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SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1.

ABSTRACT: Genomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first reported case in each Regional Health Coordination and cases from three epidemic peaks. Ninety SARS-CoV-2 genomes from RS were sequenced and analyzed through comparison with SARS-CoV-2 datasets available in GISAID for phylogenetic inference and mutation analysis. Among the first reported cases, we found the following lineages: B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), evidencing SARS-CoV-2 introduction by both international origin and community-driven transmission. We found predominance of B.1.1.33 (50.0%) and B.1.1.28 (35.0%) during the first epidemic peak (July-August 2020), emergence of P.2 (55.6%) in the second peak (November-December 2020), and massive spread of P.1 and related sequences (78.4%), such as P.1-like-II, P.1.1 and P.1.2 in the third peak (February-April, 2021). Eighteen novel mutation combinations were found among P.1 genomes, and 22 different spike mutations and/or deletions among P.1 and related sequences. This study shows the dispersion of SARS-CoV-2 lineages in Southern Brazil and describes SARS-CoV-2 diversity during three epidemic peaks, highlighting the spread of P.1 and the high genetic diversity of currently circulating lineages. Genomic monitoring of SARS-CoV-2 is essential to guide health authorities' decisions to control COVID-19 in Brazil.

SUBMITTER: Varela APM

PROVIDER: S-EPMC8595253 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Since its advent, the pandemic has caused havoc in multiple waves due partly to amplified transmissibility and immune escape to vaccines. Delhi, India also witnessed brutal multiple peaks causing exponential rise in cases. Here we had retrospectively investigated clade variation, emergence of new lineages and varied clinical characteristics during those three peaks in order to understand the trajectory of the ongoing pandemic. In this study, a total of 123,378 samples were collected for a time span of 14 months (1 June 2020 to 3 August 2021) encompassing three different peaks in Delhi. A subset of 747 samples was processed for sequencing. Complete clinical and demographic details of all the enrolled cases were also collected. We detected 26 lineages across three peaks nonuniformly from 612 quality passed samples. The first peak was driven by diverse early variants, while the second one by B.1.36 and B.1.617.2, unlike third peak caused entirely by B.1.617.2. A total of 18,316 mutations with median of 34 were reported. Majority of mutations were present in less than 1% of samples. Differences in clinical characteristics across three peaks was also reported. To be ahead of the frequently changing course of the ongoing pandemic, it is of utmost importance that novel lineages be tracked continuously. Prioritized sequencing of sudden local outburst and community hot spots must be done to swiftly detect a novel mutation/lineage of potential clinical importance. IMPORTANCE Genome surveillance of the Delhi data provides a more detailed picture of diverse circulating lineages. The added value that the current study provides by clinical details of the patients is of importance. We looked at the shifting patterns of lineages, clinical characteristics and mutation types and mutation load during each successive infection surge in Delhi. The importance of widespread genomic surveillance cannot be stressed enough to timely detect new variants so that appropriate policies can be immediately implemented upon to help control the infection spread. The entire idea of genomic surveillance is to arm us with the clues as to how the novel mutations and/or variants can prove to be more transmissible and/or fatal. In India, the densely populated cities have an added concern of the huge burden that even the milder variants of the virus combined with co-morbidity can have on the community/primary health care centers.

Project description:BackgroundThe explosive epidemics of dengue that have been occurring in various countries have stimulated investigation into new approaches to improve understanding of the problem and to develop new strategies for controlling the disease. The objective of this study was to evaluate the characteristics of diffusion of the first dengue epidemic that occurred in the city of Salvador in 1995.MethodsThe epidemiological charts and records of notified cases of dengue in Salvador in 1995 constituted the source of data. The cases of the disease were georeferenced according to census areas (spatial units) and epidemiological weeks (temporal unit). Kernel density estimation was used to identify the pattern of spatial diffusion using the R-Project computer software program.ResultsOf the 2,006 census areas in the city, 1,400 (70%) registered cases of dengue in 1995 and the spatial distribution of these records revealed that by the end of 1995 practically the entire city had been affected by the virus, with the largest concentration of cases occurring in the western region, composed of census areas with a high population density and predominantly horizontal residences compared to the eastern region of the city, where there is a predominance of vertical residential buildings.ConclusionThe pattern found in this study shows the characteristics of the classic process of spreading by contagion that is common to most infectious diseases. It was possible to identify the epicenter of the epidemic from which centrifugal waves of the disease emanated. Our results suggest that, if a more agile control instrument existed that would be capable of rapidly reducing the vector population within a few days or of raising the group immunity of the population by means of a vaccine, it would theoretically be possible to adopt control actions around the epicenter of the epidemic and consequently reduce the incidence of the disease in the city. This finding emphasizes the need for further research to improve the technology available for the prevention of this disease.

Project description:With syphilis cases on the rise, Brazil declared an epidemic in 2016. To address the consequent public health crisis, the Ministry of Health laid out a rapid response plan, namely, the "Syphilis No!" Project (SNP), a national instrument to fight the disease which encompasses four dimensions: (a) management and governance, (b) surveillance, (c) comprehensive care, and (d) strengthening of educommunication. In the dimension of education, the SNP developed the learning pathway "Syphilis and other Sexually Transmitted Infections (STIs)" to strengthen and promote Health Education. This pathway features 54 Massive Open Online Courses (MOOCs), delivered through the Virtual Learning Environment of the Brazilian Health System (AVASUS). This paper analyzes the impacts of the learning pathway "Syphilis and other STIs" on the response to the epidemic in Brazil, highlighting the educational process of the learning pathway and its social implications from the perspective of the United Nations' 2030 Agenda and its Sustainable Development Goals. Three distinct databases were used to organize the educational data: the learning pathway "Syphilis and other STIs" from AVASUS, the National Registry of HealthCare Facilities from the Brazilian Ministry of Health (MoH), and the Brazilian Occupation Classification, from the Ministry of Labor. The analysis provides a comprehensive description of the 54 courses of the learning pathway, which has 177,732 enrollments and 93,617 participants from all Brazilian regions, especially the Southeast, which accounts for the highest number of enrollees. Additionally, it is worth noting that students living abroad also enrolled in the courses. Data characterization provided a demographic study focused on the course participants' profession and level of care practiced, revealing that the majority (85%) worked in primary and secondary healthcare. These practitioners are the target audience of the learning pathway and, accordingly, are part of the personnel directly engaged in healthcare services that fight the syphilis epidemic in Brazil.

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SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1.

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