Deyvid Amgarten
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View article: A Comprehensive Molecular and Serological Investigation of Hepatitis A Virus Among Patients With Suspected Acute Hepatitis: A Brazilian Study
A Comprehensive Molecular and Serological Investigation of Hepatitis A Virus Among Patients With Suspected Acute Hepatitis: A Brazilian Study Open
Hepatitis A Virus (HAV) infects millions of individuals annually and is a major cause of acute viral hepatitis worldwide. This study aims to (1) assess HAV infection in suspected acute hepatitis patients at public healthcare institutions i…
View article: Metagenomic Next-generation Sequencing in Patients With Infectious Meningoencephalitis: A Comprehensive Systematic Literature Review and Meta-analysis
Metagenomic Next-generation Sequencing in Patients With Infectious Meningoencephalitis: A Comprehensive Systematic Literature Review and Meta-analysis Open
Background We aimed to assess the accuracy, clinical efficacy, and limitations of metagenomic next-generation sequencing (mNGS) for diagnosing infectious meningoencephalitis. Methods We performed a systematic literature review and meta-ana…
View article: Chronic Dengue Virus Encephalitis
Chronic Dengue Virus Encephalitis Open
This case highlights a challenging instance of encephalitis with unknown etiology, where metagenomic analysis detected DENV-1 RNA in brain tissue, suggesting a possible cause.
View article: Case report: Persistent COVID-19 in a patient with B cell lymphoma refractory to antiviral treatment due to resistance to Remdesivir
Case report: Persistent COVID-19 in a patient with B cell lymphoma refractory to antiviral treatment due to resistance to Remdesivir Open
the patient presented prolonged COVID-19 with persistence of virus detected by RT-PCR for several months. The strain sequenced presented a mutation different from all reported previously. Although it was no possible to sequence the initial…
View article: EP-266 - CASO DE HEPATITE AGUDA PELO VÍRUS DA HEPATITE E EM SÃO PAULO: O PAPEL DA CARACTERIZAÇÃO GENÉTICA VIRAL NO ESTABELECIMENTO DA PROVÁVEL FONTE DE INFECÇÃO
EP-266 - CASO DE HEPATITE AGUDA PELO VÍRUS DA HEPATITE E EM SÃO PAULO: O PAPEL DA CARACTERIZAÇÃO GENÉTICA VIRAL NO ESTABELECIMENTO DA PROVÁVEL FONTE DE INFECÇÃO Open
Introdução: O vírus da Hepatite E (HEV) é responsável pelo desenvolvimento da hepatite E, e sua principal via de transmissão é fecal-oral. O genótipo 3 (HEV-3), zoonótico, está globalmente distribuído, sendo o consumo de carne suína mal co…
View article: Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis
Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis Open
Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 virus was detected in the South American sea lions found dead in Santa Catarina, Brazil, in October 2023. Whole genome sequencing and comparative phylogenetic analysis were condu…
View article: Phylodynamics of avian influenza A(H5N1) viruses from outbreaks in Brazil
Phylodynamics of avian influenza A(H5N1) viruses from outbreaks in Brazil Open
Our study identified strains of the A/H5N1 virus in analyzed samples of subsistence poultry, wild birds, and mammals, belonging to clade 2.3.4.4b, genotype B3.2, with very high genetic similarity to strains from Chile, Uruguay, and Argenti…
View article: Evidence of reassortment of avian influenza A (H2) viruses in Brazilian shorebirds
Evidence of reassortment of avian influenza A (H2) viruses in Brazilian shorebirds Open
Influenza A viruses of the H2 subtype represent a zoonotic and pandemic threat to humans due to a lack of widespread specific immunity. Although A(H2) viruses that circulate in wild bird reservoirs are distinct from the 1957 pandemic A(H2N…
View article: Publisher Correction: Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium
Publisher Correction: Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium Open
View article: Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium
Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium Open
View article: Incursion of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus, Brazil, 2023
Incursion of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus, Brazil, 2023 Open
We report 4 highly pathogenic avian influenza A(H5N1) clade 2.3.4.4.b viruses in samples collected during June 2023 from Royal terns and Cabot's terns in Brazil. Phylodynamic analysis revealed viral movement from Peru to Brazil, indicating…
View article: Immune Evasion of SARS-CoV-2 Omicron Subvariants XBB.1.5, XBB.1.16 and EG.5.1 in a Cohort of Older Adults after ChAdOx1-S Vaccination and BA.4/5 Bivalent Booster
Immune Evasion of SARS-CoV-2 Omicron Subvariants XBB.1.5, XBB.1.16 and EG.5.1 in a Cohort of Older Adults after ChAdOx1-S Vaccination and BA.4/5 Bivalent Booster Open
The recently emerged SARS-CoV-2 Omicron sublineages, including the BA.2-derived XBB.1.5 (Kraken), XBB.1.16 (Arcturus), and EG.5.1 (Eris), have accumulated several spike mutations that may increase immune escape, affecting vaccine effective…
View article: Cloud-based bioinformatics platform for the analysis and diagnosis of infectious diseases
Cloud-based bioinformatics platform for the analysis and diagnosis of infectious diseases Open
Objective: Precision medicine has gained extensive use in laboratories worldwide for the diagnosis of genetic diseases, reproductive pathologies, and cancer. State-of-the-art bioinformatics pipelines and frameworks are currently available …
View article: Mortality in Sea Lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil, October 2023: Whole genome sequencing and phylogenetic analysis
Mortality in Sea Lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil, October 2023: Whole genome sequencing and phylogenetic analysis Open
Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 virus was detected in the South American sea lions found dead in Santa Catarina, Brazil, in October 2023. Whole genome sequencing and comparative phylogenetic analysis were condu…
View article: ICE volume 44 issue 12 Cover and Front matter
ICE volume 44 issue 12 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: First report and genetic characterization of the highly pathogenic avian influenza A(H5N1) virus in Cabot's tern (Thalasseus acuflavidus), Brazil
First report and genetic characterization of the highly pathogenic avian influenza A(H5N1) virus in Cabot's tern (Thalasseus acuflavidus), Brazil Open
View article: Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection
Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection Open
Background Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequenci…
View article: Risk factors for long coronavirus disease 2019 (long COVID) among healthcare personnel, Brazil, 2020–2022
Risk factors for long coronavirus disease 2019 (long COVID) among healthcare personnel, Brazil, 2020–2022 Open
Objective: To determine risk factors for the development of long coronavirus disease 2019 (COVID-19) in healthcare personnel (HCP). Methods: We conducted a case–control study among HCP who had confirmed symptomatic COVID-19 working in a Br…
View article: Detection of Hepatitis E Virus Genotype 3 in Feces of Capybaras (Hydrochoeris hydrochaeris) in Brazil
Detection of Hepatitis E Virus Genotype 3 in Feces of Capybaras (Hydrochoeris hydrochaeris) in Brazil Open
Hepatitis E virus (HEV) is an emerging zoonotic pathogen associated with relevant public health issues. The aim of this study was to investigate HEV presence in free-living capybaras inhabiting urban parks in São Paulo state, Brazil. Molec…
View article: Risk factors for long COVID among healthcare workers, Brazil, 2020–2022
Risk factors for long COVID among healthcare workers, Brazil, 2020–2022 Open
Objectives We aimed to determine risk factors for the development of long coronavirus disease (COVID) in healthcare workers (HCWs). Methods We conducted a case-control study among HCWs who had confirmed COVID-19 infection working in a Braz…
View article: First Report and Genetic Characterization of the Highly Pathogenic Avian Influenza A(H5N1) Virus in Cabot's Tern (Thalasseus Acuflavidus), Brazil
First Report and Genetic Characterization of the Highly Pathogenic Avian Influenza A(H5N1) Virus in Cabot's Tern (Thalasseus Acuflavidus), Brazil Open
View article: Longer-term effectiveness of a heterologous coronavirus disease 2019 (COVID-19) vaccine booster in healthcare workers in Brazil
Longer-term effectiveness of a heterologous coronavirus disease 2019 (COVID-19) vaccine booster in healthcare workers in Brazil Open
Objective: To compare the long-term vaccine effectiveness between those receiving viral vector [Oxford-AstraZeneca (ChAdOx1)] or inactivated viral (CoronaVac) primary series (2 doses) and those who received an mRNA booster (Pfizer/BioNTech…
View article: vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks
vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks Open
Our results suggest that vHULK represents an advance on the state of art in phage host prediction.
View article: Effectiveness of Heterologous Coronavirus Disease 2019 (COVID-19) Vaccine Booster Dosing in Brazilian Healthcare Workers, 2021
Effectiveness of Heterologous Coronavirus Disease 2019 (COVID-19) Vaccine Booster Dosing in Brazilian Healthcare Workers, 2021 Open
Background Little is currently known about vaccine effectiveness (VE) for either 2 doses of Oxford-AstraZeneca (ChAdOx1) viral vector vaccine or CoronaVac (Instituto Butantan) inactivated viral vaccine followed by a third dose of mRNA vacc…
View article: Updating the Phylodynamics of Yellow Fever Virus 2016–2019 Brazilian Outbreak With New 2018 and 2019 São Paulo Genomes
Updating the Phylodynamics of Yellow Fever Virus 2016–2019 Brazilian Outbreak With New 2018 and 2019 São Paulo Genomes Open
The recent outbreak of yellow fever (YF) in São Paulo during 2016–2019 has been one of the most severe in the last decades, spreading to areas with low vaccine coverage. The aim of this study was to assess the genetic diversity of the yell…
View article: Effectiveness of two coronavirus disease 2019 (COVID-19) vaccines (viral vector and inactivated viral vaccine) against severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in a cohort of healthcare workers
Effectiveness of two coronavirus disease 2019 (COVID-19) vaccines (viral vector and inactivated viral vaccine) against severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in a cohort of healthcare workers Open
Objective: We investigated real-world vaccine effectiveness for Oxford-AstraZeneca (ChAdOx1) and CoronaVac against laboratory-confirmed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among healthcare workers (HCWs). Me…
View article: Machine learning prediction in genomic sequences of prokaryotic viruses from metagenomic datasets
Machine learning prediction in genomic sequences of prokaryotic viruses from metagenomic datasets Open
\n Environmental viruses are extremely diverse and abundant in the biosphere. Several studies have shown prokaryotic viruses (or simply phages) as major players in determining biogeochemical cycles in oceans as well as driving microbial di…
View article: METAGENÔMICA RNA EM AMOSTRAS DE LÍQUIDO CEFALORRAQUIDIANO: RESULTADOS DE UM LABORATÓRIO PRIVADO NA CIDADE DE SÃO PAULO
METAGENÔMICA RNA EM AMOSTRAS DE LÍQUIDO CEFALORRAQUIDIANO: RESULTADOS DE UM LABORATÓRIO PRIVADO NA CIDADE DE SÃO PAULO Open
View article: Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow
Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow Open
View article: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network
SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network Open
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public …