key: cord-0791309-2fz5e7bw authors: Eisen, Ana Karolina Antunes; Gularte, Juliana Schons; Demoliner, Meriane; de Abreu Goés Pereira, Vyctoria Malayhka; Heldt, Fágner Henrique; Filippi, Micheli; de Almeida, Paula Rodrigues; Hansen, Alana Witt; Fleck, Juliane Deise; Spilki, Fernando Rosado title: Low circulation of Influenza A and coinfection with SARS‐CoV‐2 among other respiratory viruses during the COVID‐19 pandemic in a region of southern Brazil date: 2021-04-08 journal: J Med Virol DOI: 10.1002/jmv.26975 sha: 89491fb03dca7068d0c7f03df9d8fd03917ab4da doc_id: 791309 cord_uid: 2fz5e7bw With the arrival of coronavirus disease 2019 (COVID‐19) in Brazil in February 2020, several preventive measures were taken by the population aiming to avoid severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection including the use of masks, social distancing, and frequent hand washing then, these measures may have contributed to preventing infection also by other respiratory viruses. Our goal was to determine the frequencies of Influenza A and B viruses (FLUAV/FLUBV), human mastadenovirus C (HAdV‐C), Enterovirus 68 (EV‐68), and rhinovirus (RV) besides SARS‐CoV‐2 among hospitalized patients suspect of COVID‐19 with cases of acute respiratory disease syndrome (ARDS) in the period of March to December 2020 and to detect possible coinfections among them. Nucleic acid detection was performed using reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR) in respiratory samples using naso‐oropharyngeal swabs and bronchoalveolar lavage. A total of 418 samples of the 987 analyzed (42.3%) were positive for SARS‐CoV‐2, 16 (1.62%) samples were positive for FLUAV, no sample was positive for FLUBV or EV‐68, 67 (6.78%) samples were positive for HAdV‐C, 55 samples were positive for RV 1/2 (26.3%) and 37 for RV 2/2 (13.6%). Coinfections were also detected, including a triple coinfection with SARS‐CoV‐2, FLUAV, and HAdV‐C. In the present work, a very low frequency of FLUV was reported among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID‐19 and the high influenza vaccination coverage in the region in which this study was performed. By the end of 2019, scientists announced the circulation of a new type of coronavirus in China, which was later officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belonging to the Severe acute respiratory syndrome-related coronavirus species together with the first SARS-CoV. 1 Coronavirus disease 2019 , the disease caused by it, was linked to a seafood market in the city of Wuhan, Hubei province, and since then, the disease quickly spread around the world causing 87.589.206 confirmed cases by January 9th and 1.906.606 deaths. [2] [3] [4] COVID-19 was rapidly declared a pandemic, in about 3 months since its beginning. Regarding being a burden for public health, the present pandemic is only comparable to the Spanish Flu back in 1918, caused by Influenza A virus (FLUAV) H1N1. 5 Respiratory pathogens like viruses, bacteria, and fungi are commonly found infecting the same host simultaneously, in fact, coinfection with several different respiratory viruses is a common finding as well as viral-bacterial coinfection, mainly taking into account that seasonality overlaps in some of them. [6] [7] [8] Among respiratory viruses, FLUAV and Influenza B virus (FLUBV) species are prevalent, as well as Rhinovirus (RV) of Enterovirus genus and Human mastadenovirus C (HAdV-C). [8] [9] [10] [11] [12] The advent of COVID-19 forced the adoption of several nonpharmacological preventive measures aiming to avoid SARS-CoV-2 infection like wearing masks, social distancing, and frequent hand washing. Furthermore, as an attempt to contain COVID-19 and maintain the economy, the state government created a system of "controlled distancing" which has been updated weekly through a system of color-based risk flags that represent a low risk (yellow), medium risk (orange), high risk (red) and very high risk (black). Depending on the flag's color, the measures required for commerce and services establishments are more restricted and some activities may be prohibited. 13 Descriptions of primers and probes with their references can be seen in Table 1 , except for RVs and EV-68 which were not described in the kit of TaqMan® Respiratory Tract Microbiota Profiling Experiments. can be seen in Table 2 and Figure 2 . This past year had several unusual aspects due to the arrival of SARS- HAdV-C also presented a low frequency (6.78%) which was also described in similar studies during 2020 for other respiratory viruses 32 and in the case of RV, it remains present at a considerable rate (~20%) in comparison to the past years, 33 even though being higher than that find by Nowak et al. 32 Notwithstanding, in this study, a smaller number of samples were analyzed for RV. About the distribution of cases over time, in Figure 4 it is possible to evaluate that after a few weeks under the orange flag of the We have detected some viral coinfections including SARS-CoV-2 as presented in Table 2 . SARS-CoV-2 + HAdV-C and SARS-CoV-2 + RV coinfections occurred more often probably due to the greater frequency of these viruses in samples tested, and in spite of low FLUAV frequency, a dual and a triple coinfection with this virus were detected. Viral respiratory coinfections are very common and several studies already In the present work, FLUV was reported in a very low frequency among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID-19 and the high influenza vaccination coverage in 2020. We also demonstrated a relatively normal frequency of RV. Some viral coinfections were detected, including SARS-CoV-2 and FLUAV and a triple coinfection of SARS-CoV-2, FLUAV, and HAdV-C, although it is still not clear if viral coinfection is associated with more severe disease. We would like to thank to Coordenação de Aperfeiçoamento de Naming the A new coronavirus associated with human respiratory disease in China A pneumonia outbreak associated with a new coronavirus of probable bat origin COVID-19 WHO Dashboard Archived: WHO Timeline -COVID-19. 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An observational study examining current published literature including three new unpublished cases Coinfection of SARS-CoV-2 and influenza A virus SARS-CoV-2 and influenza virus co-infection Coinfection with influenza A and COVID-19 The epidemiology and clinical characteristics of co-infection of SARS-CoV-2 and influenza viruses in patients during COVID-19 outbreak Coinfection with SARS-CoV-2 and other respiratory pathogens in patients with COVID-19 in Guangzhou Low circulation of Influenza A and coinfection with SARS-CoV-2 among other respiratory viruses during the COVID-19 pandemic in a region of southern Brazil The authors declare that there are no conflict of interests. The peer review history for this article is available at https://publons. com/publon/10.1002/jmv.26975 The data that support the findings of this study are available from the corresponding author upon reasonable request.