Emergence and evolution of SARS-CoV-2 genetic variants during the Cuban epidemic.

The SARS CoV-2 D614G variant circulated in Cuba in 2020. New viral variants were detected after the opening of the border in November 2020. We show the results of the genomic surveillance in Cuba from December 28, 2020, to September 28, 2021 and their relationship to the epidemiological situation in the country. A total of 1,406 nasopharyngeal exudates from COVID-19 patients were processed for RNA extraction and the 1836 bp fragment of the spike gene was amplified and sequenced. The mutations present were determined using the GISAID database. Prevalence ratios were estimated by fitting Poisson univariate and multivariate regression models to investigate associations between SARS-CoV-2 variant group (VOC, non-VOC) and disease outcome. Seventeen genetic variants were detected including VOC Alpha, Beta, Gamma and Delta, one variant of interest (VOI) (Lambda) and two previous VOI (A.2.5.1 and Zeta/P.2). Beta (34.77%), Delta (24.89%) and D614G (19%) variants were the most frequently detected. By June, Delta increased in frequency, displacing Beta. Disease severity increased significantly with age and VOC (PR =1.98, IC 95%: 1.33-3.05, p <0.05). Genomic surveillance allowed us to identify the upsurge of novel variants. Coinciding with the higher epidemic period, multiple variants were co-circulating. Although we cannot rule out that failure in the transmission containment measures occurred, the increase in the number of cases associated with the circulation of several variants, particularly the Beta and Delta variants is highly suggestive. A greater association of Beta variant with clinical severity and Delta variant with a greater transmissibility was observed.

Correction: Cuban history of CRF19 recombinant subtype of HIV-1.

[This corrects the article DOI: 10.1371/journal.ppat.1009786.].

Arquitectura de información para la gestión de colaboración al ciudadano en salud en las áreas del municipio Pinar del Río / Information Architecture for the management of collaborative information to the Citizen on health care issues in the areas of Pinar del Río municipality

RESUMEN Introducción: las Tecnologías de la Información y las Comunicaciones actualmente son elementos fundamentales para la superación y desarrollo de un país. Por otra parte, Cuba ha identificado desde muy temprano la necesidad de introducir en la práctica social las Tecnologías de la Información y las Comunicaciones y lograr una cultura digital como una de las características imprescindibles del hombre nuevo. Cuba avanza hacia el Gobierno electrónico, a través de la alfabetización digital e informacional en los procesos decisivos, con canales que permitan aumentar la participación ciudadana. Objetivo: desarrollar la Arquitectura de Información para la Colaboración al Ciudadano en materia de Salud en las áreas del municipio Pinar del Río. Métodos: se realiza una investigación de Innovación Tecnológica sobre la gestión de la información en las áreas de salud del municipio objeto de estudio según la metodología de desarrollo de software para Programación Extrema, y con la aplicación de métodos teóricos y empíricos para el análisis, revisión y modelación de los procesos objetos de informatización. Resultados: se constató que la propuesta informática está basada en gestionar la información de los diferentes servicios médicos, como herramienta para ayudar a organizar el sistema y proporcionarle más eficiencia. Conclusión: se elaboró un prototipo informático que evitará el cumulo de personal que acude a las instituciones en busca de respuesta a preguntas dirigidas al conocimiento u orientación para una problemática determinada, en función de la proyección comunitaria.

ABSTRACT Introduction: Information Technologies are currently essential elements for the improvement and development of a country, on the other hand, Cuba has identified from very early on the need to introduce Information and Communication Technologies in social practice and achieve a digital- technology culture as one of the crucial characteristics of the new man. Cuba is moving towards electronic-government, achieving digital technology and information literacy in the decisive processes, creating channels to increase citizen participation. How to contribute to the management of collaborative information to the citizen on health care issues in the areas of Pinar del Río municipality? Objective: to develop the Information Architecture for the Citizen Collaboration in the health care issues in the areas of Pinar del Río municipality. Methods: a Technological Innovation Research on information management in the health care areas of the municipality under study is carried out following the methodology of software development for Extreme Programming, and applying theoretical and empirical methods for the analysis, review and modeling of the processes under computerization. Results: it was found that the proposal of information technology is based on managing the information of the different medical services, serving as a tool to help to the organization of the healthcare system and make it more efficient. Conclusion: a computerized prototype was created that will avoid the gathering of people who come to the institutions in search of answers to questions directed to knowledge or orientation for a determined problematic on purpose of the community projection.

Cuban history of CRF19 recombinant subtype of HIV-1.

CRF19 is a recombinant form of HIV-1 subtypes D, A1 and G, which was first sampled in Cuba in 1999, but was already present there in 1980s. CRF19 was reported almost uniquely in Cuba, where it accounts for ∼25% of new HIV-positive patients and causes rapid progression to AIDS (∼3 years). We analyzed a large data set comprising ∼350 pol and env sequences sampled in Cuba over the last 15 years and ∼350 from Los Alamos database. This data set contained both CRF19 (∼315), and A1, D and G sequences. We performed and combined analyses for the three A1, G and D regions, using fast maximum likelihood approaches, including: (1) phylogeny reconstruction, (2) spatio-temporal analysis of the virus spread, and ancestral character reconstruction for (3) transmission mode and (4) drug resistance mutations (DRMs). We verified these results with a Bayesian approach. This allowed us to acquire new insights on the CRF19 origin and transmission patterns. We showed that CRF19 recombined between 1966 and 1977, most likely in Cuban community stationed in Congo region. We further investigated CRF19 spread on the Cuban province level, and discovered that the epidemic started in 1970s, most probably in Villa Clara, that it was at first carried by heterosexual transmissions, and then quickly spread in the 1980s within the "men having sex with men" (MSM) community, with multiple transmissions back to heterosexuals. The analysis of the transmission patterns of common DRMs found very few resistance transmission clusters. Our results show a very early introduction of CRF19 in Cuba, which could explain its local epidemiological success. Ignited by a major founder event, the epidemic then followed a similar pattern as other subtypes and CRFs in Cuba. The reason for the short time to AIDS remains to be understood and requires specific surveillance, in Cuba and elsewhere.

Decay of Sabin inactivated poliovirus vaccine (IPV)-boosted poliovirus antibodies.

INTRODUCTION: We conducted a follow-on study to a phase I randomized, controlled trial conducted in Cuba, 2012, to assess the persistence of poliovirus antibodies at 21-22 months following booster dose of Sabin-IPV compared to Salk-IPV in adults who had received multiple doses of oral poliovirus vaccine (OPV) during childhood. METHODS: In 2012, 60 healthy adult males aged 19-23 were randomized to receive one booster dose, of either Sabin-inactivated poliovirus vaccine (Sabin-IPV), adjuvanted Sabin-IPV (aSabin-IPV), or conventional Salk-IPV. In the original study, blood was collected at days 0 (before) and 28 (after vaccination), respectively. In this study, an additional blood sample was collected 21-22 months after vaccination, and tested for neutralizing antibodies to Sabin poliovirus types 1, 2 and 3. RESULTS: We collected sera from 59/60 (98.3%) subjects; 59/59 (100%) remained seropositive to all poliovirus types, 21-22 months after vaccination. The decay curves were very similar among the study groups. Between day 28 and 21-22 months, there was a reduction of ⩾87.4% in median antibody levels for all poliovirus types in all study groups, with no significant differences between the study groups. CONCLUSION: The decay of poliovirus antibodies over a 21-22-month period was similar regardless of the type of booster vaccine used, suggesting the scientific data of Salk IPV long-term persistence and decay may be broadly applicable to Sabin IPV.

Reactogenicity and immunogenicity of inactivated poliovirus vaccine produced from Sabin strains: a phase I Trial in healthy adults in Cuba.

BACKGROUND: To ensure that developing countries have the option to produce inactivated poliovirus vaccine (IPV), the Global Polio Eradication Initiative has promoted the development of an IPV using Sabin poliovirus strains (Sabin IPV). This trial assessed the reactogenicity and immunogenicity of Sabin IPV and adjuvanted Sabin IPV in healthy adults in Cuba. METHODS: This is a randomized, controlled phase I trial, enrolling 60 healthy (previously vaccinated) male human volunteers, aged 19-23 years to receive one dose of either Sabin IPV (20:32:64 DU/dose), adjuvanted Sabin IPV (10:16:32 DU/dose), or conventional Salk IPV (40:8:32 DU/dose). The primary endpoint for reactogenicity relied on monitoring of adverse events. The secondary endpoint measured boosting immune responses (i.e. seroconversion or 4-fold rise) of poliovirus antibody, assessed by neutralization assays. RESULTS: Sixty subjects fulfilled the study requirements. No serious adverse events reported were attributed to trial interventions during the 6-month follow-up period. Twenty-eight days after vaccination, boosting immune responses against poliovirus types 1-3 were between 90% and 100% in all vaccination groups. There was a more than 6-fold increase in median antibody titers between pre- and post-vaccination titers in all vaccination groups. DISCUSSION: Both Sabin IPV and adjuvanted Sabin IPV were well tolerated and immunogenic against all poliovirus serotypes. This result suggests that the aluminum adjuvant may allow a 50% (or higher) dose reduction.

Coxsackievirus A6 and enterovirus 71 causing hand, foot and mouth disease in Cuba, 2011-2013.

Hand, foot and mouth disease (HFMD) is usually caused by coxsackievirus A16 or enterovirus 71 (EV71). Between 2011 and 2013, HFMD cases were reported from different Cuban provinces. A total of 42 clinical specimens were obtained from 23 patients. Detection, identification and phylogenetic analysis of enterovirus-associated HFMD were carried out by virus isolation, specific enterovirus PCR and partial VP1 sequences. HEV was detected in 11 HFMD cases. Emerging genetic variants of coxsackievirus A6 and EV71 were identified as the causative agents of the Cuban HFMD cases.