Browsing by Author "Reyes, Humberto"

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    Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution
    (2024) Solarte-Murillo, Laura; Reyes, Humberto; Ojeda, Loreto; Carcamo, Juan G.; Pontigo, Juan Pablo; Loncoman, Carlos A.
    Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.
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    Contribution of Two-Dose Vaccination Toward the Reduction of COVID-19 Cases, ICU Hospitalizations and Deaths in Chile Assessed Through Explanatory Generalized Additive Models for Location, Scale, and Shape
    (2022) Reyes, Humberto; Diethelm-Varela, Benjamin; Mendez Vejar, Constanza; Rebolledo-Zelada, Diego; Lillo-Dapremont, Bastián; Muñoz, Sergio R.; Bueno, Susan M.; González, Pablo A.; Kalergis, Alexis
    Objectives: To assess the impact of the initial two-dose-schedule mass vaccination campaign in Chile toward reducing adverse epidemiological outcomes due to SARS-CoV-2 infection. Methods: Publicly available epidemiological data ranging from 3 February 2021 to 30 September 2021 were used to construct GAMLSS models that explain the beneficial effect of up to two doses of vaccination on the following COVID-19-related outcomes: new cases per day, daily active cases, daily occupied ICU beds and daily deaths. Results: Administered first and second vaccine doses, and the statistical interaction between the two, are strong, statistically significant predictors for COVID-19-related new cases per day (R2 = 0.847), daily active cases (R2 = 0.903), ICU hospitalizations (R2 = 0.767), and deaths (R2 = 0.827). Conclusion: Our models stress the importance of completing vaccination schedules to reduce the adverse outcomes during the pandemic. Future work will continue to assess the influence of vaccines, including booster doses, as the pandemic progresses, and new variants emerge. Policy Implications: This work highlights the importance of attaining full (two-dose) vaccination status and reinforces the notion that a second dose provides increased non-additive protection. The trends we observed may also support the inclusion of booster doses in vaccination plans. These insights could contribute to guiding other countries in their vaccination campaigns.
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    Statistical explanation of the protective effect of four COVID-19 vaccine doses in the general population
    (2023) Reyes, Humberto; Mendez, Constanza; Kalergis, Alexis M.
    Objectives: To assess the effectiveness of four doses of the vaccine against SARS-CoV-2 in the general population and the impact of this on the severity of the disease by age group. Methods: By using data from the health authority public data base, we build statistical models using R and the GAMLSS library to explain the behavior of new SARS-CoV-2 infections, active COVID-19 cases, ICU bed requirement total and by age group, and deaths at the national level. Results: The four doses of vaccine and at least the interaction between the first and second doses were important explanatory factors for the protective effect against COVID-19. The R-2 for new cases per day was 0.5644 and for occupied ICU beds the R-2 is 0.9487. For occupied ICU beds for >70 years R-2 is 0.9195 and with the interaction between 4 doses as the main factor. Conclusions: Although the increase in the number of vaccine doses did not adequately explain the decrease in the number of COVID-19 cases, it explained the decrease in ICU admissions and deaths nationwide and by age group.