SUMMARY OBJECTIVE: Genome sequencing has been proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by severe acute respiratory syndrome coronavirus 2, i.e., coronavirus disease 2019. Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern. To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different variants of concern in these cases. METHODS: Nasopharyngeal swabs from infected (symptomatic and asymptomatic), vaccinated or unvaccinated individuals (n=29), and quantitative reverse transcription polymerase chain reaction cycle threshold value (Ct values) of ≤30 were subjected to viral sequencing using nanopore technology. RESULTS: Our analysis revealed that the Omicron variant was found in 99% of cases and the Delta variant was found in only one case. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of variants of concern not neutralized by the currently available vaccines. CONCLUSION: It is important to acknowledge the limitations of these vaccines and to develop new vaccines to emergent variants of concern, as is the case of influenza vaccine; going through new doses of the same coronavirus vaccines is “more of the same.” OBJECTIVE 2 ie i e i.e. 2019 Salvador Bahia Brazil METHODS symptomatic asymptomatic, asymptomatic , asymptomatic) n=29, n29 n n=29 29 (n=29) Ct values 30 ≤3 technology RESULTS 99 Infected prognosis however community CONCLUSION vaccine more same. i.e 201 n2 n=2 (n=29 3 ≤ 9 20 n= (n=2 (n= (n

ABSTRACT The outbreak of the new coronavirus (SARS-CoV-2) causing the coronavirus disease (COVID-19) has spread globally. As of June 18, 2020, a high maternal mortality rate due to SARS-CoV-2 infections was identified in Brazil, representing most of the world cases at that time. An observational, cross-sectional study was performed with pregnant women admitted in two maternity hospitals located in Salvador/Bahia and their newborns, from May 24th up to July 17th of 2020. Among 329 pregnant women enrolled at hospital admission, a high prevalence (n=28; 8.5%) of pregnant women with COVID-19 was observed, as well as a high proportion of asymptomatic cases (n=19; 67.9%). Two newborns had detectable SARS-CoV-2 but evolved without abnormalities. This data highlight the importance of identifying pregnant women with COVID-19 for proper isolation measures to prevent in-hospital transmission.

Abstract Several major epidemics of Zika fever, caused by the ZIKA virus (ZIKV), have emerged in Brazil since early 2015, eventually spreading to other countries on the South American continent. The present study describes the clinical manifestations and laboratory findings of patients with confirmed acute ZIKV infection during the first epidemic that occurred in Salvador, Brazil. All included patients were seen at the emergency room of a private tertiary hospital located in Salvador, Brazil from 2015 through 2017. Patients were considered eligible if signs of systemic viral febrile disease were present. All individuals were tested for ZIKV and Chikungunya infection using PCR, while rapid test was used to detect Dengue virus antibodies or, alternatively, the NS1 antigen. A diagnosis of acute ZIKV infection was confirmed in 78/434 (18%) individuals with systemic viral febrile illness. Positivity was mainly observed in blood, followed by saliva and urine. Coinfection with Chikungunya and/or Dengue virus was detected in 5% of the ZIKV-infected patients. The most frequent clinical findings were myalgia, arthralgia and low-grade fever. Laboratory analysis demonstrated normal levels of hematocrit, platelets and liver enzymes. In summary, in acute settings where molecular testing remains unavailable, clinicians face difficulties to confirm the diagnosis of ZIKV infection, as they rely only on clinical examinations and conventional laboratory tests.

Herein, we describe the detection of a SARS-CoV-2 genome through metatranscriptome next-generation sequencing directly from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil. Depletion of human ribosomal RNA and use of an optimized in-house developed bioinformatics strategy contributed to successful detection of the virus.

Abstract INTRODUCTION: We performed an epidemiological surveillance of the Chikungunya (CHIKV) lineages in Bahia after the 2014 East/Central/South African (ECSA) genotype outbreak. METHODS: Reverse-transcription polymerase chain reaction (RT-PCR), viral isolation, and phylogenetic analyses were conducted on serum samples from 605 patients with CHIKV-like symptoms during 2014-2018. RESULTS: Of the 605 samples, 167 were CHIKV-positive. Viral isolation was achieved for 20 samples; their phylogenetic analysis (E2 protein) revealed the presence of ECSA lineage and reinforced the phylogenetic relationship between ECSA and Indian Ocean lineages. CONCLUSIONS: The genomic surveillance of CHIKV showed that only ECSA lineage circulated in Bahia since the 2014 outbreak.

A localized Chikungunya virus (CHIKV; East/Central/South African genotype) outbreak (50 cases, 70% laboratory-confirmed; attack rate: 5.3 confirmed cases/100 people) occurred in a Salvador, Brazil neighborhood, between Apr-Jun/2017. Highly clustered cases in space and time, mostly along a single street, highlight an increased risk of CHIKV transmission among pockets of susceptible populations. This finding underscores the need for ongoing local level surveillance for arboviral outbreaks.

RESUMO CONTEXTO: Norovírus (NoV) é o agente etiológico mais importante nas gastroenterites agudas e infecta indivíduos de todas as idades, especialmente crianças no Brasil e no mundo. O NoV GII.4 é o genótipo mais prevalente em todo o mundo devido a sua elevada diversidade genética. No Brasil, principalmente no Nordeste, poucos estudos têm sido desenvolvidos a fim de identificar e caracterizar molecularmente o NoV. OBJETIVO: O presente estudo teve como objetivo detectar e descrever a epidemiologia molecular do NoV associado com gastroenterite aguda. MÉTODOS: RNA viral extraído a de amostras de fezes foi submetido a amplificação por Nested-RT-PCR e o genótipo determinado por analise da sequência de nucleotídeos. Um total de 278 amostras de pacientes atendidos no Hospital Aliança, na cidade de Salvador, com gastroenterite aguda foram examinados, entre março de 2009 a julho de 2012. RESULTADOS: Uma alta taxa de NoV (54,2%) foi identificado em crianças de até 5 anos de idade. Detectou-se a circulação de diferentes variantes de NoV GII.4 em Salvador, durante o período do estudo, tais como Den Haag 2006b, New Orleans 2009 e Sydney 2012. CONCLUSÃO: Estes achados reforçam a necessidade de maiores estudos para esclarecer a epidemiologia molecular das infecções por NoV em casos de gastroenterite aguda.

ABSTRACT BACKGROUND: Norovirus (NoV) is an important etiologic agent of acute gastroenteritis and infects individuals of all ages, especially children in Brazil and worldwide. NoV GII.4 was the most prevalent genotype worldwide because of your extensive genetic diversity. In Brazil, especially in the Northeast, few studies have been developed for identify and molecularly characterize NoV. OBJECTIVE: The present study aimed to detect and describe the molecular epidemiology of NoV associated with acute gastroenteritis. METHODS: The viral RNA extracted from stool samples were subjected to Nested RT-PCR and the genotypes were determined by nucleotide sequences analysis. In total, 278 stool samples assisted at Aliança Hospital in the city of Salvador, with acute gastroenteritis were examined, between March 2009 and July 2012. RESULTS: A high NoV rate (54.2%) was identified in children under 5 years of age. We detected the circulation of different NoV GII.4 variants in Salvador, during the study period as Den Haag 2006b, New Orleans 2009 and Sydney 2012. CONCLUSION: These findings reinforce the need to study the molecular epidemiology of NoV infections in acute gastroenteritis.

Rotavirus is a major cause of infectious diarrhea in infants and young children. The objective of this study was to characterize the genotypes of Human Rotavirus found in children hospitalized with acute diarrhea in the Pediatric Hospital Prof. Hosannah de Oliveira of the UFBA in Salvador, Bahia, Brazil, during the years of 1999, 2000 and 2002. Fecal samples were analyzed (n=358) by methods EIARA and SDS-PAGE for detection of Rotavirus. Positive samples of one or two of these methods (n=168) were submitted to RT-PCR and Multiplex-Nested PCR to determine genotypes G and P. A hundred sixty-eight (46.9%) samples were positive and 190 (53.1%) negative. Only 17 (4.7%) samples had divergent results. The distribution of genotypes G during the first year, showed that the genotype G9 was present in 96,8% of the analyzed samples, in the second year, it was responsible for 96% and in the third year, 88,1%. The characterization of genotypes P demonstrated that the genotype P1A[8] was the most outstanding in all years. In this study we discuss the benefit to control the genotypes of Rotavirus through the molecular characterization for the development of potential vaccines.

Nesta pesquisa analisamos a presença do vírus da Diarréia viral bovina em bovinos jovens através de um estudo sorológico e isolamento viral. A técnica de seroneutralização detectou de um total de 220 bovinos, 123 (56%) animais sorologicamente positivos. A distribuição dos títulos de anticorpos soroneutralizantes(TSN), mostrou que 82% das amostras apresentaram TSN de até 512, enquanto que 18% apresentaram TSN maiores que 512. O isolamento viral a partir da fração leucocitaria desses bovinos, confirmou a presença do vírus em quatro bovinos aparentemente saudáveis e de um bezerro com sintomatologia respiratória. Os cinco isolados virais não apresentaram efeito citopático nos cultivos celulares.

In this research we analyzed the presence of Bovine viral diarrhea virus in young bovines. We performed a serological study and viral isolament in 220 bovines from different counties. The serum-neutralization assay detected 123 (56%) positive bovines to BVDV and showed that 82% of the samples had SNT up to 512 and 18 %, more than 512. It was collected the buffy coats from these bovines to performed the viral isolament in culture cells and the presence of the virus was confirmed in four healthy bovines and one calves with respiratory symptoms. The five viral isolaments are non-citophatic strains.

A presença de anticorpos contra Herpesvírus Bovino tipo 1 (HBV-1) foi avaliada em bovinos jovens provenientes de quinze municípios diferentes, distribuídos nas regiões Norte, Sul e Central do estado da Bahia. Foram coletadas amostras de sangue de bovinos de 1 a 4 anos de idade, não vacinados contra HBV-1 e sem prévio diagnóstico de infecção pelo vírus HBV-1. O total de amostras correspondeu a 558 soros, equivalente a 10% da população bovina de cada fazenda. Os 558 soros foram submetidos à técnica de Microssoroneutralização (MSN) em microplacas, utilizando-se monocamadas de células MDBK e a cepa de HBV-1 Los Angeles, e ao teste de ELISA comercialmente adquirido: HerdCheck-IDDEX. Os resultados da amostragem feito pelo teste de ELISA mostraram que 56% (314/558) dos soros foram positivos e 44% (244/558), negativos. A técnica de MSN mostrou que 48% (269/558) dos soros foram negativos e 52% (289/558) foram positivos. Destes soros positivos, 54% tiveram títulos soroneutralizantes entre 4-16, 35% entre 32-64, e 11% > ou = 64. Os resultados sugerem que o HBV-1 esteja circulando ativamente na população bovina jovem. Por outra parte, a alta difusão do vírus em animais jovens representaria uma fonte contínua de infecção viral para o rebanho.

The presence of antibodies against BHV-1 was evaluated in young bovines from fifteen different counties distributed along North, South and Central regions of the state of Bahia. Bovines with age ranged from 1 to 4 years old, non-vaccinated against BHV-1 and without diagnostic of BHV-1 infection were chosen for blood collection. A total of 558 serum samples were collected equivalent to 10% of the population in each farm. The sera were submitted to ELISA (HerdCheck-IDDEX) and Microserum neutralization (MSN) tests. The MSN was performed in monolayers of MDBK cells in microplates using Los Angeles BHV-1 strain. The results of serum samples by ELISA showed that 56% (314/558) were positive and 44% (244/558) were negative. The sera assayed by MSN showed that 48% (269/558) were negative and 52% (289/558) were positive. These positive sera demonstrated that 54% had serumneutralization titer between 4-16, 35% between 32-64 and 11% > or = 64. Our results suggest that the virus is circulating actively in herds. Furthermore, the high diffusion of the BHV-1 in young bovines could represent a constant source of viral infection in the herd.