The Missing Person problem through the lens of information theory.

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.

Protection of homologous and heterologous boosters after primary schemes of rAd26-rAd5, ChAdOx1 nCoV-19 and BBIBP-CorV during the omicron outbreak in adults of 50 years and older in Argentina: a test-negative case-control study.

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.

Incorporating non-genetic evidence in large scale missing person searches: A general approach beyond filtering.

The search for missing persons implies several steps, from the preliminary investigation that involves collecting background data related to the case to the genetic kinship testing. Despite its crucial importance in identifications, only some approaches mathematically formalize the possibility of using preliminary investigation data. In some cases, a filtering strategy is applied, which implies selecting a subset of possible victims where some non-genetic variables perfectly match those of the missing. Through a Bayesian approach, we propose a mathematical model for computing the prior odds based on non-genetic variables usually collected during the preliminary investigation, such as biological sex, hair colour, and age. We use computational simulations to show how to incorporate these prior odds in DNA-database searches. Importantly, our results suggest that applying the proposed model leads to better search performance in underpowered cases from the genetic point of view, where few or distant relatives of the missing person are available for genotyping. Furthermore, the results are also helpful when using non-genetic data for prior odds in well-powered cases, where genetic data are enough to reach a reliable conclusion. It performs better than other approaches, such as using non-genetic data for filtering. The software mispitools, freely available on CRAN, implements all described methods (https://CRAN.R-project.org/package=mispitools).

Effectiveness of BBIBP-CorV, BNT162b2 and mRNA-1273 vaccines against hospitalisations among children and adolescents during the Omicron outbreak in Argentina: A retrospective cohort study.

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.

Effectiveness of the first component of Gam-COVID-Vac (Sputnik V) on reduction of SARS-CoV-2 confirmed infections, hospitalisations and mortality in patients aged 60-79: a retrospective cohort study in Argentina.

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.

Making decisions in missing person identification cases with low statistical power.

The present work proposes a general strategy for dealing with missing person identification cases through DNA-database search. Our main example is the identification of abducted children in the last civic-dictatorship of Argentina, known as the "Missing Grandchildren of Argentina". Particularly we focus on those pedigrees where few, or only distant relatives of the missing person are available, resulting in low statistical power. For such complex cases we provide a statistical method for selecting a likelihood ratio (LR) threshold for each pedigree based on error rates. Furthermore, we provide an open-source user friendly software for computing LR thresholds and error rates. The strategy described in the paper could be applied to other large-scale cases of DNA-based identification hampered by low statistical power.

Estimating COVID-19 cases and outbreaks on-stream through phone calls.

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.

Impact of vaccines against COVID-19 on new SARS-COV2 infections in health care workers of the Province of Buenos Aires / Impacto de vacunación covid-19 en las infecciones por sars-cov-2 en personal de salud de la provincia de buenos aires

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.

Impacto de vacunación de COVID-19 en las infecciones por SARS-COV-2 en personal de salud de la provincia de Buenos Aires / Impact of vaccines against COVID-19 on new SARS-COV2 infections in health care workers of the Province of Buenos Aires

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

Prioritising family members for genotyping in missing person cases: A general approach combining the statistical power of exclusion and inclusion.

Missing person identification typically involves genetic matching of a person of interest against relatives of the missing person. In cases with few available relatives, exhumations or other substantial efforts may be necessary in order to secure adequate statistical power. We propose a simulation approach for solving prioritisation problems arising in such cases. Conditioning on the already typed individuals we estimate the power of each alternative, both to detect the true person, and to exclude false candidates. Graphical summaries of the simulations are given in complementary power plots, facilitating interpretation and decision making. Through a series of examples originating from the well-known Missing grandchildren of Argentina we demonstrate that our method may untangle complex prioritisation problems and other power-related questions. In particular we offer novel insights in recent cases where only children of the potential match are available for testing. We also show that X-chromosomal markers may give high statistical power in missing person identification, but that this requires careful selection of relatives for genotyping. All simulations, power calculations and plots are done with the R package forrel.

RNA Structure Duplication in the Dengue Virus 3' UTR: Redundancy or Host Specificity?

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.

Multiscale approach to the activation and phosphotransfer mechanism of CpxA histidine kinase reveals a tight coupling between conformational and chemical steps.

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.