Prevalence of symptoms, comorbidities, and reinfections in individuals infected with Wild-Type SARS-CoV-2, Delta, or Omicron variants: a comparative study in western Mexico.

Introduction: The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been classified into variants of interest (VOIs) or concern (VOCs) to prioritize global monitoring and research on variants with potential risks to public health. The SARS-CoV-2 high-rate mutation can directly impact the clinical disease progression, epidemiological behavior, immune evasion, vaccine efficacy, and transmission rates. Therefore, epidemiological surveillance is crucial for controlling the COVID-19 pandemic. In the present study, we aimed to describe the prevalence of wild-type (WT) SARS-CoV-2 and Delta and Omicron variants in Jalisco State, Mexico, from 2021 to 2022, and evaluate the possible association of these variants with clinical manifestations of COVID-19. Methods: Four thousand and ninety-eight patients diagnosed with COVID-19 by real-time PCR (COVIFLU, Genes2Life, Mexico) from nasopharyngeal samples from January 2021 to January 2022 were included. Variant identification was performed by the RT-qPCR Master Mut Kit (Genes2Life, Mexico). A study population follow-up was performed to identify patients who had experienced reinfection after being vaccinated. Results and Discussion: Samples were grouped into variants according to the identified mutations: 46.3% were Omicron, 27.9% were Delta, and 25.8% were WT. The proportions of dry cough, fatigue, headache, muscle pain, conjunctivitis, fast breathing, diarrhea, anosmia, and dysgeusia were significantly different among the abovementioned groups (p < 0.001). Anosmia and dysgeusia were mainly found in WT-infected patients, while rhinorrhea and sore throat were more prevalent in patients infected with the Omicron variant. For the reinfection follow-up, 836 patients answered, from which 85 cases of reinfection were identified (9.6%); Omicron was the VOC that caused all reported reinfection cases. In this study, we demonstrate that the Omicron variant caused the biggest outbreak in Jalisco during the pandemic from late December 2021 to mid-February 2022 but with a less severe form than the one demonstrated by Delta and WT. The co-analysis of mutations and clinical outcomes is a public health strategy with the potential to infer mutations or variants that could increase disease severity and even be an indicator of long-term sequelae of COVID-19.

A Novel Approach to Obtain Vaccine Effectiveness Continuous Profiles. Example Case: COVID-19 in Elderly Mexicans.

Population-wide vaccination is the most promising long-term COVID-19 disease management strategy. However, the protection offered by the currently available COVID-19 vaccines wanes over time, requiring boosters to be periodically given, which represents an unattainable challenge, especially if it is necessary to apply several doses per year. Therefore, it is essential to design strategies that contribute to maximizing the control of the pandemic with the available vaccines. Achieving this objective requires knowing, as precisely and accurately as possible, the changes in vaccine effectiveness over time in each population group, considering the eventual dependence on age, sex, etc. Thus, the present work proposes a novel approach to calculating realistic effectiveness profiles against symptomatic disease. In addition, this strategy can be adapted to estimate realistic effectiveness profiles against hospitalizations or deaths. All such time-dependent profiles allow the design of improved vaccination schedules, where each dose can be administrated to the population groups so that the fulfillment of the containment objectives is maximized. As a practical example for this analysis, vaccination against COVID-19 in Mexico was considered. However, this methodology can be applied to other countries' data or to characterize future vaccines with time-dependent effectiveness values. Since this strategy uses aggregated observational data collected from massive databases, assumptions about the data validity and the course of the studied epidemic could eventually be necessary.

Severe COVID-19: Drugs and Clinical Trials.

By January of 2023, the COVID-19 pandemic had led to a reported total of 6,700,883 deaths and 662,631,114 cases worldwide. To date, there have been no effective therapies or standardized treatment schemes for this disease; therefore, the search for effective prophylactic and therapeutic strategies is a primary goal that must be addressed. This review aims to provide an analysis of the most efficient and promising therapies and drugs for the prevention and treatment of severe COVID-19, comparing their degree of success, scope, and limitations, with the aim of providing support to health professionals in choosing the best pharmacological approach. An investigation of the most promising and effective treatments against COVID-19 that are currently available was carried out by employing search terms including "Convalescent plasma therapy in COVID-19" or "Viral polymerase inhibitors" and "COVID-19" in the Clinicaltrials.gov and PubMed databases. From the current perspective and with the information available from the various clinical trials assessing the efficacy of different therapeutic options, we conclude that it is necessary to standardize certain variables-such as the viral clearance time, biomarkers associated with severity, hospital stay, requirement of invasive mechanical ventilation, and mortality rate-in order to facilitate verification of the efficacy of such treatments and to better assess the repeatability of the most effective and promising results.

Comparison of three different COVID-19 vaccine platforms (CoronaVac, BTN162b2, and Ad5-nCoV) in individuals with and without prior COVID-19: Reactogenicity and neutralizing antibodies.

Neutralizing antibodies (NAbs) can be indicators of collective immunity, vaccine efficacy, and the longevity of the humoral response. This study aimed to compare reactogenicity and NAbs generated by three different COVID-19 vaccine platforms in individuals with and without prior COVID-19. 336 individuals vaccinated (112 with CoronaVac [inactivated virus], 112 with BNT162b2 [messenger RNA], and 112 with Ad5-nCoV [non-replicating viral vector]) were included. NAbs were quantified with the cPass SARS-CoV-2 kit. Individuals immunized with the Ad5-nCoV showed higher reactogenicity than those immunized with the other vaccines (p < 0.001). The BTN162b2 vaccine-induced NAbs with higher inhibition capacity than the other platforms in the first dose. In individuals without prior COVID-19, the Ad5-nCoV vaccine generated lower NAbs against SARS-CoV-2 than those induced by two doses of the BTN162b2 (Ad5-nCoV 72.10 [55.6-93.4] vs. BTN162b2 98.41 [98.16-98.56], p < 0.0001). One individual did not generate NAbs (0.89%) after a complete immunization with CoronaVac; in BTN162b2, all generated these antibodies, and in the Ad5-nCoV group, four individuals (3.57%) did not generate NAbs. Comorbidities, gender, age, and reactogenicity did not significantly influence the generation of NAbs (p > 0.05); however, a history of COVID-19 before vaccination was associated with antibodies with greater neutralizing capacity after the first dose (p < 0.01). In conclusion, the mRNA vaccine (BTN162b2) had a remarkable better ability to produce NAbs and lower reactogenicity than the other platforms, whereas the Ad5-nCov vaccine induced the lowest NAbs response in individuals without a history of COVID-19; therefore, we suggest that a booster could benefit these individuals.

Differences in B-Cell Immunophenotypes and Neutralizing Antibodies Against SARS-CoV-2 After Administration of BNT162b2 (Pfizer-BioNTech) Vaccine in Individuals with and without Prior COVID-19 - A Prospective Cohort Study.

Purpose: Understanding the humoral immune response dynamics carried out by B cells in COVID-19 vaccination is little explored; therefore, we analyze the changes induced in the different cellular subpopulations of B cells after vaccination with BNT162b2 (Pfizer-BioNTech). Methods: This prospective cohort study evaluated thirty-nine immunized health workers (22 with prior COVID-19 and 17 without prior COVID-19) and ten subjects not vaccinated against SARS-CoV-2 (control group). B cell subpopulations (transitional, mature, naïve, memory, plasmablasts, early plasmablast, and double-negative B cells) and neutralizing antibody levels were analyzed and quantified by flow cytometry and ELISA, respectively. Results: The dynamics of the B cells subpopulations after vaccination showed the following pattern: the percentage of transitional B cells was higher in the prior COVID-19 group (p < 0.05), whereas virgin B cells were more prevalent in the group without prior COVID-19 (p < 0.05), mature B cells predominated in both vaccinated groups (p < 0.01), and memory B cells, plasmablasts, early plasmablasts, and double-negative B cells were higher in the not vaccinated group (p < 0.05). Conclusion: BNT162b2 vaccine induces changes in B cell subpopulations, especially generating plasma cells and producing neutralizing antibodies against SARS-CoV-2. However, the previous infection with SARS-CoV-2 does not significantly alter the dynamics of these subpopulations but induces more rapid and optimal antibody production.

Specific T-Cell Immune Response to SARS-CoV-2 Spike Protein over Time in Naïve and SARS-CoV-2 Previously Infected Subjects Vaccinated with BTN162b2.

Due to the COVID-19 pandemic, the rapid development of vaccines against SARS-CoV-2 has been promoted. BNT162b2 is a lipid-nanoparticle mRNA vaccine with 95% efficacy and is the most administered vaccine globally. Nevertheless, little is known about the cellular immune response triggered by vaccination and the immune behavior over time. Therefore, we evaluated the T-cell immune response against the SARS-CoV-2 spike protein and neutralization antibodies (nAbs) in naïve and SARS-CoV-2 previously infected subjects vaccinated with BTN162b2. METHODS: Forty-six BTN162b2 vaccinated subjects were included (twenty-six naïve and twenty SARS-CoV-2 previously infected subjects vaccinated with BTN162b2). Blood samples were obtained at basal (before vaccination), 15 days after the first dose, and 15 days after the second dose, to evaluate cellular immune response upon PBMC's stimulation and cytokine levels. The nAbs were determined one and six months after the second dose. RESULTS: SARS-CoV-2 previously infected subjects vaccinated with BTN162b2 showed the highest proportion of nAbs compared to naïve individuals one month after the second dose. However, women were more prone to lose nAbs percentages over time significantly. Furthermore, a diminished CD154+ IFN-γ+ CD4+ T-cell response was observed after the second BTN162b2 dose in those with previous SARS-CoV-2 infection. In contrast, naïve participants showed an overall increased CD8+ IFN-γ+ TNF-α+ T-cell response to the peptide stimulus. Moreover, a significant reduction in IP-10, IFN-λI, and IL-10 cytokine levels was found in both studied groups. Additionally, the median fluorescence intensity (MFI) levels of IL-6, IFNλ-2/3, IFN-𝛽, and GM-CSF (p < 0.05) were significantly reduced over time in the naïve participants. CONCLUSION: We demonstrate that a previous SARS-CoV-2 infection can also impact cellular T-cell response, nAbs production, and serum cytokine concentration. Therefore, the study of T-cell immune response is essential for vaccination scheme recommendations; future vaccine boost should be carefully addressed as continued stimulation by vaccination might impact the T-cell response.

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection.

SARS-CoV-2 variants surveillance is a worldwide task that has been approached with techniques such as Next Generation Sequencing (NGS); however, this technology is not widely available in developing countries because of the lack of equipment and limited funding in science. An option is to deploy a RT-qPCR screening test which aids in the analysis of a higher number of samples, in a shorter time and at a lower cost. In this study, variants present in samples positive for SARS-CoV-2 were identified with a RT-qPCR mutation screening kit and were later confirmed by NGS. A sample with an abnormal result was found with the screening test, suggesting the simultaneous presence of two viral populations with different mutations. The DRAGEN Lineage analysis identified the Delta variant, but there was no information about the other three mutations previously detected. When the sequenced data was deeply analyzed, there were reads with differential mutation patterns, that could be identified and classified in terms of relative abundance, whereas only the dominant population was reported by DRAGEN software. Since most of the software developed to analyze SARS-CoV-2 sequences was aimed at obtaining the consensus sequence quickly, the information about viral populations within a sample is scarce. Here, we present a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis.

Efficacy and Safety of Heterologous Booster Vaccination after Ad5-nCoV (CanSino Biologics) Vaccine: A Preliminary Descriptive Study.

Several studies have reported the benefits and safety of heterologous vaccination among different approved vaccines; however, there are no specific reports on the effects of vaccination with the Ad5-nCoV and other vaccines of the same or different technologies. In the present study, we evaluated the neutralizing antibodies percentage against SARS-CoV-2 in Mexican patients immunized with the Ad5-nCoV vaccine six months after its application. Moreover, the effect of the heterologous vaccination with the Ad5-nCoV vaccine and a booster dose of ChAdOx1-S-Nov-19, Ad26.COV2.S, BNT162b2, or mRNA-127 were determined. Our results suggest that a heterologous regimen of one dose with Ad5-nCoV vaccine followed by a booster dose of a different vaccine is safe and induces a stronger humoral immune response.

The PI3K/Akt/mTOR pathway: A potential pharmacological target in COVID-19.

Coronavirus disease 2019 (COVID-19) has emerged as a serious threat to global health. The disregulation of the phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR) cell signaling pathway observed in patients with COVID-19 has attracted attention for the possible use of specific inhibitors of this pathway for the treatment of the disease. Here, we review emerging data on the involvement of the PI3K/Akt/mTOR pathway in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the clinical studies investigating its tailored inhibition in COVID-19. Current in silico, in vitro, and in vivo data convergently support a role for the PI3K/Akt/mTOR pathway in COVID-19 and suggest the use of specific inhibitors of this pathway that, by a combined mechanism entailing downregulation of excessive inflammatory reactions, cell protection, and antiviral effects, could ameliorate the course of COVID-19.

Overview of Neutralizing Antibodies and Their Potential in COVID-19.

The antibody response to respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a major focus of COVID-19 research due to its clinical relevance and importance in vaccine and therapeutic development. Neutralizing antibody (NAb) evaluations are useful for the determination of individual or herd immunity against SARS-CoV-2, vaccine efficacy, and humoral protective response longevity, as well as supporting donor selection criteria for convalescent plasma therapy. In the current manuscript, we review the essential concepts of NAbs, examining their concept, mechanisms of action, production, and the techniques used for their detection; as well as presenting an overview of the clinical use of antibodies in COVID-19.

[The involvement of vitamin A in the production of secretory IgA in the respiratory epithelium for potential protection against SARS-CoV-2 infection]. / Participación de la vitamina A en la producción de IgA secretora en el epitelio del tracto respiratorio para la potencial protección de infección por SARS-CoV-2.

SARS-CoV-2 continues to infect thousands of people around the world. It has been established that the main transmission mechanism of this virus is via airborne route, which is why it initially infects the respiratory tract. Currently, the effectiveness of medications used against COVID-19 is limited, and although immunization programs have been initiated, there is international inequality in the distribution of vaccines. Accordingly, the search for adjuvant therapies continues to be an alternative for research. Supplementation with vitamin A has been associated to the decrease of mortality from infection; this effect could be mediated by retinoic acid (RA), which is the active metabolite of vitamin A that exerts immunomodulatory functions. According to preclinical studies, RA favors the production of secretory immunoglobulin A (IgA) in the respiratory tract. In addition to this, the retinol-binding protein has been correlated with the concentration of IgA and neutralizing antibodies in patients with influenza. Therefore, this review aims to address the involvement of vitamin A in the production of secretory IgA in the respiratory epithelium in order to highlight its potential protection against SARS-CoV-2 infection.

El SARS-CoV-2 continúa infectando a miles de personas a nivel mundial. Se ha establecido que el principal mecanismo de transmisión del SARS-CoV-2 es por vía aérea, por lo que infecta inicialmente el tracto respiratorio. Actualmente, la eficacia de los fármacos utilizados contra COVID-19 es limitada y a pesar de que los programas de inmunización han iniciado, existe una desigualdad internacional en la distribución de vacunas. En este sentido, la búsqueda de terapias coadyuvantes continúa siendo una alternativa para su investigación. La suplementación con vitamina A se ha asociado con la reducción de mortalidad por infecciones; este efecto podría ser mediado por el ácido retinoico (AR), un metabolito activo de esta vitamina, que ejerce funciones inmunomoduladoras. De acuerdo con estudios preclínicos, el AR favorece la producción de inmunoglobulina A (IgA) secretora en el tracto respiratorio. Aunado a esto, la proteína de unión a retinol se ha correlacionado con la concentración de IgA y anticuerpos neutralizantes en pacientes con influenza. Por lo tanto, la presente revisión tiene como objetivo abordar la participación de la vitamina A en la producción de la inmunoglobulina A secretora en el epitelio del tracto respiratorio para resaltar su potencial función protectora contra la infección por SARS-CoV-2.

Neutralizing Antibodies against SARS-CoV-2, Anti-Ad5 Antibodies, and Reactogenicity in Response to Ad5-nCoV (CanSino Biologics) Vaccine in Individuals with and without Prior SARS-CoV-2.

This is the first study outside of clinical trials (phase I-III) evaluating the ability of the Ad5-nCoV vaccine to generate neutralizing antibodies and the factors associated with optimal or suboptimal response. In a longitudinal assay, 346 people (117 with prior COVID-19 and 229 without prior COVID-19) vaccinated with Ad5-nCoV were recruited. The percentage of neutralizing antibodies against SARS-CoV-2 (Surrogate Virus Neutralization Test) and antibodies against Ad5 (ADV-Ad5 IgG ELISA) were quantified pre and post-vaccination effects. The Ad5-nCoV vaccine induces higher neutralizing antibodies percentage in individuals with prior COVID-19 than those without prior COVID-19 (median [IQR]: 98% [97-98.1] vs. 72% [54-90], respectively; p < 0.0001). Furthermore, a natural infection (before vaccination) induces more neutralizing antibodies percentage than immunized individuals without prior COVID-19 (p < 0.01). No patient had vaccine-severe adverse effects. The age, antidepressant, and immunosuppressive treatments, reactogenicity, and history of COVID-19 are associated with impaired antibody production. The anti-Ad5 antibodies increased after 21 days of post-vaccination in all groups (p < 0.01). We recommend the application of a booster dose of Ad5-nCoV, especially for those individuals without previous COVID-19 infection. Finally, the induction of anti-Ad5 antibodies after vaccination should be considered if a booster with the same vaccine is planned.

COVID-19 Screening by Anti-SARS-CoV-2 Antibody Seropositivity: Clinical and Epidemiological Characteristics, Comorbidities, and Food Intake Quality.

Developing countries have reported lower molecular diagnostic testing levels due to a lack of resources. Therefore, antibody tests represent an alternative to detect exposure to SARS-CoV-2 and analyze possible risk factors. We aimed to describe and compare the clinical-epidemiological characteristics and the quality of food intake in Mexican individuals with a positive or negative test to antibodies against SARS-CoV-2. We carried out antibody tests and applied a survey to 1799 individuals; 42% were positive, and diabetes was more prevalent in these cases (p < 0.01). No differences were identified in the blood type nor influenza vaccination between groups. Coughing, respiratory distress, muscle pain, joint pain, and anosmia were the most prevalent symptoms among seropositive cases (p < 0.0001). Food intake quality was similar in both groups, except for the most consumed type of fat (p = 0.006). In conclusion, this study supports the association of diabetes as a principal risk factor for SARS-CoV-2 infection in the Mexican population. The results do not support previous associations between blood group or influenza vaccination as protective factors against SARS-CoV-2 infection. However, frequent consumption of polyunsaturated fats is highlighted as a new possible associated factor with COVID-19, which more studies should corroborate as with all novel findings.

Neutralizing Antibodies Titers and Side Effects in Response to BNT162b2 Vaccine in Healthcare Workers with and without Prior SARS-CoV-2 Infection.

The main expected result of a vaccine against viruses is the ability to produce neutralizing antibodies. Currently, several vaccines against SARS-CoV-2 are being applied to prevent mortal complications, being Pfizer-BioNTech (BNT162b2) one of the first to be authorized in the USA and Mexico (11 December 2020). This study evaluated the efficacy of this vaccine on antibody production with neutralizing capacity and its side effects in healthcare workers with and without prior SARS-CoV-2 infection and in a group of unvaccinated individuals with prior COVID-19. The main findings are the production of 100% neutralizing antibodies in both groups after the second dose, well-tolerated adverse effects, the possible presence of immunosenescence, and finally, we support that a single dose of this vaccine in individuals with prior COVID-19 would be sufficient to achieve an immunization comparable to people without prior COVID-19 with a complete vaccination program (2 doses).

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact.

Background: Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population. Methods: Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico. Results: In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. Conclusion: This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

Vitamin D Levels in COVID-19 Outpatients from Western Mexico: Clinical Correlation and Effect of Its Supplementation.

BACKGROUND: The immunomodulatory effects of vitamin D are known to be beneficial in viral infections; it is also known that its deficiency is associated with a prognosis more critical of Coronavirus Disease 2019. This study aimed to determine baseline vitamin D serum concentrations and the effects of its supplementation in asymptomatic or mildly symptomatic Coronavirus Disease 2019 outpatients. METHODS: 42 outpatients were included, 22 of which received a supplement of 10,000 IU of vitamin D3 for 14 days; the remaining 20 outpatients were designated as a control group. Serum levels of transferrin, ferritin, vitamin D, and D-dimer were measured at baseline in both groups. After 14 days, serum levels of total vitamin D were determined in the supplemented group. RESULTS: At baseline, only 19% of infected outpatients had vitamin D levels corresponding to sufficiency. All outpatients with vitamin D insufficiency had at least one symptom associated with the disease, while only 75% of patients with symptoms presented sufficiency. On the seventh and fourteenth day of follow-up, the supplemented group presented fewer symptoms with respect to those non-supplemented. A vitamin D3 dose of 10,000 IU/daily for 14 days was sufficient to raise vitamin D serum concentrations. CONCLUSIONS: Immunomodulatory effects of vitamin D appear to be linked to the development of symptoms in positive outpatients. Vitamin D supplementation could have significant benefits in the Western Mexican population.

Potential immunomodulatory effects of vitamin D in the prevention of severe coronavirus disease 2019: An ally for Latin America (Review).

Currently, the world is under a pandemic of severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2), responsible for coronavirus disease 2019 (COVID­19). This disease is characterized by a respiratory syndrome that can progress to an acute respiratory distress syndrome. To date, limited effective therapies are available for the prevention or treatment of COVID­19; therefore, it is necessary to propose novel treatment options with immunomodulatory effects. Vitamin D serves functions in bone health and has been recently reported to exert protective effects against respiratory infections. Observational studies have demonstrated an association between vitamin D deficiency and a poor prognosis of COVID­19; this is alarming as vitamin D deficiency is a global health problem. In Latin America, the prevalence of vitamin D deficiency is unknown, and currently, this region is in the top 10 according to the number of confirmed COVID­19 cases. Supplementation with vitamin D may be a useful adjunctive treatment for the prevention of COVID­19 complications. The present review provides an overview of the current knowledge of the potential immunomodulatory effects of vitamin D in the prevention of COVID­19 and sets out vitamin D recommendations for the Latin American population.