Relationship between the Viral Load in Patients with Different COVID-19 Severities and SARS-CoV-2 Variants.

SARS-CoV-2 has spread throughout the world since 2019, changing in its genome and leading to the appearance of new variants. This gave it different evolutionary advantages, such as greater infectivity and/or a greater ability to avoid the immune response, which could lead to an increased severity of COVID-19 cases. There is no consistent information about the viral load that occurs in infection with the different SARS-CoV-2 variants, hence, in this study we quantify the viral load of more than 16,800 samples taken from the Mexican population with confirmed diagnosis of COVID-19 and we analyze the relation between different demographic and disease variables. We detected that the viral load caused by different variants differs only in the first two days after the onset of symptoms, being higher when infections are caused by the delta variant and lower when caused by omicron. Furthermore, the viral load appears to be higher in outpatients compared to hospitalized patients or in cases of death. On the other hand, no differences were found in the viral load produced in vaccinated and unvaccinated patients, nor did it differ between genders.

A Potential Association between Abdominal Obesity and the Efficacy of Humoral Immunity Induced by COVID-19 and by the AZD1222, Convidecia, BNT162b2, Sputnik V, and CoronaVac Vaccines.

Abdominal obesity is highly prevalent in Mexico and has a poor prognosis in terms of the severity of coronavirus disease (COVID-19) and low levels of antibodies induced by infection and vaccination. We evaluated the humoral immune response induced by COVID-19 and five different vaccination schedules in Mexican individuals with abdominal obesity and the effects of other variables. This prospective longitudinal cohort study included 2084 samples from 389 participants. The levels of anti-S1/S2 and anti-RBD IgG antibodies were measured at various time points after vaccination. A high prevalence of hospitalization and oxygen use was observed in individuals with abdominal obesity (AO) who had COVID-19 before vaccination; however, they also had high levels of anti-S1/S2 and anti-RBD-neutralizing IgG antibodies. The same was true for vaccination-induced antibody levels. However, their longevity was low. Interestingly, we did not observe significant differences in vaccine reactogenicity between abdominally obese and abdominally non-obese groups. Finally, individuals with a higher body mass index, older age, and previous COVID-19 had higher levels of antibodies induced by COVID-19 and vaccination. Therefore, it is important to evaluate other immunological and inflammatory factors to better understand the pathogenesis of COVID-19 in the presence of risk factors and to propose effective vaccination schedules for vulnerable populations.

Association of Obesity with SARS-CoV-2 and Its Relationship with the Humoral Response Prior to Vaccination in the State of Mexico: A Cross-Sectional Study.

Obesity is associated with an increased risk of contracting infections. This study aimed to estimate the risk of COVID-19 infection associated with obesity and to assess its role in the specific antibody response against SARS-CoV-2 in 2021. This study included 980 participants from the State of Mexico who participated in a serological survey where they were tested for SARS-CoV-2 IgG anti-S1/S2 and anti-RBD antibodies and asked for height, weight, and previous infection data via a questionnaire. Of the cohort of 980 participants, 451 (46.02%) were seropositive at the time of recruitment (45.2% symptomatic and 54.8% asymptomatic). The risk of SARS-CoV-2 infection with obesity was 2.18 (95% CI: 1.51-3.16), 2.58 (95% CI: 1.63-4.09), and 1.88 (95% CI: 1.18-2.98) for seropositive, asymptomatic, and symptomatic individuals, respectively, compared to those with normal weight. Anti-S1/S2 and anti-RBD IgG antibodies tended to be higher in overweight and obese participants in the seropositive group and stratified by different obesity classes. Additionally, there was a positive correlation between anti-S1/S2 and anti-RBD IgG antibodies and BMI in both men and women in the seropositive group. Obesity is an independent risk factor for SARS-CoV-2 infection when adjusted for confounding variables; however, the relationship between BMI and anti-S1/S2 and anti-RBD IgG antibody levels differed markedly in the presence or absence of symptoms.

Impact of vaccination on infection or death from COVID-19 in individuals with laboratory-confirmed cases: Case-control study.

OBJECTIVES: The objective of this study is to estimate the effectiveness of COVID-19 vaccines in people treated within the social security system whose vaccination status was reported to the epidemiological surveillance system. STUDY DESIGN: Case-control study. METHODS: This was a case-control study conducted. The records of individuals with suspected cases of COVID-19 registered in the epidemiological surveillance system between February 1 and June 30, 2021, were studied. RT-qPCR was performed to determine SARS-CoV-2 infection; those with a positive result were considered cases, and those with a negative result were considered controls. The ratio between cases and controls was 1:1.3. The crude and adjusted vaccine effectiveness was considered the prevention of symptomatic infection and death and calculated as the difference between the dose and the risk, with a survival analysis among vaccinated people. RESULTS: A total of 94,416 individuals were included, of whom 40,192 were considered cases and 54,224 controls; 3,781 (4.00%) had been vaccinated against COVID-19. Vaccination also proved to be a protective factor against COVID-19, especially in the population who received a second dose (OR = 0.31; 95% CI 0.28-0.35). With the application of the vaccine, there was a protective effect against mortality (OR = 0.76; 95% CI 0.66-0.87). Disease prevention was higher for the BNT162-2 mRNA vaccine (82%) followed by the ChAdOx1 vaccine (33%). In the survival analysis, vaccination provided a protective effect. CONCLUSIONS: There was a positive impact of vaccines for the prevention of symptomatic COVID-19, with a second dose generating greater efficacy and a reduction in deaths.

Diversity, composition, and networking of saliva microbiota distinguish the severity of COVID-19 episodes as revealed by an analysis of 16S rRNA variable V1-V3 region sequences.

Studies on the role of the oral microbiome in SARS-CoV-2 infection and severity of the disease are limited. We aimed to characterize the bacterial communities present in the saliva of patients with varied COVID-19 severity to learn if there are differences in the characteristics of the microbiome among the clinical groups. We included 31 asymptomatic subjects with no previous COVID-19 infection or vaccination; 176 patients with mild respiratory symptoms, positive or negative for SARS-CoV-2 infection; 57 patients that required hospitalization because of severe COVID-19 with oxygen saturation below 92%, and 18 fatal cases of COVID-19. Saliva samples collected before any treatment were tested for SARS-CoV-2 by PCR. Oral microbiota in saliva was studied by amplification and sequencing of the V1-V3 variable regions of 16S gene using an Illumina MiSeq platform. We found significant changes in diversity, composition, and networking in saliva microbiota of patients with COVID-19, as well as patterns associated with severity of disease. The presence or abundance of several commensal species and opportunistic pathogens were associated with each clinical stage. Patterns of networking were also found associated with severity of disease: a highly regulated bacterial community (normonetting) was found in healthy people whereas poorly regulated populations (disnetting) were characteristic of severe cases. Characterization of microbiota in saliva may offer important clues in the pathogenesis of COVID-19 and may also identify potential markers for prognosis in the severity of the disease. IMPORTANCE SARS-CoV-2 infection is the most severe pandemic of humankind in the last hundred years. The outcome of the infection ranges from asymptomatic or mild to severe and even fatal cases, but reasons for this remain unknown. Microbes normally colonizing the respiratory tract form communities that may mitigate the transmission, symptoms, and severity of viral infections, but very little is known on the role of these microbial communities in the severity of COVID-19. We aimed to characterize the bacterial communities in saliva of patients with different severity of COVID-19 disease, from mild to fatal cases. Our results revealed clear differences in the composition and in the nature of interactions (networking) of the bacterial species present in the different clinical groups and show community-patterns associated with disease severity. Characterization of the microbial communities in saliva may offer important clues to learn ways COVID-19 patients may suffer from different disease severities.

Longevity and Neutralizing Capacity of IgG Antibodies against SARS-CoV-2 Generated by the Application of BNT162b2, AZD1222, Convidecia, Sputnik V, and CoronaVac Vaccines: a Cohort Study in the Mexican Population.

The WHO has approved the use of several vaccines during the COVID-19 pandemic; experience over the last 2 years has indicated that dose demand can only be covered using more than one design. Therefore, having scientific evidence of the performance of the different vaccines applied in a country is highly relevant. In Mexico, 5 vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were used, allowing a cohort study to analyze the generation of anti-S1/S2 IgG antibodies and anti-RBD antibodies with neutralizing activity at 0, 21, 90, and 180 days after vaccination. Five groups of participants were formed on the basis of the type of vaccine received and were divided on the basis of whether they previously had or did not have COVID-19. After completing the vaccination schedule, the seroprevalence was 95.5, 97.5, 81.0, 95.2, and 90.0% (BNT162b2, AZD1222, Convidecia, Sputnik V, and CoronaVac, respectively). Among the participants without COVID-19 prior to vaccination, the largest amount of antibodies in the 90-day period was observed in the BNT162b2 group, and the amount of antibodies in the Sputnik V group decreased the least over time. Even though the percentages of seroconversion obtained in this study were lower than those currently reported in other parts of the world, the tested vaccines are able, in most cases, to induce a good production of IgG antibodies anti-S1/S2 and neutralizing capacity. The fact that there are people who have not produced antibodies during the study leaves open some questions that must be investigated to avoid the appearance of serious cases of COVID-19. IMPORTANCE Since the start of the vaccination programs against COVID-19 in 2020, it was evident that due to global shortages, the demand for the dose required in Mexico could only be covered by acquiring different vaccines. Therefore, determining the effectiveness of these and the longevity of acquired immunity is extremely important in a scenario where SARS-CoV-2 circulation becomes endemic and booster doses are required periodically. Our data reveal significant differences both in the generation of antibodies as well as in their longevity for the vaccines applied in the country but suggest that, in general, the Mexican population can reach a high capacity to neutralize the virus, therefore, regarding less the variant for which they were designed.

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.

[Coinfections by SARS-CoV-2 and other respiratory viruses and their clinical outcome]. / Coinfecciones por SARS-CoV-2 y otros virus respiratorios y su desenlace clínico.

Background: SARS-CoV-2 is a coronavirus described for the first time in China, in December 2019. This virus can cause a disease with a very variable spectrum that ranges from asymptomatic cases to deaths. The most severe cases are normally associated with comorbidities and with the age of the patient. However, there are patients who are not part of these risk groups and develop severe cases. Objetive: To determine the association between coinfections by SARS-CoV-2 and other respiratory viruses and their clincal outcome. Material and methods: RT-qPCR was performed to determine the presence of 16 respiratory viruses in 103 confirmed COVID-19 cases. Demographic and comorbid data were collected, and statistical analyzes were performed to determine associations with severity. Results: Of the 103 analyzed cases, 14 (13.6%) presented a coinfection, of these, 92% did not require hospitalization, even in those cases in which the patient presented advanced age and some comorbidities. Conclusions: These results suggest that coinfection of SARS-CoV-2 and other respiratory viruses is not related to a more severe form of COVID-19 and, in some cases, depending on the virus involved, it could even lead to a better prognosis. These findings lay the foundations for the development of new studies that could determine the biological mechanism of this phenomenon.

Introducción: el SARS-CoV-2 es un coronavirus que fue descrito por primera vez en diciembre de 2019 en Wuhan, China. Este virus causa una enfermedad que varía en un espectro de severidad que va desde casos asintomáticos hasta defunciones. Los casos más severos se asocian normalmente con algunas comorbilidades y con la edad del paciente. Sin embargo, existen pacientes que no son parte de estos grupos de riesgo y aun así desarrollan casos graves. Objetivo: determinar la asociación entre las coinfecciones por SARS-CoV-2 y otros virus respiratorios y su desenlace clínico. Material y métodos: se realizó RT-qPCR para determinar la presencia de 16 virus respiratorios en 103 casos confirmados de COVID-19. Se recolectaron datos demográficos y de comorbilidades, y se realizaron análisis estadísticos para determinar asociaciones con gravedad. Resultados: el 13.6% de los casos (14/103) presentaron alguna coinfección, de estos, el 92% nunca requirió ingreso hospitalario, aun en aquellos casos en los que el paciente presentara comorbilidades y edad avanzada. Conclusiones: estos resultados sugieren que la coinfección no está relacionada con un COVID-19 más grave y que, dependiendo del virus involucrado, incluso podría conducir a un mejor pronóstico. Estos hallazgos sientan las bases para nuevos estudios dirigidos a determinar el mecanismo biológico por el cual ocurre este fenómeno y a proponer las estrategias correspondientes para limitar la progresión a casos severos de COVID-19.

Impact of the introduction of chikungunya and zika viruses on the incidence of dengue in endemic zones of Mexico.

BACKGROUND: With the arrival of chikungunya (CHIKV) and zika (ZIKV) viruses in Mexico, there was a decrease in diagnosed dengue virus (DENV) cases. During the first years of cocirculation (2015-2017), the algorithms established by epidemiological surveillance systems and the installed capacity limited us to one diagnostic test per sample, so there was an underestimation of cases until September 2017, when a multiplex algorithm was implemented. Therefore, the objective of this study was determine the impact of the introduction of CHIKV and ZIKV on the incidence of diagnosed DENV in endemic areas of Mexico, when performing the rediagnosis, using the multiplex algorithm, in samples from the first three years of co-circulation of these arboviruses. METHODOLOGY AND PRINCIPAL FINDINGS: For this, 1038 samples received by the Central Laboratory of Epidemiology between 2015 and 2017 were selected for this work. Viruses were identified by multiplex RT-qPCR, and the χ2 test was used to compare categorical variables. With the new multiplex algorithm, we identified 2.4 times the rate of arbovirosis as originally reported, evidencing an underestimation of the incidence of the three viruses. Even so, significantly less dengue was observed than in previous years. The high incidence rates of chikungunya and Zika coincided with periods of dengue decline. The endemic channel showed that the cases caused by DENV rose again after the circulation of CHIKV and ZIKV decreased. In addition, 23 cases of coinfection were identified, with combinations between all viruses. CONCLUSIONS AND SIGNIFICANCE: The results obtained in this study show for the first time the real impact on the detected incidence of dengue after the introduction of CHIKV and ZIKV in Mexico, the degree of underestimation of these arboviruses in the country, as well as the co-infections between these viruses, whose importance clinical and epidemiological are still unknown.

Coinfecciones por SARS-CoV-2 y otros virus respiratorios y su desenlace clínico / Coinfections by SARS-CoV-2 and other respiratory viruses and their clinical outcome

Introducción: el SARS-CoV-2 es un coronavirus que fue descrito por primera vez en diciembre de 2019 en Wuhan, China. Este virus causa una enfermedad que varía en un espectro de severidad que va desde casos asintomáticos hasta defunciones. Los casos más severos se asocian normalmente con algunas comorbilidades y con la edad del paciente. Sin embargo, existen pacientes que no son parte de estos grupos de riesgo y aun así desarrollan casos graves. Objetivo: determinar la asociación entre las coinfecciones por SARS-CoV-2 y otros virus respiratorios y su desenlace clínico. Material y métodos: se realizó RT-qPCR para determinar la presencia de 16 virus respiratorios en 103 casos confirmados de COVID-19. Se recolectaron datos demográficos y de comorbilidades, y se realizaron análisis estadísticos para determinar asociaciones con gravedad. Resultados: el 13.6% de los casos (14/103) presentaron alguna coinfección, de estos, el 92% nunca requirió ingreso hospitalario, aun en aquellos casos en los que el paciente presentara comorbilidades y edad avanzada. Conclusiones: estos resultados sugieren que la coinfección no está relacionada con un COVID-19 más grave y que, dependiendo del virus involucrado, incluso podría conducir a un mejor pronóstico. Estos hallazgos sientan las bases para nuevos estudios dirigidos a determinar el mecanismo biológico por el cual ocurre este fenómeno y a proponer las estrategias correspondientes para limitar la progresión a casos severos de COVID-19.

Background: SARS-CoV-2 is a coronavirus described for the first time in China, in December 2019. This virus can cause a disease with a very variable spectrum that ranges from asymptomatic cases to deaths. The most severe cases are normally associated with comorbidities and with the age of the patient. However, there are patients who are not part of these risk groups and develop severe cases. Objetive: To determine the association between coinfections by SARS-CoV-2 and other respiratory viruses and their clincal outcome. Material and methods: RT-qPCR was performed to determine the presence of 16 respiratory viruses in 103 confirmed COVID-19 cases. Demographic and comorbid data were collected, and statistical analyzes were performed to determine associations with severity. Results: Of the 103 analyzed cases, 14 (13.6%) presented a coinfection, of these, 92% did not require hospitalization, even in those cases in which the patient presented advanced age and some comorbidities. Conclusions: These results suggest that coinfection of SARS-CoV-2 and other respiratory viruses is not related to a more severe form of COVID-19 and, in some cases, depending on the virus involved, it could even lead to a better prognosis. These findings lay the foundations for the development of new studies that could determine the biological mechanism of this phenomenon.

SARS-CoV-2 IgG Antibodies Seroprevalence and Sera Neutralizing Activity in MEXICO: A National Cross-Sectional Study during 2020.

Until recently, the incidence of COVID-19 was primarily estimated using molecular diagnostic methods. However, the number of cases is vastly underreported using these methods. Seroprevalence studies estimate cumulative infection incidences and allow monitoring of transmission dynamics, and the presence of neutralizing antibodies in the population. In February 2020, the Mexican Social Security Institute began conducting anonymous unrelated sampling of residual sera from specimens across the country, excluding patients with fever within the previous two weeks and/or patients with an acute respiratory infection. Sampling was carried out weekly and began 17 days before Mexico's first officially confirmed case. The 24,273 sera obtained were analyzed by chemiluminescent-linked immunosorbent assay (CLIA) IgG S1/S2 and, later, positive cases using this technique were also analyzed to determine the rate of neutralization using the enzyme-linked immunosorbent assay (ELISA). We identified 40 CLIA IgG positive cases before the first official report of SARS-CoV-2 infection in Mexico. The national seroprevalence was 3.5% in February and 33.5% in December. Neutralizing activity among IgG positives patients during overall study period was 86.1%. The extent of the SARS-CoV-2 infection in Mexico is 21 times higher than that reported by molecular techniques. Although the general population is still far from achieving herd immunity, epidemiological indicators should be re-estimated based on serological studies of this type.

Zika and dengue but not chikungunya are associated with Guillain-Barré syndrome in Mexico: A case-control study.

Background Zika, dengue and chikungunya viruses (ZIKV, CHIKV and DENV) are temporally associated with neurological diseases, such as Guillain-Barré syndrome (GBS). Because these three arboviruses coexist in Mexico, the frequency and severity of GBS could theoretically increase. This study aims to determine the association between these arboviruses and GBS in a Mexican population and to establish the clinical characteristics of the patients, including the severity of the infection. A case-control study was conducted (2016/07/01-2018/06/30) in Instituto Mexicano del Seguro Social (Mexican Social Security Institute) hospitals, using serum and urine samples that were collected to determine exposure to ZIKV, DENV, CHIKV by RT-qPCR and serology (IgM). For the categorical variables analysis, Pearson's χ2 or Fisher exact tests were used, and the Mann-Whitney U test for continuous variables. To determine the association of GBS and viral infection diagnosis through laboratory and symptomatology before admission, we calculated the odds ratio (OR) and 95% confidence intervals (95%CI) using a 2x2 contingency table. A p-value ≤ 0.05 was considered as significant. Ninety-seven GBS cases and 184 controls were included. The association of GBS with ZIKV acute infection (OR, 8.04; 95% CI, 0.89-73.01, p = 0.047), as well as laboratory evidence of ZIKV infection (OR, 16.45; 95% CI, 2.03-133.56; p = 0.001) or Flavivirus (ZIKV and DENV) infection (OR, 6.35; 95% CI, 1.99-20.28; p = 0.001) was observed. Cases of GBS associated with ZIKV demonstrated a greater impairment of functional status and a higher percentage of mechanical ventilation. According to laboratory results, an association between ZIKV or ZIKV and DENV infection in patients with GBS was found. Cases of GBS associated with ZIKV exhibited a more severe clinical picture. Cases with co-infection were not found.

Modification of HIF-1α, NF-aκB, IGFBP-3, VEGF and adiponectin in diabetic foot ulcers treated with hyperbaric oxygen.

Introduction: Diabetic foot ulcers are a frequent complication of diabetes and the first cause of non-traumatic lower limb amputation. They affect quality of life, restrict social productivity and generate a high economic burden for health care systems. Hyperbaric oxygen (HBO2) therapy is an adjunctive treatment option because it improves wound healing in the short term. However, its ability to modulate the pro- and anti-inflammatory balance and the hypoxic cell response in the clinical setting has not been fully described. Objective: To determine modifications in HIF-1α, NF-κB, IGFBP-3, and VEGF expression in wounds as well as circulating inflammatory cytokines in patients with diabetic foot ulcers subjected to HBO2. Materials and methods: We studied 17 ambulatory patients and one hospitalized patient with diabetic foot ulcers classified as Grade 3 or 4 according to the Wagner scale. All underwent HBO2 therapy. Tissue expression of HIF-1α, NF-κB, IGFBP-3, and VEGF was determined by immunohistochemistry. Plasma levels of adiponectin, IL-6, IFN-γ, IL-10 and IL-4 were measured by ELISA and chemiluminescence. Fibrosis and angiogenesis were determined by Masson's trichrome staining. Results: Ulcers in all patients healed after one month of HBO2, and none presented relapses at the one-year follow-up. At the beginning of treatment, HIF-1α and NF-κB expression was observed mainly in the nucleus, whereas these proteins were localized in the cytoplasm at the end of HBO2. There were significant modifications in VEGF expression after therapy, an increase in the plasma level of proinflammatory IL-6, and a decrease in that of IFN-γ. IGFBP-3 expression and plasma levels of adiponectin were increased at the end of HBO2. Increases in fibrosis and angiogenesis were also observed. Conclusion: These results suggest that adjuvant HBO2 modifies the proinflammatory balance related to the cellular response to hypoxia.

Evolutionary analysis of the Chikungunya virus epidemic in Mexico reveals intra-host mutational hotspots in the E1 protein.

The epidemic potential of Chikungunya virus (CHIKV) was recently made evident by its introduction and rapid expansion in the Caribbean and the Americas. We sought to gain a detailed understanding of the dynamics of the epidemic in Mexico, the country with the highest number of confirmed CHIKV cases in the Americas, and to characterise viral evolution at the population and intra-host level. Analysis of the spatiotemporal distribution of 2,739 diagnosed cases in Mexico from December 2014 to December 2015 showed a rapid nationwide expansion of the epidemic with focalisation in the South West of the country. We sequenced the envelope glycoprotein 1 gene (E1) from 25 patients using the Illumina MiSeq platform and report synonymous and non-synonymous consensus mutations. Bayesian phylogenetic analysis using 249 Asian lineage E1 sequences gave updated estimates of nucleotide substitution rates for E1 and time to most recent common ancestor of major lineages. The analysis indicates phylogenetically-related emergent Latin American clusters in South Western Mexico, Nicaragua and Honduras and transmission of American strains in the Pacific islands. Detailed analysis showed that intra-host changes in E1 mainly occurred in two variable regions (E1:189-220 and E1:349-358) in domains II and III, respectively, in residues involved in inter and intra-envelope spike interactions. At the population level, this study sheds light on the introduction and evolutionary dynamics of CHIKV in the Americas. At the intra-host level, this study identifies mutational hotspots of the E1 protein with implications for understanding the relationship between the CHIKV quasispecies, viral fitness and pathogenesis.

Differential Detection of Enterovirus and Herpes Simplex Virus in Cerebrospinal Fluid by Real-Time RT-PCR.

BACKGROUND: Enterovirus (EV) and herpes simplex virus 1 and 2 (HSV1 and HSV2) are the main etiologic agents of central nervous system infections. Early laboratory confirmation of these infections is performed by viral culture of the cerebrospinal fluid (CSF), or the detection of specific antibodies in serum (e.g., HSV). The sensitivity of viral culture ranges from 65 to 75%, with a recovery time varying from 3 to 10 days. Serological tests are faster and easy to carry out, but they exhibit cross-reactivity between HSV1 and HSV2. Although molecular techniques are more sensitive (sensitivity >95%), they are more expensive and highly susceptible to cross-contamination. METHODS: A real-time RT-PCR for the detection of EV, HSV1, and HSV2 was compared with end-point nested PCR. RESULTS: We tested 87 CSF samples of patients with a clinical diagnosis of viral meningitis or encephalitis. Fourteen samples were found to be positive by RT-PCR, but only 8 were positive by end-point PCR. The RT-PCR showed a specificity range of 94-100%, the negative predictive value was 100%, and the positive predictive value was 62, 100, and 28% for HSV1, HSV2, and EV, respectively. CONCLUSION: Real-time RT-PCR detected EV, HSV1, and HSV2 with a higher sensitivity and specificity than end-point nested RT-PCR.

Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico.

BACKGROUND: Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections. METHODS: This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR. RESULTS: The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age. CONCLUSION: In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses.

In Silico Identification of Highly Conserved Epitopes of Influenza A H1N1, H2N2, H3N2, and H5N1 with Diagnostic and Vaccination Potential.

The unpredictable, evolutionary nature of the influenza A virus (IAV) is the primary problem when generating a vaccine and when designing diagnostic strategies; thus, it is necessary to determine the constant regions in viral proteins. In this study, we completed an in silico analysis of the reported epitopes of the 4 IAV proteins that are antigenically most significant (HA, NA, NP, and M2) in the 3 strains with the greatest world circulation in the last century (H1N1, H2N2, and H3N2) and in one of the main aviary subtypes responsible for zoonosis (H5N1). For this purpose, the HMMER program was used to align 3,016 epitopes reported in the Immune Epitope Database and Analysis Resource (IEDB) and distributed in 34,294 stored sequences in the Pfam database. Eighteen epitopes were identified: 8 in HA, 5 in NA, 3 in NP, and 2 in M2. These epitopes have remained constant since they were first identified (~91 years) and are present in strains that have circulated on 5 continents. These sites could be targets for vaccination design strategies based on epitopes and/or as markers in the implementation of diagnostic techniques.