Typical epidemiology of respiratory virus infections in a Brazilian slum

Abstract

Host population size, density, immune status, age structure, and contact rates are critical elements of virus epidemiology. Slum populations stand out from other settings and may present differences in the epidemiology of acute viral infections. We collected nasopharyngeal specimens from 282 children aged ≤5 years with acute respiratory tract infection (ARI) during 2005 to 2006 in one of the largest Brazilian slums. We conducted real-time reverse transcription-polymerase chain reaction (RT-PCR) for 16 respiratory viruses, nested RT-PCR-based typing of rhinoviruses (HRVs), and collected clinical symptoms. Viruses were common causes of respiratory disease;with ≥1 virus being detected in 65.2% of patients. We detected 15 different viruses during 1 year with a predominance of HRV (33.0%) and human respiratory syncytial virus (hRSV, 12.1%) infections, and a high rate of viral coinfections (28.3%). We observed seasonality of hRSV, HRV and human coronavirus infections, more severe symptoms in hRSV and influenza virus (FLU) infections and prolonged circulation of seven HRV clusters likely representing distinct serotypes according to genomic sequence distances. Potentially unusual findings included the absence of human metapneumovirus detections and lack of typical FLU seasonal patterns, which may be linked to the population size and density of the slum. Nonetheless, most epidemiological patterns were similar to other studies globally, suggesting surprising similarities of virus-associated ARI across highly diverse settings and a complex impact of population characteristics on respiratory virus epidemiology. K E Y W O R D S acute respiratory infection, Brazil, epidemiology, real-time polymerase chain reaction, respiratory tract infections, slum, viruses ---

Potential impact of seasonal forcing on a SARS-CoV-2 pandemic

“…As a result, many respiratory viruses show clear seasonal variation in prevalence; the most well-known example being seasonal influenza which peaks every winter in the temperate zone of the Northern Hemisphere [14]. A similar pattern is seen for the four seasonal human coronaviruses: HKU1, NL63, OC43 and 229E (hereafter collectively referred to as "seasonal CoVs") [15][16][17][18][19][20]. These viruses cause respiratory infections which usually are mild and primarily affect young children.…”

The virus and socioeconomic inequality: An agent-based model to simulate and assess the impact of interventions to reduce the spread of COVID-19 in Rio de Janeiro, Brazil

“…Several works have demonstrated the importance in consider the slums and its specific life conditions to understand the spread and control of epidemics scenarios, such as for Influenza [Adiga et al 2018, Verma et al 2018 and Ebola [Long et al 2018]. In the same way, other studies pointed out to the impact of the population's characteristics on respiratory diseases like influenza, tuberculosis and also human coronaviruses (HCoV) in Brazilian favelas [Góes et al 2019, Pereira et al 2015. However, despite the great number of works being published about COVID-19 in the last weeks, to the best of our knowledge, at this moment, there is no work considering using agent-based modeling to simulate the COVID-19 spread in the contexts of the slums in other countries nor in the Brazilian favelas.…”

“…The favelas are human settlement areas that combine the lack of sanitation and water, compounded by insufficient living space for families, which means more than three people sharing the same room 2 . Virus transmission may be facilitated in these dense populations, characterized by frequent inter-individual contact, crowded housing, improper sanitation systems, poor education, and poor nutritional status [Góes et al 2019]. Furthermore, in this period, most of Brazilian states faces a high incidence of Severe Acute Respiratory Infection (SARI), compared to the same period in previous years [da Saúde 2020] 3 .…”

SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network

“…In Brazil, the four endemic CoVs circulate annually 6 - 11 and the first case of coronavirus disease 2019 (COVID-19) was reported on February 26, 2020 (https://covid.saude.gov.br) when SARS-CoV-2 was detected in a 61-year-old male traveller from Lombardia region, Italy, that returned to the São Paulo city, Brazil. Until the first reported case in Brazil, also the first in South American region, 12 there were 81,109 confirmed COVID-19 cases in 38 countries.…”