Comparative analysis of chemical breath-prints through olfactory technology for the discrimination between SARS-CoV-2 infected patients and controls.

BACKGROUND: We identified a global chemical pattern of volatile organic compounds in exhaled breath capable of discriminating between COVID-19 patients and controls (without infection) using an electronic nose. METHODS: The study focused on 42 SARS-CoV-2 RT-qPCR positive subjects as well as 42 negative subjects. Principal component analysis indicated a separation of the study groups and provides a cumulative percentage of explanation of the variation of 98.3%. RESULTS: The canonical analysis of principal coordinates model shows a separation by the first canonical axis CAP1 (r2 = 0.939 and 95.23% of correct classification rate), the cut-off point of 0.0089; 100% sensitivity (CI 95%:91.5-100%) and 97.6% specificity (CI 95%:87.4-99.9%). The predictive model usefulness was tested on 30 open population subjects without prior knowledge of SARS-CoV-2 RT-qPCR status. Of these 3 subjects exhibited COVID-19 suggestive breath profiles, all asymptomatic at the time, two of which were later shown to be SARS-CoV-2 RT-qPCR positive. An additional subject had a borderline breath profile and SARS-CoV-2 RT-qPCR positive. The remaining 27 subjects exhibited healthy breath profiles as well as SARS-CoV-2 RT-qPCR test results. CONCLUSIONS: In all, the use of olfactory technologies in communities with high transmission rates as well as in resource-limited settings where targeted sampling is not viable represents a practical COVID-19 screening approach capable of promptly identifying COVID-19 suspect patients and providing useful epidemiological information to guide community health strategies in the context of COVID-19.

Prevalence of Drug Resistance Mutations in Protease, Reverse Transcriptase, and Integrase Genes of North Central Mexico HIV Isolates.

This study set out to determine the frequency of antiretroviral drug resistance mutations in treatment-naive subjects of the north central Mexican state of San Luis Potosí. Mexican studies of antiretroviral drug resistance mutations have focused mainly on large metropolitan areas and border towns subjected to intense international migrations. This study set forth to describe the frequency of these mutations in a Mexican region less subjected to such migratory influences and more representative of smaller Mexican cities. Thirty-eight full-length pol sequences spanning the protease, reverse-transcriptase, and integrase-encoding regions were obtained from 42 treatment-naive human immunodeficiency virus (HIV)-infected subjects. Most exhibited subtype B homology, but CRF02_AG was also detected. Evidence of APOBEC3 hypermutation was seen in two samples. Calibrated population analysis revealed a surveillance drug resistance mutation prevalence of 4.9% for protease inhibitors, of 2.7% for nucleoside reverse transcriptase inhibitors, of 8.1% for non-nucleoside reverse transcriptase inhibitors, and an overall prevalence of 9.5%. This corresponds to an intermediate level of transmitted drug resistance according to the World Health Organization. The identification of integrase mutations suggests that transmitted drug mutations are being imported, as inhibitors targeting integrase have not been widely used in Mexico. Our results provide a greater understanding of HIV diversity in Mexico and highlight the way internal migrations allow HIV mutations and genetic features to permeate regions less subjected to international migrations. The implications of these findings will become more evident as Mexico hosts increased repatriations of migrants in the coming years.

Maxiprep genomic DNA extractions for molecular epidemiology studies and biorepositories.

Molecular epidemiology and genomic characterisation studies require the screening of large numbers of individuals to achieve statistical significance. Although many of the novel DNA extraction methods offer convenient, high-throughput capabilities, their use for the processing of larger sample volumes becomes very expensive. We are currently compiling the Mexican Genomic DNA Collection in order to address specific health priorities through molecular techniques. Our approach employs a low-cost laundry detergent based DNA extraction technique that maximizes DNA yield and quality. We have optimised four different modalities (maxiprep, midiprep, miniprep and microprep) for two different sources (leukocyte concentrates and whole blood). Our optimised protocol produces 4.5 mg of DNA from 15 ml of blood-bank discarded leukocyte concentrates with spectrophotometric quality, genomic integrity and PCR suitability that rivals that of phenol-chloroform extracted samples. We present evidence of many PCR applications that we have carried out on samples extracted with this technique including Killer-cell Immunoglobulin-like Receptor genotyping, Short Tandem Repeat profiling as well as nucleic acid screening for hepatitis B and human immunodeficiency type-1 viruses. This paper highlights many of the advantages that this DNA extraction technique provides over existing methodologies, whether it is used to establish large genomic DNA collections (as was our main intention) or as a routine DNA extraction method for PCR applications.