COVID-19 reinfections in Mexico City: implications for public health

BackgroundSince its appearance, COVID-19 has immensely impacted our society. Public health measures, from the initial lockdowns to vaccination campaigns, have mitigated the crisis. However, SARS-CoV-2’s persistence and evolving variants continue to pose global threats, increasing the risk of reinfections. Despite vaccination progress, understanding reinfections remains crucial for informed public health responses.MethodsWe collected available data on clinical and genomic information for SARS-CoV-2 samples from patients treated in Mexico City from 2020 epidemiological week 10 to 2023 epidemiological week 06 encompassing the whole public health emergency’s period. To identify clinical data we utilized the SISVER (Respiratory Disease Epidemiological Surveillance System) database for SARS-CoV-2 patients who received medical attention in Mexico City. For genomic surveillance we analyzed genomic data previously uploaded to GISAID generated by Mexican institutions. We used these data sources to generate descriptors of case number, hospitalization, death and reinfection rates, and viral variant prevalence throughout the pandemic period.FindingsThe fraction of reinfected individuals in the COVID-19 infected population steadily increased as the pandemic progressed in Mexico City. Most reinfections occurred during the fifth wave (40%). This wave was characterized by the coexistence of multiple variants exceeding 80% prevalence; whereas all other waves showed a unique characteristic dominant variant (prevalence >95%). Shifts in symptom patient care type and severity were observed, 2.53% transitioned from hospitalized to ambulatory care type during reinfection and 0.597% showed the opposite behavior; also 7.23% showed a reduction in severity of symptoms and 6.05% displayed an increase in severity. Unvaccinated individuals accounted for the highest percentage of reinfections (41.6%), followed by vaccinated individuals (31.9%). Most reinfections occurred after the fourth wave, dominated by the Omicron variant; and after the vaccination campaign was already underway.InterpretationOur analysis suggests reduced infection severity in reinfections, evident through shifts in symptom severity and care patterns. Unvaccinated individuals accounted for most reinfections. While our study centers on Mexico City, its findings may hold implications for broader regions, contributing insights into reinfection dynamics

A Molecular Characterization of the Allelic Expression of the BRCA1 Founder Δ9–12 Pathogenic Variant and Its Potential Clinical Relevance in Hereditary Cancer:International Journal of Molecular Sciences

Hereditary breast and ovarian cancer (HBOC) syndrome is a genetic condition that increases the risk of breast cancer by 80% and that of ovarian cancer by 40%. The most common pathogenic variants (PVs) causing HBOC occur in the BRCA1 gene, with more than 3850 reported mutations in the gene sequence. The prevalence of specific PVs in BRCA1 has increased across populations due to the effect of founder mutations. Therefore, when a founder mutation is identified, it becomes key to improving cancer risk characterization and effective screening protocols. The only founder mutation described in the Mexican population is the deletion of exons 9 to 12 of BRCA1 (BRCA1Δ9–12), and its description focuses on the gene sequence, but no transcription profiles have been generated for individuals who carry this gene. In this study, we describe the transcription profiles of cancer patients and healthy individuals who were heterozygous for PV BRCA1Δ9–12 by analyzing the differential expression of both alleles compared with the homozygous BRCA1 control group using RT–qPCR, and we describe the isoforms produced by the BRCA1 wild-type and BRCA1Δ9–12 alleles using nanopore long-sequencing. Using the Kruskal–Wallis test, our results showed a similar transcript expression of the wild-type allele between the healthy heterozygous group and the homozygous BRCA1 control group. An association between the recurrence and increased expression of both alleles in HBOC patients was also observed. An analysis of the sequences indicated four wild-type isoforms with diagnostic potential for discerning individuals who carry the PV BRCA1Δ9–12 and identifying which of them has developed cancer

Insights in the regulatory role of non-coding RNAs in cancer metabolism

Cancer represents a complex disease originated from alterations in several genes leading to the disturbances of important signaling pathways in tumor biology favoring heterogeneity that promotes adaptability and pharmacological resistance of tumor cells. Metabolic reprogramming has emerged as an important hallmark of cancer characterized by the presence of aerobic glycolysis, increased glutaminolysis and fatty acid biosynthesis, as well as an altered mitochondrial energy production. The metabolic switches that support energetic requirements of cancer cells are closely related to either activation of oncogenes or down-modulation of tumor-suppressor genes, finally leading to dysregulation of cell proliferation, metastasis and drug resistance signals. Non coding RNAs (ncRNAs) have emerged as one important kind of regulatory molecules of the altered genes contributing to the establishment of metabolic reprogramming. Moreover, diverse metabolic signals can regulate ncRNAs expression and activity at genetic, transcriptional or epigenetic level. The regulatory landscape of ncRNAs may provide a new approach for understanding and treatment of different kind of malignancies. In this review we discuss the regulatory role exerted by ncRNAs on metabolic enzymes and pathways involved in glucose, lipid and amino acid metabolism. We also review how the metabolic stress conditions and tumoral microenvironment influence ncRNA expression and activity. Furthermore, we comment the therapeutic potential of metabolism-related ncRNAs in cancer

Data_Sheet_2_COVID-19 reinfections in Mexico City: implications for public health.xlsx

BackgroundSince its appearance, COVID-19 has immensely impacted our society. Public health measures, from the initial lockdowns to vaccination campaigns, have mitigated the crisis. However, SARS-CoV-2’s persistence and evolving variants continue to pose global threats, increasing the risk of reinfections. Despite vaccination progress, understanding reinfections remains crucial for informed public health responses.MethodsWe collected available data on clinical and genomic information for SARS-CoV-2 samples from patients treated in Mexico City from 2020 epidemiological week 10 to 2023 epidemiological week 06 encompassing the whole public health emergency’s period. To identify clinical data we utilized the SISVER (Respiratory Disease Epidemiological Surveillance System) database for SARS-CoV-2 patients who received medical attention in Mexico City. For genomic surveillance we analyzed genomic data previously uploaded to GISAID generated by Mexican institutions. We used these data sources to generate descriptors of case number, hospitalization, death and reinfection rates, and viral variant prevalence throughout the pandemic period.FindingsThe fraction of reinfected individuals in the COVID-19 infected population steadily increased as the pandemic progressed in Mexico City. Most reinfections occurred during the fifth wave (40%). This wave was characterized by the coexistence of multiple variants exceeding 80% prevalence; whereas all other waves showed a unique characteristic dominant variant (prevalence >95%). Shifts in symptom patient care type and severity were observed, 2.53% transitioned from hospitalized to ambulatory care type during reinfection and 0.597% showed the opposite behavior; also 7.23% showed a reduction in severity of symptoms and 6.05% displayed an increase in severity. Unvaccinated individuals accounted for the highest percentage of reinfections (41.6%), followed by vaccinated individuals (31.9%). Most reinfections occurred after the fourth wave, dominated by the Omicron variant; and after the vaccination campaign was already underway.InterpretationOur analysis suggests reduced infection severity in reinfections, evident through shifts in symptom severity and care patterns. Unvaccinated individuals accounted for most reinfections. While our study centers on Mexico City, its findings may hold implications for broader regions, contributing insights into reinfection dynamics.</p

Data_Sheet_1_COVID-19 reinfections in Mexico City: implications for public health.docx

BackgroundSince its appearance, COVID-19 has immensely impacted our society. Public health measures, from the initial lockdowns to vaccination campaigns, have mitigated the crisis. However, SARS-CoV-2’s persistence and evolving variants continue to pose global threats, increasing the risk of reinfections. Despite vaccination progress, understanding reinfections remains crucial for informed public health responses.MethodsWe collected available data on clinical and genomic information for SARS-CoV-2 samples from patients treated in Mexico City from 2020 epidemiological week 10 to 2023 epidemiological week 06 encompassing the whole public health emergency’s period. To identify clinical data we utilized the SISVER (Respiratory Disease Epidemiological Surveillance System) database for SARS-CoV-2 patients who received medical attention in Mexico City. For genomic surveillance we analyzed genomic data previously uploaded to GISAID generated by Mexican institutions. We used these data sources to generate descriptors of case number, hospitalization, death and reinfection rates, and viral variant prevalence throughout the pandemic period.FindingsThe fraction of reinfected individuals in the COVID-19 infected population steadily increased as the pandemic progressed in Mexico City. Most reinfections occurred during the fifth wave (40%). This wave was characterized by the coexistence of multiple variants exceeding 80% prevalence; whereas all other waves showed a unique characteristic dominant variant (prevalence >95%). Shifts in symptom patient care type and severity were observed, 2.53% transitioned from hospitalized to ambulatory care type during reinfection and 0.597% showed the opposite behavior; also 7.23% showed a reduction in severity of symptoms and 6.05% displayed an increase in severity. Unvaccinated individuals accounted for the highest percentage of reinfections (41.6%), followed by vaccinated individuals (31.9%). Most reinfections occurred after the fourth wave, dominated by the Omicron variant; and after the vaccination campaign was already underway.InterpretationOur analysis suggests reduced infection severity in reinfections, evident through shifts in symptom severity and care patterns. Unvaccinated individuals accounted for most reinfections. While our study centers on Mexico City, its findings may hold implications for broader regions, contributing insights into reinfection dynamics.</p

Data_Sheet_3_COVID-19 reinfections in Mexico City: implications for public health.csv

BackgroundSince its appearance, COVID-19 has immensely impacted our society. Public health measures, from the initial lockdowns to vaccination campaigns, have mitigated the crisis. However, SARS-CoV-2’s persistence and evolving variants continue to pose global threats, increasing the risk of reinfections. Despite vaccination progress, understanding reinfections remains crucial for informed public health responses.MethodsWe collected available data on clinical and genomic information for SARS-CoV-2 samples from patients treated in Mexico City from 2020 epidemiological week 10 to 2023 epidemiological week 06 encompassing the whole public health emergency’s period. To identify clinical data we utilized the SISVER (Respiratory Disease Epidemiological Surveillance System) database for SARS-CoV-2 patients who received medical attention in Mexico City. For genomic surveillance we analyzed genomic data previously uploaded to GISAID generated by Mexican institutions. We used these data sources to generate descriptors of case number, hospitalization, death and reinfection rates, and viral variant prevalence throughout the pandemic period.FindingsThe fraction of reinfected individuals in the COVID-19 infected population steadily increased as the pandemic progressed in Mexico City. Most reinfections occurred during the fifth wave (40%). This wave was characterized by the coexistence of multiple variants exceeding 80% prevalence; whereas all other waves showed a unique characteristic dominant variant (prevalence >95%). Shifts in symptom patient care type and severity were observed, 2.53% transitioned from hospitalized to ambulatory care type during reinfection and 0.597% showed the opposite behavior; also 7.23% showed a reduction in severity of symptoms and 6.05% displayed an increase in severity. Unvaccinated individuals accounted for the highest percentage of reinfections (41.6%), followed by vaccinated individuals (31.9%). Most reinfections occurred after the fourth wave, dominated by the Omicron variant; and after the vaccination campaign was already underway.InterpretationOur analysis suggests reduced infection severity in reinfections, evident through shifts in symptom severity and care patterns. Unvaccinated individuals accounted for most reinfections. While our study centers on Mexico City, its findings may hold implications for broader regions, contributing insights into reinfection dynamics.</p

Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection

SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem

Analytical Performances of the COVISTIXTM Antigen Rapid Test for SARS-CoV-2 Detection in an Unselected Population (All-Comers)

The performance and validity of the COVISTIXTM rapid antigen test for the detection of SARS-CoV-2 were evaluated in an unselected population. Additionally, we assessed the influence of the Omicron SARS-CoV-2 variant in the performance of this antigen rapid test. Swab samples were collected at two point-of-care facilities in Mexico City from individuals that were probable COVID-19 cases, as they were either symptomatic or asymptomatic persons at risk of infection due to close contact with SARS-CoV-2 positive cases. Detection of the Omicron SARS-CoV-2 variant was performed in 91 positive cases by Illumina sequencing. Specificity and sensitivity of the COVISTIXTM rapid antigen test was 96% (CI 95% 94&ndash;98) and 81% (CI 95% 76&ndash;85), respectively. The accuracy parameters were not affected in samples collected after 7 days of symptom onset, and it was possible to detect almost 65% of samples with a Ct-value between 30 and 34. The COVISTIXTM antigen rapid test is highly sensitive (93%; CI 95% 88&ndash;98) and specific (98%; CI 95% 97&ndash;99) for detecting Omicron SARS-CoV-2 variant carriers. The COVISTIXTM rapid antigen test is adequate for examining asymptomatic and symptomatic individuals, including those who have passed the peak of viral shedding, as well as carriers of the highly prevalent Omicron SARS-CoV-2 variant

SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma

Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection. Case presentation. We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin’s lymphoma and COVID-19. We used RT-qPCR to quantify SARS-CoV-2 viral load over time and whole-virus genome sequencing to identify viral lineage and mutation profile. The patient presented with a persistent infection through 102 days while being treated with cytotoxic chemotherapy for non-Hodgkin’s lymphoma and received targeted therapy for COVID-19 with remdesivir and hyperimmune plasma. All sequenced samples belonged to the BA.1.1 lineage. We detected nine amino acid substitutions in five viral genes (Nucleocapsid, ORF1a, ORF1b, ORF13a, and ORF9b), grouped in two clusters: the first cluster with amino acid substitutions only detected on days 39 and 87 of sample collection, and the second cluster with amino acid substitutions only detected on day 95 of sample collection. The Spike gene remained unchanged in all samples. Viral load was dynamic but consistent with the disease flares. Conclusions. This report shows that the multiple mutations that occur in an immunocompromised patient with persistent COVID-19 could provide information regarding viral evolution and emergence of new SARS-CoV-2 variants