/immunology , Humans , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/immunology , SARS-CoV-2