Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil.

The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.

Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil.

The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly Δ144 or Δ141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we did not find an increased incidence of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sublineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting more infectious variants or antibody evasion mutations is expected to increase. IMPORTANCE The continuous evolution of SARS-CoV-2 is an expected phenomenon that will continue to happen due to the high number of cases worldwide. The present study analyzed how a Variant of Concern (VOC) could still circulate in a population hardly affected by two COVID-19 waves and with vaccination in progress. Our results showed that the answer behind that was a new generation of Gamma-like viruses, which emerged locally carrying mutations that made it more transmissible and more capable of spreading, partially evading prior immunity triggered by natural infections or vaccines. With thousands of new cases daily, the current pandemics scenario suggests that SARS-CoV-2 will continue to evolve and efforts to reduce the number of infected subjects, including global equitable access to COVID-19 vaccines, are mandatory. Thus, until the end of pandemics, the SARS-CoV-2 genomic surveillance will be an essential tool to better understand the drivers of the viral evolutionary process.

Intra-urban differences in rates of admissions for ambulatory care sensitive conditions in Brazil's Center-West region. / Desigualdades intraurbanas de taxas de internações por condições sensíveis à atenção primária na região central do Brasil.

Admissions for ambulatory care sensitive conditions (ACSCs) represent a useful indicator of assess to and the effectiveness of primary health care. This article examined rates of admissions for ACSCs and the main causes of admissions in intra-urban areas of the municipality of Goiânia, capital of the State of Goiás. An ecological study was conducted to determine rates of admissions in Goiânia's seven health districts between 2008 and 2013 using data from Hospital Admission Authorization forms obtained from the municipality's Hospital Information System. Admissions were georeferenced throughout the seven health districts. Age-adjusted rates of admissions for ACSCs were calculated and the most common causes of admissions were identified for each age group. A 95% confidence interval was calculated as a measure of precision of the rates. The average overall rate of admissions for ACSCs was 155.5 per 10,000 population. Rates were highest in the Southern District and lowest in the Southwest District. Rates were highest in the youngest and oldest age groups. The Northwest District showed the highest rates in nine groups of causes, notably chronic non-communicable diseases among adults. Our findings showed that there are major differences in rates across health districts, pointing to shortfalls in primary health coverage, quality problems and an inadequate care model in districts with high coverage.

Desigualdades intraurbanas de taxas de internações por condições sensíveis à atenção primária na região central do Brasil / Intra-urban differences in rates of admissions for ambulatory care sensitive conditions in Brazil´s Center-West region

Resumo Internações por condições sensíveis à atenção primária (ICSAP) é um indicador útil para avaliar efetividade da atenção primária (APS). Este artigo avaliou as taxas de ICSAP e as causas nas áreas intraurbanas do município de Goiânia-Goiás. Estudo ecológico das taxas de ICSAP nos Distritos Sanitários (DS) de Goiânia, de 2008 a 2013. Utilizou-se dados das Autorizações de Internação Hospitalar (AIH) do SIH municipal, georreferenciadas nos 07 DS. Calculou-se taxas padronizadas de ICSAP por DS, e grupos de causas e faixa etária com respectivos Intervalos de Confiança de 95%. A taxa média de ICSAP foi de 155,5 por 10.000 habitantes. O Distrito Sul teve a maior taxa e o Sudoeste a menor. O grupo de Gastroenterites apresentou a maior taxa e o grupo Anemia a menor. As faixas etárias de 0 a 9 anos e idosos tiveram as taxas mais elevadas. No Distrito Noroeste houve maiores taxas em 09 grupos de causas, destaque para as Doenças Crônicas não Transmissíveis na faixa etária adulta. Os resultados possibilitaram identificar as desigualdades nas taxas de ICSAP entre os DS, apontou deficiências de cobertura de APS, problemas de qualidade e insuficiência do modelo assistencial em regiões com alta cobertura.

Abstract Admissions for ambulatory care sensitive conditions (ACSCs) represent a useful indicator of assess to and the effectiveness of primary health care. This article examined rates of admissions for ACSCs and the main causes of admissions in intra-urban areas of the municipality of Goiânia, capital of the State of Goiás. An ecological study was conducted to determine rates of admissions in Goiânia’s seven health districts between 2008 and 2013 using data from Hospital Admission Authorization forms obtained from the municipality’s Hospital Information System. Admissions were georeferenced throughout the seven health districts. Age-adjusted rates of admissions for ACSCs were calculated and the most common causes of admissions were identified for each age group. A 95% confidence interval was calculated as a measure of precision of the rates. The average overall rate of admissions for ACSCs was 155.5 per 10,000 population. Rates were highest in the Southern District and lowest in the Southwest District. Rates were highest in the youngest and oldest age groups. The Northwest District showed the highest rates in nine groups of causes, notably chronic non-communicable diseases among adults. Our findings showed that there are major differences in rates across health districts, pointing to shortfalls in primary health coverage, quality problems and an inadequate care model in districts with high coverage.

Caracterização dos casos suspeitos de dengue internados na capital do estado de Goiás em 2013: período de grande epidemia / Characteristics of suspected dengue patients admitted to hospital in Goiás state capital in 2013: a period of severe outbreak / Caracterización de los casos sospechosos de dengue hospitalizados en la capital de Goiás en 2013: período de gran epidemia

OBJETIVO: descrever o perfil clínico-epidemiológico e a distribuição espacial dos casos suspeitos de dengue com hospitalização em Goiânia-GO, Brasil, durante a epidemia de 2013. MÉTODOS: estudo descritivo sobre dados do Sistema de Informação de Agravos de Notificação, Sistema Gerenciador de Ambiente Laboratorial, Sistema de Regulação de Leitos, e do Sistema da Companhia de Processamento de Dados de Goiânia. RESULTADOS: foram incluídos 616 casos suspeitos de dengue com idade média de 36 anos (desvio-padrão: 14,8), 55,2% do sexo feminino, 9,3% confirmados laboratorialmente e 9,7% apresentando comorbidades; a comorbidade mais frequente foi hipertensão arterial (20%); os sinais de alarme mais frequentes foram vômitos persistentes (23,7%) e plaquetopenia (22,7%); verificou-se positividade dos resultados laboratoriais inclusive nas coletas inoportunas, após cinco dias do inicio dos sintomas, e grande dispersão na distribuição espacial dos casos. CONCLUSÃO: entre os casos suspeitos de dengue internados, predominaram adultos e com presença de sinais e sintomas de alarme.

OBJECTIVE: to describe the clinical and epidemiological features and the spatial distribution of suspected dengue cases admitted to hospital in Goiânia, state of Goiás, during the 2013 epidemic. METHODS: this was a descriptive study of suspected dengue cases admitted to hospital in Goiânia based on four databases. RESULTS: 616 suspected dengue cases were included in the study; patients' mean age was 36 years (SD: 14.8), 55.2% were female, 9.3% were laboratory confirmed and 9.7% had comorbidities; the most common comorbidity was hypertension (20%); the most common warning signs were persistent vomiting (23.7%) and thrombocytopenia (22.7%); laboratory results were positive including for late sample collections taken five days after the onset of symptoms. There was great dispersion in the spatial distribution of cases. CONCLUSION: the majority of suspected dengue cases admitted to hospital were adults who had warning signs and symptoms.

OBJETIVO: describir el perfil clínico-epidemiológico y la distribución espacial de los casos sospechosos de dengue con hospitalización en Goiania-GO, durante la epidemia de 2013. MÉTODOS: estudio descriptivo basado en datos del "Sistema de información de Enfermedades de Declaración Obligatoria", "Sistema de gestión ambiental y laboratorio", "Sistema de regulación de camas" y "Sistema de la compañía de procesamiento de datos de Goiana". RESULTADOS: se incluyeron 616 casos sospechosos de dengue; la media de edad fue de 36 años (Desviación Estándar: 14,8), el 55,2% eran mujeres, 9,3% fueron confirmados en laboratorio y 9,7% presentaron comorbilidades; la comorbilidad más frecuente fue hipertensión arterial (20%). Las señales de alarma más frecuentes fueron vómitos persistentes (23,7%) y trombocitopenia (22,7%); hubo resultados positivos de laboratorio inclusive en las colectas inadvertidas, después de cinco días del inicio de los síntomas y hubo gran variación en la distribución espacial de los casos. CONCLUSIÓN: entre los casos sospechosos de dengue internados, predominaron los adultos y la presencia de signos y síntomas de alarma.