Polymorphisms located within the MHC have been linked to many disease outcomes by mechanisms not yet fully understood in most cases. Variants located within untranslated regions of HLA genes are involved in allele-specific expression and may therefore underlie some of these disease associations. We determined sequences extending nearly 2 kb upstream of the transcription start site for 68 alleles from 57 major lineages of classical HLA class I genes. The nucleotide diversity within this promoter segment roughly follows that seen within the coding regions, with HLA-B showing the highest (∼1.9%), followed by HLA-A (∼1.8%), and HLA-C showing the lowest diversity (∼0.9%). Despite its greater diversity, HLA-B mRNA expression levels determined in 178 European Americans do not vary in an allele- or lineage-specific manner, unlike the differential expression levels of HLA-A or HLA-C reported previously. Close proximity of promoter sequences in phylogenetic trees is roughly reflected by similarity of expression pattern for most HLA-A and -C loci. Although promoter sequence divergence might impact promoter activity, we observed no clear link between the phylogenetic structures as represented by pairwise nucleotide differences in the promoter regions with estimated differences in mRNA expression levels for the classical class I loci. Further, no pair of class I loci showed coordinated expression levels, suggesting that distinct mechanisms across loci determine their expression level under nonstimulated conditions. These data serve as a foundation for more in-depth analysis of the functional consequences of promoter region variation within the classical HLA class I loci.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in young children. During the COVID-19 pandemic, a significant change in the epidemiology of RSV and other viruses occurred worldwide, leading to a reduction in the circulation of these infectious agents. After the pandemic, the resurgence of seasonal respiratory viruses occurred, but some features of these infections contrast to those registered prior to the pandemic. In the present work, we studied 390 children <5 years old admitted to the hospital to determine the contribution of RSV, SARS-CoV-2, human metapneumovirus (hMPV), and influenza viruses to acute respiratory infections during the 2023–2024 winter season in Mexico. RSV was the most frequently detected virus (n = 160, 41%), followed by SARS-CoV-2 (n = 69, 17.7%), hMPV (n = 68, 17.4%), and influenza A or B (n = 40, 10.26%). Fourteen patients required admission to the intensive care unit, including six (42.8%) with RSV infection. Four children died (1%). At least one of the four viruses was detected in all deceased patients: SARS-CoV-2 in one; SARS-CoV-2 and hMPV in two; and RSV, influenza A, and SARS-CoV-2 in one. The high impact of RSV and other respiratory viruses indicates the need to implement specific preventive programs to reduce the morbidity and mortality associated with them.

The viral infectivity factor (Vif) is an HIV accessory protein that counteracts host antiviral proteins of the APOBEC3 family. Accumulating evidence highlights the pivotal role that accessory HIV proteins have on disease pathogenesis, a fact that has made them targets of interest for novel therapeutic and preventive strategies. Little is known about Vif sequence diversity outside of African or white populations. Mexico is home to Americas' third largest HIV-affected population and Mexican Hispanics represent an ever-increasing U.S. minority. This study provides a detailed analysis of the diversity seen in 77 Mexican Vif protein sequences. Phylogenetic analysis shows that most sequences cluster with HIV-1 subtype B, while less than 10% exhibit greater similarity to subtype D and A subtypes. Although most functional motifs are conserved among the Mexican sequences, substantial diversity was seen in some APOBEC binding sites, the nuclear localization inhibitory signal, and the CBFβ interaction sites.

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.

In recent years, wastewater (WW)-based epidemiology has been increasingly used for surveillance of SARS-CoV-2 and has emerged as a potential tool for monitoring other respiratory viruses. Most evidence on the use of WW for detecting multiple respiratory viruses comes from developed countries. In this study, we assessed the feasibility of multi-respiratory virus sewage surveillance in a middle-income country and explored signals that may be potentially used as early warning signs for Public Health authorities. We examined the presence of SARS-CoV-2, influenza virus, respiratory syncytial virus (RSV), and human metapneumovirus (hMPV) in 238 WW samples collected from three treatment plants in San Luis Potosí, Mexico, over one year. The weekly detection of each virus was compared with the weekly number of hospital admissions for respiratory infections caused by that virus in pediatric patients. SARS-CoV-2, influenza, hMPV, and RSV were detected in 152 (63.9%), 108 (45.4%), 95 (39.9%), and 24 (10.1%) samples, respectively. There was no significant correlation between viral detection in WW and the number of hospitalizations during that week. However, analyses of WW viral detection with hospitalizations in subsequent weeks showed an increasing correlation reaching a maximum correlation for a lag of 12 weeks for SARS-CoV-2 (r_s = 0.63, p = 0.001), 9 weeks for influenza (r_s 0.62, p = 0.0001), 2 weeks for RSV (r_s = 0.30, p = 0.05), and 3 weeks for hMPV (r_s = 0.39, p = 0.009). In addition, we identified time-periods of SARS-CoV-2, influenza, and RSV widespread circulation (several consecutive weeks in which viruses were detected in the three treatment plants); most hospitalizations caused by these viruses occurred after widespread circulation was detected in WW, suggesting this may be used as an early alert for public health systems. Overall, our results show that WW-based surveillance of multiple respiratory viruses is feasible and has potential applications as an early warning system in middle-income countries.

Protease is one of three enzymes encoded within HIV’s pol gene, responsible for the cleavage of viral Gag-Pol polypeptide into mature viral proteins and a target of current anti-retroviral therapy. Protease diversity analysis in Latin America has been lacking in spite of extensive studies of protease-inhibitor resistance mutations. We studied the diversity of 777 Mexican protease sequences and found all were subtype B except one (CRF02_AG). Phylogenetic analysis suggested the existence of six different clades with geospecific contributions. 33% of sites were conserved, 25% had conservative substitutions and 41% exhibited physicochemical changes. The most conserved regions surrounded the active site, most of the flap domain and a region between the 60’s loop and C-terminal triad. A single sequence exhibited an active site mutation (T26S). Variable sites were mapped to a crystallographic structure, providing further insight into the distribution and functional relevance of variable sites among Mexican isolates.