RESUMEN

Missing person cases typically require a genetic kinship test to determine the relationship between an unidentified individual and the relatives of the missing person. When not enough genetic evidence has been collected the lack of statistical power of these tests might lead to unreliable results. This is particularly true when just a few distant relatives are available for genotyping. In this contribution, we considered a Bayesian network approach for kinship testing and proposed several information theoretic metrics in order to quantitatively evaluate the information content of pedigrees. We show how these statistics are related to the widely used likelihood ratio values and could be employed to efficiently prioritize family members in order to optimize the statistical power in missing person problems. Our methodology seamlessly integrates with Bayesian modeling approaches, like the GENis platform that we have recently developed for high-throughput missing person identification tasks. Furthermore, our approach can also be easily incorporated into Elston-Stewart forensic frameworks. To facilitate the application of our methodology, we have developed the forensIT package, freely available on CRAN repository, which implements all the methodologies described in our manuscript.

Asunto(s)

RESUMEN

Background: After primary vaccination schemes with rAd26-rAd5 (Sputnik V), ChAdOx1 nCoV-19, BBIBP-CorV or heterologous combinations, the effectiveness of homologous or heterologous boosters (Sputnik V, ChAdOx, Pfizer-BioNTech, Moderna) against SARS-CoV-2 infections, hospitalisations and deaths has been scarcely studied. Methods: Test-negative, case-control study, conducted in Argentina during omicron BA.1 predominance, in adults ≥50 years old tested for SARS-CoV-2 who had received two or three doses of COVID-19 vaccines. Outcomes were COVID-associated infections, hospitalisations and deaths after administering mRNA and vectored boosters, < or ≥60 days from the last dose. Findings: Of 422,124 individuals tested for SARS-CoV-2, 221,993 (52.5%) tested positive; 190,884 (45.2%) and 231,260 (54.8%) had received 2-dose and 3-dose vaccination schemes, respectively. The 3-dose scheme reduced infections, hospitalisations and death (OR 0.81 [0.80-0.83]; 0.28 [0.25-0.32] and 0.25 [0.22-0.28] respectively), but protection dropped after 60 days to 1.04 [1.01-1.06]; 0.52 [0.44-0.61] and 0.38 [0.33-0.45]). Compared with 2-dose-schemes, homologous boosters after primary schemes with vectored-vaccines provided lower protection against infections < and ≥60 days (0.94 [0.92-0.97] and 1.05 [1.01-1.09], respectively) but protected against hospitalisations (0.30 [0.26-0.35]) and deaths (0.29 [0.25-0.33]), decreasing after 60 days (0.59 [0.47-0.74] and 0.51 [0.41-0.64], respectively). Heterologous boosters protected against infections (0.70 [0.68-0.71]) but decreased after 60 days (1.01 [0.98-1.04]) and against hospitalisations and deaths (0.26 [0.22-0.31] and 0.22 [0.18-0.25], respectively), which also decreased after 60 days (0.43 [0.35-0.53] and 0.33 [0.26-0.41], respectively). Heterologous boosters protected against infections when applied <60 days (0.70 [0.68-0.71], p < 0.001), against hospitalisations when applied ≥60 days (0.43 [0.35-0.53], p < 0.01), and against deaths < and ≥60 days (0.22 [0.18-0.25], p < 0.01 and 0.33 [0.26-0.41], p < 0.001). Interpretation: During omicron predominance, heterologous boosters such as viral vectored and mRNA vaccines, following Sputnik V, ChAdOx1, Sinopharm or heterologous primary schemes might provide better protection against death; this effect might last longer in individuals aged ≥50 than homologous boosters. Funding: None.

RESUMEN

Objetivo: Evaluar la efectividad de esquemas primarios de Sputnik V, Astra-Zeneca, Sinopharm o combinaciones heterólogas seguidos de refuerzos a vector viral (Sputnik V, Astra-Zeneca) o ARNm (Pfizer-BioNTech, Moderna) frente a infecciones, hospitalizaciones y muertes por SARS-CoV-2. Material y métodos: Estudio de casos y controles con test negativo realizado en la provincia de Buenos Aires, durante el predominio de ómicron BA.1, que incluyó individuos ≥ 50 años con test positivo para SARS-CoV-2 que habían recibido 2 o 3 dosis de vacunas. Se registraron infecciones, hospitalizaciones y muertes después de administrar refuerzos con Sputnik V, Astra-Zeneca o ARNm. Resultados: De 422 124 personas analizadas para SARS-Cov-2, 221 993 (52.5%) presentaron test positivos; 190 884 (45.2%) y 231.260 (54.8%) recibieron esquemas de vacunación de 2 y 3 dosis, respectivamente. Los esquemas primarios con Astra-Zeneca, Sputnik V o vector viral, combinados con un refuerzo a vector viral, mostraron protección contra infecciones (OR: 0.94 [0.92 a 0.97]), hospitalizaciones (OR: 0.30 [0.26 a 0.35]) y muertes (OR: 0.29 [0.25 a 0.33]. Los esquemas primarios con Astra-Zeneca y Sputnik V más refuerzo de ARNm, o con Sinopharm más refuerzo de ARNm o vector viral otorgaron protección adicional contra infecciones (OR: 0.70 [0.68 a 0.71]). Hubo un efecto protector frente a hospitalizaciones y muertes (OR: 0.26 [0.22 a 0.31] y 0.22 [0.18 a 0.25]) en todos los casos. Conclusiones: Durante el predominio de ómicron, los refuerzos heterólogos con vacunas a vector viral y de ARNm, posteriores a los esquemas primarios de Sputnik V, Astra-Zeneca, Sinopharm o heterólogos, podrían proporcionar mejor protección y mayor duración del efecto contra la muerte en personas mayores de 50 años, en comparación con refuerzos homólogos

Objective: To evaluate the effectiveness of primary vaccination regimens involving Sputnik V, Astra-Zeneca, Sinopharm, or heterologous combinations followed by viral vector boosters (Sputnik V, As-traZeneca) or mRNA boosters (Pfizer-BioNTech, Moderna) against infections, hospitalizations and deaths caused by SARS-CoV-2. Material and methods: Case-control studies with negative tests conducted in the Buenos Aires province during the Omicron BA.1 predominance. The study included patients ≥ 50 years of age, who tested positive for SARS-CoV-2 and had received two or three doses of vaccines. Infections, hospitalizations, and deaths were registered following the administration of Sputnik V, AstraZeneca, or mRNA boosters. Findings: Out of 422 124 people tested for SARS-Cov-2, 221 993 (52.5%) had positive test results; 190,884 (45.2%) and 231 260 (54.8%) received two-dose and three-dose vaccination schemes, respectively. Primary regimens with AstraZeneca, Sputnik V, or viral vector, combined with a viral vector booster demonstrated protection against infections (OR 0.94 [0.92 to 0.97]), hospitalizations (OR 0.30 [0.26 to 0.35]) and deaths (OR 0.29 [0.25 to 0.33]. Primary regimens with AstraZeneca and Sputnik V combined with mRNA boosters, as well as pri-mary schemes with Sinopharm combined with mRNA or viral vectored boosters showed additional protection against infections (OR 0.70 [0.68 to 0.71]). There was a protective effect against hospi-talizations and deaths (OR 0.26 [0.22-0.31] and 0.22 [0.18 -0.25]) in all cases. Conclusions: During Omicron predominance, heterologous boosters with viral-vector and mRNA vaccines, administered after Sputnik V, AstraZeneca, Sinopharm, or heterologous primary regimens, could provide enhanced protection and prolonged effectiveness against mortality in individuals aged ≥ 50, compared to ho-mologous boosters

Asunto(s)

RESUMEN

Background: Although paediatric clinical presentations of COVID-19 are usually less severe than in adults, serious illness and death have occurred. Many countries started the vaccination rollout of children in 2021; still, information about effectiveness in the real-world setting is scarce. The aim of our study was to evaluate vaccine effectiveness (VE) against COVID-19-associated-hospitalisations in the 3-17-year population during the Omicron outbreak. Methods: We conducted a retrospective cohort study including individuals aged 3-17 registered in the online vaccination system of the Buenos Aires Province, Argentina. mRNA-1273 and BNT162b2 were administered to 12-17-year subjects; and BBIBP-CorV to 3-11-year subjects. Vaccinated group had received a two-dose scheme by 12/1/2021. Unvaccinated group did not receive any COVID-19 vaccine between 12/14/2021 and 3/9/2022, which was the entire monitoring period. Vaccine effectiveness (VE) against COVID-19-associated hospitalisations was calculated as (1-OR)x100. Findings: By 12/1/2021, 1,536,435 individuals aged 3-17 who had received zero or two doses of SARS-CoV-2 vaccines were included in this study. Of the latter, 1,440,389 were vaccinated and 96,046 not vaccinated. VE were 78.0%[68.7-84.2], 76.4%[62.9-84.5] and 80.0%[64.3-88.0] for the entire cohort, 3-11-year (BBIBP-CorV) subgroup and 12-17 (mRNA vaccines) subgroup, respectively. VE for the entire population was 82.7% during the period of Delta and Omicron overlapping circulation and decreased to 67.7% when Omicron was the only variant present. Interpretation: This report provides evidence of high vaccine protection against associated hospitalisations in the paediatric population during the Omicron outbreak but suggests a decrease of protection when Omicron became predominant. Application of a booster dose in children aged 3-11-year warrants further consideration. Funding: None.

RESUMEN

BACKGROUND: A first-dose of various vaccines provides acceptable protection against infections by SARS-CoV-2 and evolution to the most severe forms of COVID-19. The recombinant adenovirus (rAd)-based vaccine, Gam-COVID-Vac (Sputnik V), was proven efficacious but information about effectiveness in the real-world setting is lacking. The aim of our study was to investigate the association between the rollout of the first component (rAd26) of Gam-COVID-Vac and PCR-positive tests, hospitalisations and deaths. METHODS: We conducted a retrospective cohort study which analyzed individuals aged 60-79 who self-registered in the online vaccination system of the Province of Buenos Aires, Argentina, from December 29, 2020 to March 21, 2021. Exclusion criteria were having a previous positive RT-PCR or antigen tests for SARS-CoV-2, having received other vaccines, or two doses of any vaccine.Proportions of new laboratory-confirmed SARS-CoV-2 infections, hospitalisations and deaths until 83 days of vaccination were compared between vaccinated and unvaccinated subjects. Vaccine effectiveness for the three outcomes was calculated as (1-OR) × 100. Kaplan-Meier cumulative incidence curves were constructed. FINDINGS: During the study period 415995 registered subjects received the first component of Gam-COVID-Vac; 40387 belonged to the 60-79 age group, and were compared to 38978 unvaccinated. Vaccine effectiveness for preventing laboratory-confirmed infections was 78•6% [CI95% 74·8 - 81·7]; and for reducing hospitalizations and deaths was, respectively, 87·6% [CI95% 80·3 - 92·2] and 84·8% [CI95% 75·0 - 90·7]. Effectiveness was high across all subgroups. INTERPRETATION: Similarly to other vaccines, the administration of one dose of Gam-COVID-Vac was effective for a wide range of COVID-19-related outcomes. FUNDING: This study did not receive any funding.

RESUMEN

One of the main problems in controlling COVID-19 epidemic spread is the delay in confirming cases. Having information on changes in the epidemic evolution or outbreaks rise before laboratory-confirmation is crucial in decision making for Public Health policies. We present an algorithm to estimate on-stream the number of COVID-19 cases using the data from telephone calls to a COVID-line. By modelling the calls as background (proportional to population) plus signal (proportional to infected), we fit the calls in Province of Buenos Aires (Argentina) with coefficient of determination R 2 > 0.85. This result allows us to estimate the number of cases given the number of calls from a specific district, days before the laboratory results are available. We validate the algorithm with real data. We show how to use the algorithm to track on-stream the epidemic, and present the Early Outbreak Alarm to detect outbreaks in advance of laboratory results. One key point in the developed algorithm is a detailed track of the uncertainties in the estimations, since the alarm uses the significance of the observables as a main indicator to detect an anomaly. We present the details of the explicit example in Villa Azul (Quilmes) where this tool resulted crucial to control an outbreak on time. The presented tools have been designed in urgency with the available data at the time of the development, and therefore have their limitations which we describe and discuss. We consider possible improvements on the tools, many of which are currently under development.

RESUMEN

RESUMEN INTRODUCCIÓN : La vacunación en la provincia de Buenos Aires inició con personal de salud (PS). El objetivo de este trabajo es evaluar el impacto de la vacunación sobre la evolución de los casos de infección por SARS-CoV-2 en el PS, comparado con la de la población general (PG). MÉTODOS : Estudio obsewacional descriptivo de series temporales de casos confirmados de COVID-19, entre abril de 2020 y marzo de 2021. Se utilizó el sistema de información VacunatePBA y el SNVS. Se tomó el grado de inmunización a 14 días de la aplicación de la vacuna. RESULTADOS : A partir de septiembre de 2020, el número de casos disminuyó en el PS, en comparación con la PG. Para fines de febrero de 2021 estaba inmunizado con primera dosis (PD) el 42% del PS y con segunda dosis (SD) el 24%, mientras que en PG solo estaba inmunizado el 0,06% con PD y nadie SD. En marzo de 2021 mientras la cantidad de casos en PG (con 2% inmunizada) aumentó un 10% con respecto a febrero, en PS disminuyó un 35% (95% de esa población inmunizada). Esto indica una disminución significativa entre los nuevos casos de febrero y de marzo en PS (p <0,00001). DISCUSIÓN : A partir del inicio de la vacunación contra COVID-19 a finales de diciembre 2020, se muestra una disminución de casos nuevos de COVID-19 en PS. Este trabajo describe una disminución relativa de los casos en PS luego de la vacunación en la provincia de Buenos Aires y aporta los primeros datos del país sobre el impacto de las vacunas contra COVID-19.

ABSTRACT INTRODUCTION : The vaccination in the province of Buenos Aires has initiated with the health care workers (HCW). The present work aims to evaluate the impact of vaccination on the evolution of confirmed SARS- CoV2 cases in HCW compared to that of the general population (GP). METHODS : The study design is descriptive observational of series were developed confirmed cases, period April 2020 to March 2021. The Sistema Nacional de Vigilancia en Salud (SNVS), and VacunatePBA were used. The grade immunization was estimated at 14 days from the application of the first dose. RESULTS : As of September, the number of cases begins to decrease more sharply in HCW than in the general population. By February 2021, 42% of the HCW had been immunized with the first dose (FD) and 24% with the second dose (SD), while in GP only 0.06% had been immunized with FD and 0% of SD. In March, while the number of GP cases increased by 10% compared to February (only 2% immunized), HCW decreased by 35% (95% immunized). This indicates a significant decrease between the new cases of February and March in HCW (p-value <0.00001). DISCUSSION: Since the introduction of COVID-19 vaccines at the end of December in different countries, a decrease in new cases of COVID-19 in HCW has begun to be reported. The present work describes a relative decrease in HCW cases in a post-vaccination context in the province of Buenos Aires, providing the first data in the country on the impact of COVID-19 vaccines on HCW.

RESUMEN

INTRODUCCIÓN: La vacunación en la provincia de Buenos Aires inició con personal de salud (PS). El objetivo de este trabajo es evaluar el impacto de la vacunación sobre la evolución de los casos de infección por SARS-CoV-2 en el PS, comparado con la de la población general (PG). MÉTODOS: Estudio observacional descriptivo de series temporales de casos confirmados de COVID-19, entre abril de 2020 y marzo de 2021. Se utilizó el sistema de información VacunatePBA y el SNVS. Se tomó el grado de inmunización a 14 días de la aplicación de la vacuna. RESULTADOS: A partir de septiembre de 2020, el número de casos disminuyó en el PS, en comparación con la PG. Para fines de febrero de 2021 estaba inmunizado con primera dosis (PD) el 42% del PS y con segunda dosis (SD) el 24%, mientras que en PG solo estaba inmunizado el 0,06% con PD y nadie SD. En marzo de 2021 mientras la cantidad de casos en PG (con 2% inmunizada) aumentó un 10% con respecto a febrero, en PS disminuyó un 35% (95% de esa población inmunizada). Esto indica una disminución significativa entre los nuevos casos de febrero y de marzo en PS (p <0,00001). DISCUSIÓN: A partir del inicio de la vacunación contra COVID-19 a finales de diciembre 2020, se muestra una disminución de casos nuevos de COVID-19 en PS. Este trabajo describe una disminución relativa de los casos en PS luego de la vacunación en la provincia de Buenos Aires y aporta los primeros datos del país sobre el impacto de las vacunas contra COVID-19

Asunto(s)

RESUMEN

Flaviviruses include a diverse group of medically important viruses that cycle between mosquitoes and humans. During this natural process of switching hosts, each species imposes different selective forces on the viral population. Using dengue virus (DENV) as model, we found that paralogous RNA structures originating from duplications in the viral 3' untranslated region (UTR) are under different selective pressures in the two hosts. These RNA structures, known as dumbbells (DB1 and DB2), were originally proposed to be enhancers of viral replication. Analysis of viruses obtained from infected mosquitoes showed selection of mutations that mapped in DB2. Recombinant viruses carrying the identified variations confirmed that these mutations greatly increase viral replication in mosquito cells, with low or no impact in human cells. Use of viruses lacking each of the DB structures revealed opposite viral phenotypes. While deletion of DB1 reduced viral replication about 10-fold, viruses lacking DB2 displayed a great increase of fitness in mosquitoes, confirming a functional diversification of these similar RNA elements. Mechanistic analysis indicated that DB1 and DB2 differentially modulate viral genome cyclization and RNA replication. We found that a pseudoknot formed within DB2 competes with long-range RNA-RNA interactions that are necessary for minus-strand RNA synthesis. Our results support a model in which a functional diversification of duplicated RNA elements in the viral 3' UTR is driven by host-specific requirements. This study provides new ideas for understanding molecular aspects of the evolution of RNA viruses that naturally jump between different species.IMPORTANCE Flaviviruses constitute the most relevant group of arthropod-transmitted viruses, including important human pathogens such as the dengue, Zika, yellow fever, and West Nile viruses. The natural alternation of these viruses between vertebrate and invertebrate hosts shapes the viral genome population, which leads to selection of different viral variants with potential implications for epidemiological fitness and pathogenesis. However, the selective forces and mechanisms acting on the viral RNA during host adaptation are still largely unknown. Here, we found that two almost identical tandem RNA structures present at the viral 3' untranslated region are under different selective pressures in the two hosts. Mechanistic studies indicated that the two RNA elements, known as dumbbells, contain sequences that overlap essential RNA cyclization elements involved in viral RNA synthesis. The data support a model in which the duplicated RNA structures differentially evolved to accommodate distinct functions for viral replication in the two hosts.

Asunto(s)

RESUMEN

Sensor histidine kinases (SHKs) are an integral component of the molecular machinery that permits bacteria to adapt to widely changing environmental conditions. CpxA, an extensively studied SHK, is a multidomain homodimeric protein with each subunit consisting of a periplasmic sensor domain, a transmembrane domain, a signal-transducing HAMP domain, a dimerization and histidine phospho-acceptor sub-domain (DHp) and a catalytic and ATP-binding subdomain (CA). The key activation event involves the rearrangement of the HAMP-DHp helical core and translation of the CA towards the acceptor histidine, which presumably results in an autokinase-competent complex. In the present work we integrate coarse-grained, all-atom, and hybrid QM-MM computer simulations to probe the large-scale conformational reorganization that takes place from the inactive to the autokinase-competent state (conformational step), and evaluate its relation to the autokinase reaction itself (chemical step). Our results highlight a tight coupling between conformational and chemical steps, underscoring the advantage of CA walking along the DHp core, to favor a reactive tautomeric state of the phospho-acceptor histidine. The results not only represent an example of multiscale modelling, but also show how protein dynamics can promote catalysis.

Asunto(s)