α-IRAK-4 Suppresses the Activation of RANK/RANKL Pathway on Macrophages Exposed to Endodontic Microorganisms.

Periapical lesions are common pathologies affecting the alveolar bone, often initiated by intraradicular lesions resulting from microbial exposure to dental pulp. These microorganisms trigger inflammatory and immune responses. When endodontic treatment fails to eliminate the infection, periapical lesions persist, leading to bone loss. The RANK/RANKL/OPG pathway plays a crucial role in both the formation and the destruction of the bone. In this study, the objective was to inhibit the RANK/RANKL pathway in vitro within exposed Thp-1 macrophages to endodontic microorganisms, specifically Enterococcus faecalis, which was isolated from root canals of 20 patients with endodontic secondary/persistent infection, symptomatic and asymptomatic, and utilizing an α-IRAK-4 inhibitor, we introduced endodontic microorganisms and/or lipoteichoic acid from Streptococcus spp. to cellular cultures in a culture plate, containing thp-1 cells and/or PBMC from patients with apical periodontitis. Subsequently, we assessed the percentages of RANK+, RANKL+, and OPG+ cells through flow cytometry and measured the levels of several inflammatory cytokines (IL-1ß, TNF-α, IL-6, IL-8, IL-10, and IL-12p70) in the cellular culture supernatant through a CBA kit and performed analysis by flow cytometry. A significant difference was observed in the percentages of RANK+RANKL+, OPG+ RANKL+ cells in thp-1 cells and PBMCs from patients with apical periodontitis. The findings revealed significant differences in the percentages of the evaluated cells, highlighting the novel role of the IRAK-4 inhibitor in addressing this oral pathology, apical periodontitis, where bone destruction is observed.

Respiratory Syncytial Virus-A ON1 Genotype Emergence in Central Mexico in 2009 and Evidence of Multiple Duplication Events.

Background: Respiratory syncytial virus (RSV) is a leading cause of respiratory infections. An RSV-A genotype (ON1) that contains a 72-nt duplication was reported in 2012 and has since extended worldwide. Methods: We analyzed 345 respiratory samples obtained between 2003 and 2014 to assess the relevance of ON1 infections. Nucleotidic and deduced amino acid sequences from viruses detected in San Luis Potosí and sequences previously reported were analyzed. Results: RSV ON1 was detected in 105 samples. The earliest case of ON1 infection was detected in November 2009, almost 1 year prior to detection of this virus in Canada. Amino acid sequence analysis of the duplication region showed the presence of Y273N and L274P substitutions in RSV GA2 viruses that, when combined, resulted in 4 different GXXSPSQ sequence motifs at positions 272-278. Three of these motifs were present in both the original and duplicated regions of ON1 strains. Additional signature amino acid substitutions were observed in ON1 strains that have the different sequence motifs. Conclusions: ON1 strains include viruses that appear to be the result of at least 3 independent duplication events. Molecular data of strains from diverse geographical regions should help define the frequency and implications of this evolution mechanism.

Risk factors for severe influenza A-related pneumonia in adult cohort, Mexico, 2013-14.

During the 2013-14 influenza season, we assessed characteristics of 102 adults with suspected influenza pneumonia in a hospital in Mexico; most were unvaccinated. More comorbidities and severity of illness were found than for patients admitted during the 2009-10 influenza pandemic. Vaccination policies should focus on risk factors.

Ultrastructural and Functional Characterization of Mitochondrial Dynamics Induced by Human Respiratory Syncytial Virus Infection in HEp-2 Cells.

Human respiratory syncytial virus (hRSV) is the leading cause of acute lower respiratory tract infections in children under five years of age and older adults worldwide. During hRSV infection, host cells undergo changes in endomembrane organelles, including mitochondria. This organelle is responsible for energy production in the cell and plays an important role in the antiviral response. The present study focuses on characterizing the ultrastructural and functional changes during hRSV infection using thin-section transmission electron microscopy and RT-qPCR. Here we report that hRSV infection alters mitochondrial morphodynamics by regulating the expression of key genes in the antiviral response process, such as Mfn1, VDAC2, and PINK1. Our results suggest that hRSV alters mitochondrial morphology during infection, producing a mitochondrial phenotype with shortened cristae, swollen matrix, and damaged membrane. We also observed that hRSV infection modulates the expression of the aforementioned genes, possibly as an evasion mechanism in the face of cellular antiviral response. Taken together, these results advance our knowledge of the ultrastructural alterations associated with hRSV infection and might guide future therapeutic efforts to develop effective antiviral drugs for hRSV treatment.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico.

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

Killer-cell immunoglobulin-like receptors (KIR) in severe A (H1N1) 2009 influenza infections.

Introduction of a novel influenza virus into the human population leads to the occurrence of pandemic events, such as the one caused by pandemic influenza A (H1N1) 2009 virus. The severity of infections caused by this virus in young adults was greater than that observed in patients with seasonal influenza. Fatal cases have been associated with an abnormal innate, proinflammatory immune response. A critical role for natural killer cells during the initial responses to influenza infections has been suggested. In this study, we assessed the association of killer-cell immunoglobulin-like receptors (KIRs) with disease severity by comparing KIR gene content in patients with mild and severe pandemic influenza virus infections to a control group. We found that activator (KIR3DS1 and KIR2DS5) and inhibitory (KIR2DL5) genes, encoded in group B haplotypes containing the cB01, cB03 and tB01 motifs, are associated with severe pandemic influenza A (H1N1) 2009 infections. Better understanding of how genetic variability contributes to influenza virus pathogenesis may help to the development of immune intervention strategies aiming at controlling the severity of disease.

Neutralizing antibodies levels are increased in individuals with heterologous vaccination and hybrid immunity with Ad5-nCoV in the north of Mexico.

The coordinated efforts to stop the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) include massive immunization of the population at a global scale. The humoral immunity against COVID-19 is conferred by neutralizing antibodies (NAbs) that occur during the post-infection period and upon vaccination. Here, we provide robust data showing that potent neutralizing antibodies are induced in convalescent patients of SARS-CoV-2 infection who have been immunized with different types of vaccines, and patients with no previous history of COVID-19 immunized with a mixed vaccination schedule regardless of the previous infection. More importantly, we showed that a heterologous prime-boost in individuals with Ad5-nCoV (Cansino) vaccine induces higher NAbs levels in comparison to a single vaccination scheme alone.

The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico.

During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.

Respiratory syncytial virus B sequence analysis reveals a novel early genotype.

Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

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.

Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.

Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1-S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.

Peripheral Blood Mitochondrial DNA Levels Were Modulated by SARS-CoV-2 Infection Severity and Its Lessening Was Associated With Mortality Among Hospitalized Patients With COVID-19.

Introduction: During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the virus hijacks the mitochondria causing damage of its membrane and release of mt-DNA into the circulation which can trigger innate immunity and generate an inflammatory state. In this study, we explored the importance of peripheral blood mt-DNA as an early predictor of evolution in patients with COVID-19 and to evaluate the association between the concentration of mt-DNA and the severity of the disease and the patient's outcome. Methods: A total 102 patients (51 COVID-19 cases and 51 controls) were included in the study. mt-DNA obtained from peripheral blood was quantified by qRT-PCR using the NADH mitochondrial gene. Results: There were differences in peripheral blood mt-DNA between patients with COVID-19 (4.25 ng/µl ± 0.30) and controls (3.3 ng/µl ± 0.16) (p = 0.007). Lower mt-DNA concentrations were observed in patients with severe COVID-19 when compared with mild (p= 0.005) and moderate (p= 0.011) cases of COVID-19. In comparison with patients with severe COVID-19 who survived (3.74 ± 0.26 ng/µl) decreased levels of mt-DNA in patients with severe COVID-19 who died (2.4 ± 0.65 ng/µl) were also observed (p = 0.037). Conclusion: High levels of mt-DNA were associated with COVID-19 and its decrease could be used as a potential biomarker to establish a prognosis of severity and mortality of patients with COVID-19.

Health Sentinel: A mobile crowdsourcing platform for self-reported surveys provides early detection of COVID-19 clusters in San Luis Potosí, Mexico.

BACKGROUND: The Health Sentinel (Centinela de la Salud, CDS), a mobile crowdsourcing platform that includes the CDS app, was deployed to assess its utility as a tool for COVID-19 surveillance in San Luis Potosí, Mexico. METHODS: The CDS app allowed anonymized individual surveys of demographic features and COVID-19 risk of transmission and exacerbation factors from users of the San Luis Potosí Metropolitan Area (SLPMA). The platform's data processing pipeline computed and geolocalized the risk index of each user and enabled the analysis of the variables and their association. Point process analysis identified geographic clustering patterns of users at risk and these were compared with the patterns of COVID-19 cases confirmed by the State Health Services. RESULTS: A total of 1554 COVID-19 surveys were administered through the CDS app. Among the respondents, 50.4 % were men and 49.6 % women, with an average age of 33.5 years. Overall risk index frequencies were, in descending order: no-risk 77.8 %, low risk 10.6 %, respiratory symptoms 6.7 %, medium risk 1.4 %, high risk 2.0 %, very high risk 1.5 %. Comorbidity was the most frequent vulnerability category (32.4 %), followed by the inability to keep home lockdown (19.2 %). Statistically significant risk clusters identified at a spatial scale between 5 and 730 m coincided with those in neighborhoods containing substantial numbers of confirmed COVID-19 cases. CONCLUSIONS: The CDS platform enables the analysis of the sociodemographic features and spatial distribution of individual risk indexes of COVID-19 transmission and exacerbation. It is a useful epidemiological surveillance and early detection tool because it identifies statistically significant and consistent risk clusters in neighborhoods with a substantial number of confirmed COVID-19 cases.

Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic.

During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.

Severe pneumonia associated with pandemic (H1N1) 2009 outbreak, San Luis Potosí, Mexico.

We describe the clinical characteristics and outcomes of adults hospitalized with pneumonia during the pandemic (H1N1) 2009 outbreak. Patients admitted to a general hospital in San Luis Potosí, Mexico, from April 10 through May 11, 2009, suspected to have influenza virus-associated pneumonia were evaluated. We identified 50 patients with suspected influenza pneumonia; the presence of influenza virus was confirmed in 18: 11 with pandemic (H1N1) 2009 virus, 5 with unsubtypeable influenza A virus, 1 with seasonal influenza A virus (H3N2), and 1 in whom assay results for seasonal and pandemic (H1N1) 2009 viruses were positive. Eighteen patients were treated in the intensive care unit, and 10 died. During the pandemic (H1N1) 2009 outbreak, severe pneumonia developed in young adults who had no identifiable risk factors; early diagnosis and treatment of influenza virus infections may have a determinant role in outcome.

Clinical impact and direct costs of nosocomial respiratory syncytial virus infections in the neonatal intensive care unit.

BACKGROUND: Nosocomial infections are a leading cause of morbidity, costs, and mortality in preterm newborns. Most reports regarding nosocomial infections in neonatal intensive care units (NICU) are focused on bacterial infections and there is limited information regarding the impact of nosocomial viruses. The objective of this study was to assess the impact of nosocomial respiratory syncytial virus (RSV) infections in a NICU. METHODS: This was a retrospective cohort design from a NICU in a general hospital in Mexico. We included 24 newborn infants with nosocomial RSV infection and 24 infants without RSV matched by gestational age, birth weight, and the period of time of hospitalization. RESULTS: Infants with nosocomial RSV infection had longer hospitalization duration (median 24 days vs. 13 days; P = .05), increased antibiotic use (45.8% vs. 8.3%; P = .003), more mechanical ventilation requirement (54.2% vs. 0.4%; P <.001), more frequent nosocomial infections (45.8% vs. 0%; P <.001), and higher hospitalization direct costs (median 3,587.20 USD vs. 1,123.60 USD; P = .001) after nosocomial RSV detection. CONCLUSIONS: Nosocomial RSV infections are associated to a significant increase of costs in infants hospitalized in the NICU. Evaluation of interventions that may reduce the incidence of nosocomial RSV infections in this setting is warranted.

Computational Forecasting Methodology for Acute Respiratory Infectious Disease Dynamics.

The study of infectious disease behavior has been a scientific concern for many years as early identification of outbreaks provides great advantages including timely implementation of public health measures to limit the spread of an epidemic. We propose a methodology that merges the predictions of (i) a computational model with machine learning, (ii) a projection model, and (iii) a proposed smoothed endemic channel calculation. The predictions are made on weekly acute respiratory infection (ARI) data obtained from epidemiological reports in Mexico, along with the usage of key terms in the Google search engine. The results obtained with this methodology were compared with state-of-the-art techniques resulting in reduced root mean squared percentage error (RMPSE) and maximum absolute percent error (MAPE) metrics, achieving a MAPE of 21.7%. This methodology could be extended to detect and raise alerts on possible outbreaks on ARI as well as for other seasonal infectious diseases.

Respiratory syncytial virus A genotype classification based on systematic intergenotypic and intragenotypic sequence analysis.

Respiratory syncytial virus (RSV), a leading cause of lower respiratory tract infections, is classified in two major groups (A and B) with multiple genotypes within them. Continuous changes in spatiotemporal distribution of RSV genotypes have been recorded since the identification of this virus. However, there are no established criteria for genotype definition, which affects the understanding of viral evolution, immunity, and development of vaccines. We conducted a phylogenetic analysis of 4,353 RSV-A G gene ectodomain sequences, and used 1,103 complete genome sequences to analyze the totallity of RSV-A genes. Intra- and intergenotype p-distance analysis and identification of molecular markers associated to specific genotypes were performed. Our results indicate that previously reported genotypes can be classified into nine distinct genotypes: GA1-GA7, SAA1, and NA1. We propose the analysis of the G gene ectodomain with a wide set of reference sequences of all genotypes for an accurate genotype identification.