RESUMO
Bovine rabies is endemic in most Brazilian States, including Rio Grande do Sul (RS), which has faced an unprecedented rabies outbreak between 2011 and 2018. We described a real-time reverse transcription quantitative PCR (RT-rtPCR) for detection of rabies virus (RABV) in bovine samples. The primers were designed targeting a highly conserved region of the nucleoprotein (N) gene of RABV obtained from cattle. The detection limit corresponded to 13 DNA copies and the intra- and inter-run repeatability was adequate (CV<9%) in all dilutions tested. Amplification of other pathogens associated with neurological disease in cattle or cross-contamination was not observed. Brain samples from cattle suspicious of rabies (n=21) were tested in triplicate by the RT-rtPCR and by the gold-standard direct fluorescent antibody test (DFAT), resulting in 100% of sensitivity and specificity of the RT-rtPCR. Testing of additional 41 bovine brain samples submitted to the routine DFAT testing yielded 37 (90.2%) concordant results (30 positive/7 negative) and 4 (9.7%) inconclusive in DFAT and RT-rtPCR positive. These results showed a good concordance between the tests and a higher sensitivity of the RT-rtPCR. This assay represents an alternative for RABV detection, either as a confirmatory test or for large-scale diagnosis in endemic regions.
A raiva bovina é endêmica na maioria dos estados brasileiros, inclusive no Rio Grande do Sul (RS), que enfrentou um surto de raiva sem precedentes entre 2011 e 2018. Descrevemos um PCR quantitativo de transcrição reversa em tempo real (RT-rtPCR) para detecção do vírus da raiva (RABV) em bovinos. Os primers foram desenhados visando uma região altamente conservada do gene da nucleoproteína (N) de RABV obtido de bovinos. O limite de detecção correspondeu a 13 cópias de DNA e a repetibilidade intra e inter-ensaios foi adequada (CV <9%) em todas as diluições testadas. Não foi observada amplificação de outros patógenos associados a doenças neurológicas em bovinos ou contaminação cruzada. Amostras de cérebro de bovinos com suspeita de raiva (n = 21) foram testadas em triplicata no RT-rtPCR e pelo teste de anticorpo fluorescente padrão ouro (DFAT), resultando em 100% de sensibilidade e especificidade do RT-rtPCR. O teste de 41 amostras de cérebro bovino adicionais submetidas ao teste de DFAT de rotina rendeu 37 (90,2%) resultados concordantes (30 positivos / sete negativos) e quatro (9,7%) inconclusivos em DFAT e RT-rtPCR positivo. Esses resultados mostraram boa concordância entre os testes e maior sensibilidade do RT-rtPCR. Este ensaio representa uma alternativa para a detecção do vírus da raiva, seja como teste confirmatório ou para diagnóstico em larga escala em regiões endêmicas.
Assuntos
Bovinos , Raiva , Transcrição Reversa , Diagnóstico , BovinosRESUMO
ABSTRACT: Bovine rabies is endemic in most Brazilian States, including Rio Grande do Sul (RS), which has faced an unprecedented rabies outbreak between 2011 and 2018. We described a real-time reverse transcription quantitative PCR (RT-rtPCR) for detection of rabies virus (RABV) in bovine samples. The primers were designed targeting a highly conserved region of the nucleoprotein (N) gene of RABV obtained from cattle. The detection limit corresponded to 13 DNA copies and the intra- and inter-run repeatability was adequate (CV<9%) in all dilutions tested. Amplification of other pathogens associated with neurological disease in cattle or cross-contamination was not observed. Brain samples from cattle suspicious of rabies (n=21) were tested in triplicate by the RT-rtPCR and by the gold-standard direct fluorescent antibody test (DFAT), resulting in 100% of sensitivity and specificity of the RT-rtPCR. Testing of additional 41 bovine brain samples submitted to the routine DFAT testing yielded 37 (90.2%) concordant results (30 positive/7 negative) and 4 (9.7%) inconclusive in DFAT and RT-rtPCR positive. These results showed a good concordance between the tests and a higher sensitivity of the RT-rtPCR. This assay represents an alternative for RABV detection, either as a confirmatory test or for large-scale diagnosis in endemic regions.
RESUMO: A raiva bovina é endêmica na maioria dos estados brasileiros, inclusive no Rio Grande do Sul (RS), que enfrentou um surto de raiva sem precedentes entre 2011 e 2018. Descrevemos um PCR quantitativo de transcrição reversa em tempo real (RT-rtPCR) para detecção do vírus da raiva (RABV) em bovinos. Os primers foram desenhados visando uma região altamente conservada do gene da nucleoproteína (N) de RABV obtido de bovinos. O limite de detecção correspondeu a 13 cópias de DNA e a repetibilidade intra e inter-ensaios foi adequada (CV <9%) em todas as diluições testadas. Não foi observada amplificação de outros patógenos associados a doenças neurológicas em bovinos ou contaminação cruzada. Amostras de cérebro de bovinos com suspeita de raiva (n = 21) foram testadas em triplicata no RT-rtPCR e pelo teste de anticorpo fluorescente padrão ouro (DFAT), resultando em 100% de sensibilidade e especificidade do RT-rtPCR. O teste de 41 amostras de cérebro bovino adicionais submetidas ao teste de DFAT de rotina rendeu 37 (90,2%) resultados concordantes (30 positivos / sete negativos) e quatro (9,7%) inconclusivos em DFAT e RT-rtPCR positivo. Esses resultados mostraram boa concordância entre os testes e maior sensibilidade do RT-rtPCR. Este ensaio representa uma alternativa para a detecção do vírus da raiva, seja como teste confirmatório ou para diagnóstico em larga escala em regiões endêmicas.
RESUMO
The SARS-CoV-2 variant of concern (VOC) gamma (P.1) has increased transmissibility and resulted in elevated hospitalization and mortality rates in Brazil. We investigated the clinical course of COVID-19 caused by gamma and non-VOCs at a reference hospital in Brazil in a retrospective cohort study with nonelderly hospitalized patients from two periods, before and after the emergence of gamma. Cohort 1 included patients from both periods whose samples would be eligible for whole-genome sequencing (WGS). Cohort 2 was composed of randomly selected patients from Cohort 1 whose samples were submitted to WGS. A total of 433 patients composed Cohort 1: 259 from the first and 174 from the second period. Baseline characteristics were similar, except for a higher incidence of severe distress respiratory syndrome at admission in patients from the second period. Patients from the second period had significantly higher incidence rates of advanced respiratory support (adjusted hazard ratio [aHR]: 2.04; 95% confidence interval [CI], 1.60-2.59), invasive ventilatory support (aHR: 2.72; 95% CI: 2.05-3.62), and 28-day mortality from the onset of symptoms (aHR: 2.62; 95% CI: 1.46-4.72). A total of 86 (43 gamma and 43 non-gamma) patients composed Cohort 2. Patients with confirmed gamma VOC infections had higher advanced ventilatory support and mortality rates than non-gamma-infected patients. Our study suggests that non-elderly patients hospitalized for COVID-19 in the second period (used as a proxy of gamma infection) had a more severe clinical course. This might have contributed to higher hospitalization and death rates observed in the second wave in Brazil.
Assuntos
COVID-19 , Humanos , Pessoa de Meia-Idade , Brasil/epidemiologia , Estudos Retrospectivos , SARS-CoV-2 , Progressão da DoençaRESUMO
The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM.
Assuntos
COVID-19/virologia , Genoma Viral , SARS-CoV-2/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Brasil/epidemiologia , COVID-19/epidemiologia , Criança , Pré-Escolar , Feminino , Genômica , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Mutação , Filogenia , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação , Glicoproteína da Espícula de Coronavírus/genética , Sequenciamento Completo do Genoma , Adulto JovemAssuntos
COVID-19 , SARS-CoV-2 , Humanos , Brasil/epidemiologia , COVID-19/diagnóstico , Diagnóstico PrecoceRESUMO
The emergence of SARS-CoV-2 P.1 lineage coincided with a surge in hospitalisations in the North region of Brazil. In the South region's Rio Grande do Sul state, severe COVID-19 case numbers rose 3.8 fold in February 2021. During that month, at a COVID-19 referral hospital in this state, whole-genome sequencing of a subset of cases' specimens (n = 27) revealed P.1 lineage SARS-CoV-2 in most (n = 24). Findings raise concerns regarding a possible association between lineage P.1 and rapid case and hospitalisation increases.
Assuntos
COVID-19/diagnóstico , COVID-19/virologia , SARS-CoV-2/isolamento & purificação , Brasil/epidemiologia , Hospitalização/estatística & dados numéricos , Humanos , Sequenciamento Completo do GenomaRESUMO
The envelope glycoprotein E2 of pestiviruses is a major target for neutralizing antibodies. In this study, we analyzed the E2 DA domain of 43 pestiviruses from Southern Brazil. The isolates were identified as Bovine viral diarrhea virus (BVDV) subtypes 1a and 1b or BVDV-2b. Compared to reference strains, the BVDV-1 and -2 isolates had four and two mutations in the DA domain, respectively. All BVDV-2 isolates had a deletion of residues 724 and 725. All mutated amino acids in the BVDV isolates had the same aa substitution, and all were in previously identified antibody binding sites. It is possible that an immunity-mediated selection is acting on the pestiviruses circulating in Southern Brazil.
Assuntos
Vírus da Diarreia Viral Bovina/genética , Vírus da Diarreia Viral Bovina/isolamento & purificação , Proteínas do Envelope Viral/genética , Animais , Antígenos Virais/genética , Sítios de Ligação de Anticorpos/genética , Doença das Mucosas por Vírus da Diarreia Viral Bovina/epidemiologia , Doença das Mucosas por Vírus da Diarreia Viral Bovina/virologia , Brasil/epidemiologia , Bovinos , Vírus da Diarreia Viral Bovina/classificação , Vírus da Diarreia Viral Bovina/imunologia , Mutação , Filogenia , RNA Viral/genética , Proteínas do Envelope Viral/imunologiaRESUMO
Bees are fundamental in several aspects, especially in relation to plant biodiversity and pollination. Recently, immense losses are being faced in the number of Brazilian colonies, mainly in southern states of the country, which has a strong beekeeping activity. There are indications that, among the reasons for the losses, pathogens that affect the health of bees may be involved. Among them, the microsporidium Nosema and the black queen cell virus (BQCV) stand out for their prevalence. In this study, 92 colonies of 17 apiaries from southern Brazil were evaluated for infection by Nosema ceranae, Nosema apis and BQCV. Nucleic acid extractions and cDNA synthesis were performed from adult bee samples, followed by Reverse Transcription Polymerase Chain Reaction (RT-PCR) and multiplex PCR. Eight BQCV positive samples were subjected to sequencing. The results showed that N. ceranae and BQCV are circulating in the Southern region of the country, which may be the reason for the loss of colonies. N. apis was not found. N. ceranae was found in 57.6% (53/92) of the colonies and BQCV in 32.6% (30/92). Co-infection was found in 25% (23/92) of the colonies studied, a factor that is suggested to be reducing the hosts' longevity due to the synergistic action of the pathogens. The samples submitted to sequencing indicated similarity of 96.8 to 100% between them, in addition to strong similarity with sequences from Asia, United States, Germany and Peru. This study reports the circulation of N. ceranae and BQCV in apiaries in southern Brazil, in addition to being the first phylogenetic analysis of the Brazilian BQCV sequence.(AU)
As abelhas mostram-se fundamentais em diversos aspectos, especialmente com relação à biodiversidade de plantas e polinização. Recentemente, estão sendo enfrentadas imensas perdas no número de colônias brasileiras, principalmente nos estados do sul do país, com forte atividade apícola. Há indicativos de que, dentre as razões para as perdas, possam estar envolvidos patógenos que afetam a saúde das abelhas. Dentre eles, o microsporídio Nosema e o vírus da realeira negra (BQCV) destacam-se pela prevalência. Neste estudo, foram avaliadas 92 colônias, de 17 apiários do sul do Brasil, a respeito da infecção por Nosema ceranae, Nosema apis e BQCV. Foram realizadas extrações de ácidos nucleicos e síntese de cDNA a partir de amostras de abelhas adultas, seguidos de Reação em Cadeia da Polimerase-Transcriptase Reversa (RT-PCR). Oito amostras positivas para BQCV foram submetidas a sequenciamento. Os resultados mostraram que N. ceranae e BQCV estão circulando na região sul do país, podendo ser a razão para as perdas de colônias. N. apis não foi encontrado. N. ceranae foi encontrado em 57.6% (53/92) das colônias e BQCV em 32.6% (30/92). Foi encontrada coinfecção por ambos em 25% (23/92) das colônias estudadas, fator que sugere a diminuição da longevidade do hospedeiro por ação sinérgica dos patógenos. As amostras submetidas ao sequenciamento indicaram similaridade de 96.8 a 100% entre elas, além de forte similaridade com sequências da Ásia, Estados Unidos, Alemanha e Peru. Este estudo relata a circulação de N. ceranae e BQCV nos apiários do sul do Brasil, além de ser a primeira análise filogenética da sequência do BQCV brasileiro.(AU)
Assuntos
Animais , Abelhas/microbiologia , Nosema/isolamento & purificação , Microsporidiose/epidemiologia , Dicistroviridae/isolamento & purificação , Coinfecção , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
Bees are fundamental in several aspects, especially in relation to plant biodiversity and pollination. Recently, immense losses are being faced in the number of Brazilian colonies, mainly in southern states of the country, which has a strong beekeeping activity. There are indications that, among the reasons for the losses, pathogens that affect the health of bees may be involved. Among them, the microsporidium Nosema and the black queen cell virus (BQCV) stand out for their prevalence. In this study, 92 colonies of 17 apiaries from southern Brazil were evaluated for infection by Nosema ceranae, Nosema apis and BQCV. Nucleic acid extractions and cDNA synthesis were performed from adult bee samples, followed by Reverse Transcription Polymerase Chain Reaction (RT-PCR) and multiplex PCR. Eight BQCV positive samples were subjected to sequencing. The results showed that N. ceranae and BQCV are circulating in the Southern region of the country, which may be the reason for the loss of colonies. N. apis was not found. N. ceranae was found in 57.6% (53/92) of the colonies and BQCV in 32.6% (30/92). Co-infection was found in 25% (23/92) of the colonies studied, a factor that is suggested to be reducing the hosts' longevity due to the synergistic action of the pathogens. The samples submitted to sequencing indicated similarity of 96.8 to 100% between them, in addition to strong similarity with sequences from Asia, United States, Germany and Peru. This study reports the circulation of N. ceranae and BQCV in apiaries in southern Brazil, in addition to being the first phylogenetic analysis of the Brazilian BQCV sequence.(AU)
As abelhas mostram-se fundamentais em diversos aspectos, especialmente com relação à biodiversidade de plantas e polinização. Recentemente, estão sendo enfrentadas imensas perdas no número de colônias brasileiras, principalmente nos estados do sul do país, com forte atividade apícola. Há indicativos de que, dentre as razões para as perdas, possam estar envolvidos patógenos que afetam a saúde das abelhas. Dentre eles, o microsporídio Nosema e o vírus da realeira negra (BQCV) destacam-se pela prevalência. Neste estudo, foram avaliadas 92 colônias, de 17 apiários do sul do Brasil, a respeito da infecção por Nosema ceranae, Nosema apis e BQCV. Foram realizadas extrações de ácidos nucleicos e síntese de cDNA a partir de amostras de abelhas adultas, seguidos de Reação em Cadeia da Polimerase-Transcriptase Reversa (RT-PCR). Oito amostras positivas para BQCV foram submetidas a sequenciamento. Os resultados mostraram que N. ceranae e BQCV estão circulando na região sul do país, podendo ser a razão para as perdas de colônias. N. apis não foi encontrado. N. ceranae foi encontrado em 57.6% (53/92) das colônias e BQCV em 32.6% (30/92). Foi encontrada coinfecção por ambos em 25% (23/92) das colônias estudadas, fator que sugere a diminuição da longevidade do hospedeiro por ação sinérgica dos patógenos. As amostras submetidas ao sequenciamento indicaram similaridade de 96.8 a 100% entre elas, além de forte similaridade com sequências da Ásia, Estados Unidos, Alemanha e Peru. Este estudo relata a circulação de N. ceranae e BQCV nos apiários do sul do Brasil, além de ser a primeira análise filogenética da sequência do BQCV brasileiro.(AU)