Comparative Analysis of Antimicrobial Antibodies between Mild and Severe COVID-19.

Patients with 2019 coronavirus disease (COVID-19) exhibit a broad spectrum of clinical presentations. A person's antimicrobial antibody profile, as partially shaped by past infection or vaccination, can reflect the immune system health that is critical to control and resolve the infection. We performed an explorative immunoproteomics study using microbial protein arrays displaying 318 full-length antigens from 77 viruses and 3 bacteria. We compared antimicrobial antibody profiles between 135 patients with mild COVID-19 disease and 215 patients with severe disease in 3 independent cohorts from Mexico and Italy. Severe disease patients were older with higher prevalence of comorbidities. We confirmed that severe disease patients elicited a stronger anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) response. We showed that antibodies against HCoV-229E and HcoV-NL63 but not against HcoV-HKU1 and HcoV-OC43 were also higher in those who had severe disease. We revealed that for a set of IgG and IgA antibodies targeting coronaviruses, herpesviruses, and other respiratory viruses, a subgroup of patients with the highest reactivity levels had a greater incidence of severe disease compared to those with mild disease across all three cohorts. On the contrary, fewer antibodies showed consistent greater prevalence in mild disease in all 3 cohorts. IMPORTANCE The clinical presentations of COVID-19 range from asymptomatic to critical illness that may lead to intensive care or even death. The health of the immune system, as partially shaped by past infections or vaccinations, is critical to control and resolve the infection. Using an innovative protein array platform, we surveyed antibodies against hundreds of full-length microbial antigens from 80 different viruses and bacteria in COVID-19 patients from different geographic regions with mild or severe disease. We not only confirmed the association of severe COVID-19 disease with higher reactivity of antibody responses to SARS-CoV-2 but also uncovered known and novel associations with antibody responses against herpesviruses and other respiratory viruses. Our study represents a significant step forward in understanding the factors contributing to COVID-19 disease severity. We also demonstrate the power of comprehensive antimicrobial antibody profiling in deciphering risk factors for severe COVID-19. We anticipate that our approach will have broad applications in infectious diseases.

Contribution of APOA5, APOC3, CETP, ABCA1 and SIK3 genetic variants to hypertriglyceridemia development in Mexican HIV-patients receiving antiretroviral therapy.

OBJECTIVE: To investigate the impact of single nucleotide polymorphisms (SNPs) from APOA5, APOC3, CETP, ATP binding cassette transporter A1 and SIK3 genes in the development of hypertriglyceridemia in HIV patients under antiretroviral therapy. MATERIAL AND METHODS: A case-control study was developed. Leukocytic genomic DNA was extracted and genotyping for SNPs rs662799, rs964184, rs5128, rs2854116, rs2854117, rs3764261, rs4149310, rs4149267 and rs139961185 was performed by real time-PCR using TaqMan allelic discrimination assays, in Mexican mestizo patients with HIV infection, with hypertriglyceridemia (>1.7 mmol/L) under antiretroviral therapy. Genetic variants were also investigated in a control group of normolipidemic HIV patients (≤ 1.7 mmol/L). Haplotypes and gene interactions were analyzed. RESULTS: A total of 602 HIV patients were genotyped (316 cases and 286 controls). Age and antiretroviral regimen based on protease inhibitors were associated with hypertriglyceridemia (P = 0.0001 and P = 0.0002. respectively). SNP rs964184 GG genotype in APOA5 gene exhibited the highest association with hypertriglyceridemia risk (OR, 3.2, 95% CI, 1.7-5.8, P = 0.0001); followed by SNP rs139961185 in SIK3 gene (OR = 2.3; (95% CI, 1.1-4.8; P = 0.03 for AA vs. AG genotype; and APOC3 rs5128 GG genotype, (OR, 2.2; 95% CI, 1.1-4.9; P = 0.04) under codominant models. These associations were maintained in the adjusted analysis by age and protease inhibitors based antiretroviral regimens. CONCLUSIONS: This study reveals an association between rs964184 in APOA5; rs5128 in APOC3 and rs139961185 in SIK3 and high triglyceride concentrations in Mexican HIV-patients receiving protease inhibitors. These genetic factors may influence the adverse effects related to antiretroviral therapy.

Detection of cytomegalovirus in plasma of patient's HIV by duplex real time PCR / Detección de citomegalovirus en plasma de pacientes con VIH mediante PCR dúplex en tiempo real

BACKGROUND: Cytomegalovirus (CMV) is able to cause serious and even deadly diseases in immunocompromised patients. It is important to have a sensitive, specific and molecular viral tests for its detection, using as targets, key genes for viral replication. The following genes have been used in the molecular detection of CMV: UL122 (replication) and UL83 (most abundant protein of the tegument). OBJECTIVE: Detect and quantify CMV, by real-time duplex PCR, from a minimum amount of plasma. MATERIAL AND METHODS: The UL122 and UL83 genes were amplified with different fluorophores, by real-time duplex PCR. To quantify CMV, curves were generated, starting with DNA-CMV (1.0-0.0000001 ng). RESULTS: The dynamic range of "master" duplex straight had a pendent (m) −3.0, the amplification efficiency was 115.44% plasmas from patients with HIV viral load ≥ 100,000 copies/mL, 11.36% were true positive for CMV and 88.64% had no amplifications or they were outside of the linear range of molecular detection. CONCLUSIONS: This test identified two important CMV genes (UL122 and UL83) in a single reaction (FAM:VIC), viral detection was confirmed from a minimum amount of plasma. This mean a smaller amount of biological sample required and would add a tool to the clinical area, as well as a lower consumption of reagents and materials.

INTRODUCCIÓN: El citomegalovirus (CMV) es capaz de provocar enfermedades graves e incluso mortales en pacientes inmunocomprometidos. Es importante contar con pruebas moleculares de detección viral, sensibles y específicas, utilizando como blanco los genes clave para la replicación viral. En la detección molecular de CMV se han utilizado los genes UL122 (replicación) y UL83 (proteína más abundante del tegumento). OBJETIVO: Detectar y cuantificar el CMV mediante reacción en cadena de la polimerasa (PCR) dúplex en tiempo real, a partir de una mínima cantidad de plasma. MATERIAL Y MÉTODOS: Los genes UL122 y UL83 se amplificaron con diferentes fluoróforos mediante PCR dúplex en tiempo real. Para cuantificar el CMV se generó una recta estándar, a partir de DNA del CMV (1.0-0.0000001 ng). RESULTADOS: El rango dinámico de la «recta maestra¼ tuvo una pendiente (m) de -3.0; la eficiencia de amplificación fue del 115.44%; de los plasmas de pacientes con infección por el virus de la inmunodeficiencia humana (VIH) con una carga viral ≥ 100,000 copias/ml, el 11.36% fueron verdaderos positivos para CMV y el 88.64% no tuvieron amplificaciones o estuvieron fuera del rango lineal de detección molecular. CONCLUSIONES: Esta prueba identificó dos genes importantes del CMV (UL122 y UL83) en una sola reacción (FAM:VIC), y se ratificó la detección viral a partir de una mínima cantidad de plasma. Esto se traduce en una menor cantidad de muestra biológica requerida y sumaría una herramienta al área clínica, así como un menor consumo de reactivos y materiales.

Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico.

Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.

Prevalence of gene rearrangements in Mexican children with acute lymphoblastic leukemia: a population study-report from the Mexican Interinstitutional Group for the identification of the causes of childhood leukemia.

Mexico has one of the highest incidences of childhood leukemia worldwide and significantly higher mortality rates for this disease compared with other countries. One possible cause is the high prevalence of gene rearrangements associated with the etiology or with a poor prognosis of childhood acute lymphoblastic leukemia (ALL). The aims of this multicenter study were to determine the prevalence of the four most common gene rearrangements [ETV6-RUNX1, TCF3-PBX1, BCR-ABL1, and MLL rearrangements] and to explore their relationship with mortality rates during the first year of treatment in ALL children from Mexico City. Patients were recruited from eight public hospitals during 2010-2012. A total of 282 bone marrow samples were obtained at each child's diagnosis for screening by conventional and multiplex reverse transcription polymerase chain reaction to determine the gene rearrangements. Gene rearrangements were detected in 50 (17.7%) patients. ETV6-RUNX1 was detected in 21 (7.4%) patients, TCF3-PBX1 in 20 (7.1%) patients, BCR-ABL1 in 5 (1.8%) patients, and MLL rearrangements in 4 (1.4%) patients. The earliest deaths occurred at months 1, 2, and 3 after diagnosis in patients with MLL, ETV6-RUNX1, and BCR-ABL1 gene rearrangements, respectively. Gene rearrangements could be related to the aggressiveness of leukemia observed in Mexican children.