Low prevalence of influenza A strains with resistance markers in Brazil during 2017-2019 seasons.

The influenza A virus (IAV) is of a major public health concern as it causes annual epidemics and has the potential to cause pandemics. At present, the neuraminidase inhibitors (NAIs) are the most widely used anti-influenza drugs, but, more recently, the drug baloxavir marboxil (BXM), a polymerase inhibitor, has also been licensed in some countries. Mutations in the viral genes that encode the antiviral targets can lead to treatment resistance. Worldwide, a low prevalence of antiviral resistant strains has been reported. Despite that, this situation can change rapidly, and resistant strain surveillance is a priority. Thus, the aim of this was to evaluate Brazilian IAVs antiviral resistance from 2017 to 2019 through the identification of viral mutations associated with reduced inhibition of the drugs and by testing the susceptibility of IAV isolates to oseltamivir (OST), the most widely used NAI drug in the country. Initially, we analyzed 282 influenza A(H1N1)pdm09 and 455 A(H3N2) genetic sequences available on GISAID. The amino acid substitution (AAS) NA:S247N was detected in one A(H1N1)pdm09 strain. We also identified NA:I222V (n = 6) and NA:N329K (n = 1) in A(H3N2) strains. In addition, we performed a molecular screening for NA:H275Y in 437 A(H1N1)pdm09 samples, by pyrosequencing, which revealed a single virus harboring this mutation. Furthermore, the determination of OST IC50 values for 222 A(H1N1)pdm09 and 83 A(H3N2) isolates revealed that all isolates presented a normal susceptibility profile to the drug. Interestingly, we detected one A(H3N2) virus presenting with PA:E119D AAS. Moreover, the majority of the IAV sequences had the M2:S31N adamantanes resistant marker. In conclusion, we show a low prevalence of Brazilian IAV strains with NAI resistance markers, in accordance with what is reported worldwide, indicating that NAIs still remain an option for the treatment of influenza infections in Brazil. However, surveillance of influenza resistance should be strengthened in the country for improving the representativeness of investigated viruses and the robustness of the analysis.

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.

Importation and early local transmission of COVID-19 in Brazil, 2020.

We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil.

Genetic evolution of influenza viruses among selected countries in Latin America, 2017-2018.

OBJECTIVE: Since the 2009 influenza pandemic, Latin American (LA) countries have strengthened their influenza surveillance systems. We analyzed influenza genetic sequence data from the 2017 through 2018 Southern Hemisphere (SH) influenza season from selected LA countries, to map the availability of influenza genetic sequence data from, and to describe, the 2017 through 2018 SH influenza seasons in LA. METHODS: We analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers (NICs) in ten countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Ecuador, Mexico, Paraguay, Peru and Uruguay) with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018. These sequences were generated by the NIC or the WHO Collaborating Center (CC) at the U.S Centers for Disease Control and Prevention, uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform, and used for phylogenetic reconstruction. FINDINGS: Influenza hemagglutinin sequences from the participating countries (A/H1pdm09 n = 326, A/H3 n = 636, B n = 433) were highly concordant with the genetic groups of the influenza vaccine-recommended viruses for influenza A/H1pdm09 and influenza B. For influenza A/H3, the concordance was variable. CONCLUSIONS: Considering the constant evolution of influenza viruses, high-quality surveillance data-specifically genetic sequence data, are important to allow public health decision makers to make informed decisions about prevention and control strategies, such as influenza vaccine composition. Countries that conduct influenza genetic sequencing for surveillance in LA should continue to work with the WHO CCs to produce high-quality genetic sequence data and upload those sequences to open-access databases.

Importation and early local transmission of COVID-19 in Brazil, 2020

We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil. (AU)

Caracterização genética da hemaglutinina (HA) dos vírus da influenza tipos A e B, nas regiões de abrangência do Instituto Adolfo Lutz, no período de 2013-2015 / Genetic characterization of hemagglutinin (HA) of influenza virus types A and B, in the regions covered by the Adolfo Lutz Institute, in the period of 2013-2015

A constante evolução do vírus da Influenza requer o monitoramento global contínuo e a reformulação frequente das vacinas. O presente estudo analisou a dinâmica genética da hemaglutinina (HA) dos vírus da Influenza do tipo A, subtipos H1 e H3, e do tipo B, linhagens Yamagata e Victoria, através de sua caracterização pelo sequenciamento de Sanger e pela análise filogenética, realizados no período de 2013 a 2015, nos estados de abrangência do Instituto Adolfo Lutz (IAL) (São Paulo, Goiás, Mato Grosso, Mato Grosso do Sul, Distrito Federal, Piauí, Rondônia e Tocantins). Os resultados encontrados mostraram que na análise do segmento 4 do genoma viral, que codifica a HA, foram identificadas mutações em sítios antigênicos nos subtipos H1 e H3 dos vírus da Influenza A e nas linhagens Yamagata e Victoria dos vírus da Influenza B, com consequentes alterações das estirpes vacinais. Os vírus da Influenza A(H1N1)pdm09 foram incluídos no grupo genético 6B e permaneceram similares à estirpe da vacina A/California/7/2009, quando caracterizados antigenicamente com antissoro de furão, desde o ano de 2013...(AU)

Molecular epidemiology of influenza A(H1N1)PDM09 hemagglutinin gene circulating in São Paulo State , Brazil: 2016 anticipated influenza season.

Compared to previous years, seasonal influenza activity commenced early in São Paulo State, Brazil, Southern hemisphere during the 2016 year. In order to investigate the genetic pattern of influenza A(H1N1)pdm09 in the State of Sao Paulo a total of 479 respiratory samples, collected in January by Sentinel Surveillance Units, were screened by real-time RT-PCR. A total of 6 Influenza viruses A(H1N1)pdm09 presenting ct values ≤ 30 were sequenced following phylogenetic analysis. The present study identified the circulation of the new 6B.1 subgroup (A/Sao Paulo/10-118/2016 and A/Sao Paulo/3032/2016). In addition, influenza A(H1N1)pdm09 group 6B has also been identified during January in the State of Sao Paulo. Despite amino acid changes and changes in potential glycosylation motifs, 6B.1 viruses were well inhibited by the reference ferret antiserum against A/California/07/2009 virus, the A(H1N1)pdm09 component of the vaccine for the 2016 influenza season.

Mumps virus genotypes identified during disease outbreaks in the state of São Paulo, Brazil: 2011 – 2016 / Genótipos dos vírus da caxumba identificados durante surtos da doença no estado de São Paulo, Brasil: 2011 - 2016

In São Paulo the mumps virus (MuV) outbreaks have been increasing from 2011 to nowadays. MuV epidemiological surveillance has been improving by using the polymerase chain reaction in real time (rRT-PCR) in addition to the specific IgM antibody (IgM-Ab) detection; in some cases, genome sequencing studies were performed. Increased virus transmission and recent outbreaks have raised interest on MuV genotyping, as a means to understand the transmission pathways and to identify the vaccine-associated cases. From January 2011 to August 2016, MuV infection was analyzed at Institute Adolfo Lutz. A total of 232 (77.33 %) throat wash samples showed positivity to mumps genome, and 68 (22.66 %) were negative when analyzed by rRT-PCR. Among 15 samples for molecular analysis, 10 serum samples from respective patients were also available for detecting anti-MuV IgM-Ab; and from these, four (40%) samples were seropositive. Vaccination status was available only for patients from Cedral and Araraquara. Phylogenetic analysis revealed the circulation of the following mumps virus genotypes in the investigated periods: 2011(M), 2012, and 2013 (K); 2014 (N); 2015 (G, K, and N); 2016 (G). Knowledge on MuV molecular epidemiology in São Paulo-Brazil could contribute to the surveillance and epidemiological program in Brazil, and globally as well.

No estado de São Paulo têm ocorrido surtos de caxumba desde 2011. O diagnóstico laboratorial tem sido realizado no Instituto Adolfo Lutz utilizando-se a técnica de identificação de material genético viral por meio de reação de cadeia de polimerase-em tempo real (rRT-PCR) e pela detecção de anticorpos IgM (Ac-IgM) específicos circulantes. Os recentes surtos de caxumba têm aumentado o interesse em investigar os genótipos dos vírus prevalentes para identificar os casos associadas à vacina. De janeiro de 2011 a agosto de 2016, 300 amostras de lavados da orofaringe coletadas de pacientes suspeitos de infecção foram analisadas. O material genético viral específico foi detectado em 232 (77,33 %) amostras e 68 (22,66 %) foram negativas. Das 10 amostras analisadas pelo teste sorológico, quatro (40 %) demonstraram positividade para Ac-IgM específicos anti-vírus da caxumba e seis foram negativas. Somente os municípios Cedral e Araraquara forneceram os dados referentes à vacinação. Análise filogenética mostrou a circulação dos seguintes genótipos do vírus da caxumba no período investigado: 2011 (M), 2012 e 2013 (K); 2014 (N); 2015 (GKN); 2016 (G). A vigilância virológica é mundialmente imprescindível, para identificar a diversidade e a distribuição dos diferentes genótipos, com vistas à composição de vacinas específicas.

Mumps virus genotypes identified during disease outbreaks in the state of São Paulo, Brazil: 2011-2016 / Genótipos dos vírus da caxumba identificados durantesurtos da doença no estado de São Paulo, Brasil: 2011 - 2016

In São Paulo the mumps virus (MuV) outbreaks have been increasing from In São Paulo the mumps virus (MuV) outbreaks have been increasing from 2011 to nowadays. MuV epidemiological surveillance has been improving by using the polymerase chain reaction in real time (rRT-PCR) in addition to the specific IgM antibody (IgM-Ab) detection; in some cases,genome sequencing studies were performed. Increased virus transmission and recent outbreakshave raised interest on MuV genotyping, as a means to understand the transmission pathways andto identify the vaccine-associated cases. From January 2011 to August 2016, MuV infection was analyzed at Institute Adolfo Lutz. A total of 232 (77.33 %) throat wash samples showed positivity to mumps genome, and 68 (22.66 %) were negative when analyzed by rRT-PCR. Among 15 samples for molecular analysis, 10 serum samples from respective patients were also available for detecting anti-MuV IgM-Ab; and from these, four (40%) samples were seropositive. Vaccination statuswas available only for patients from Cedral and Araraquara. Phylogenetic analysis revealed the circulation of the following mumps virus genotypes in the investigated periods: 2011(M), 2012, and 2013 (K); 2014 (N); 2015 (G, K, and N); 2016 (G). Knowledge on MuV molecular epidemiology in São Paulo-Brazil could contribute to the surveillance and epidemiological program in Brazil, and globally as well.

No estado de São Paulo têm ocorrido surtos de caxumba desde 2011. O diagnóstico laboratorialtem sido realizado no Instituto Adolfo Lutz utilizando-se a técnica de identificação de material genético viral por meio de reação de cadeia de polimerase-em tempo real (rRT-PCR) e peladetecção de anticorpos IgM (Ac-IgM) específicos circulantes. Os recentes surtos de caxumbatêm aumentado o interesse em investigar os genótipos dos vírus prevalentes para identificaros casos associadas à vacina. De janeiro de 2011 a agosto de 2016, 300 amostras de lavadosda orofaringe coletadas de pacientes suspeitos de infecção foram analisadas. O material genéticoviral específico foi detectado em 232 (77,33 %) amostras e 68 (22,66 %) foram negativas.Das 10 amostras analisadas pelo teste sorológico, quatro (40 %) demonstraram positividadepara Ac-IgM específicos anti-vírus da caxumba e seis foram negativas. Somente os municípios Cedral e Araraquara forneceram os dados referentes à vacinação. Análise filogenética mostroua circulação dos seguintes genótipos do vírus da caxumba no período investigado: 2011 (M),2012 e 2013 (K); 2014 (N); 2015 (GKN); 2016 (G). A vigilância virológica é mundialmente imprescindível, para identificar a diversidade e a distribuição dos diferentes genótipos, com vistasà composição de vacinas específicas.