RESUMO
An immunocompetent toddler came to medication attention with gastroenteritis, complicated by encephalopathy and hepatitis. Multiplexed testing using a polymerase chain reaction meningitis panel was positive for human herpesvirus 6 (HHV-6). Clinical correlation, quantitative HHV-6 polymerase chain reaction, and metagenomic next-generation sequencing supported a likely diagnosis of primary HHV-6B infection.
Assuntos
Encefalopatias/virologia , Exantema Súbito/virologia , Gastroenterite/virologia , Hepatite/virologia , Herpesvirus Humano 6/isolamento & purificação , Reação em Cadeia da Polimerase Multiplex , Herpesvirus Humano 6/genética , Humanos , Imunocompetência , Lactente , Masculino , Medição de RiscoRESUMO
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.
Assuntos
Genoma Viral/genética , Mosquitos Vetores/virologia , Infecção por Zika virus/epidemiologia , Infecção por Zika virus/transmissão , Zika virus/genética , Adolescente , Adulto , Brasil/epidemiologia , América Central/epidemiologia , Criança , Pré-Escolar , Humanos , Imunidade Coletiva/imunologia , Metagenômica , México/epidemiologia , Filogenia , Análise de Sequência de RNA , Zika virus/imunologia , Infecção por Zika virus/sangue , Infecção por Zika virus/urinaRESUMO
Sequencing of isolates from patients in Bahia, Brazil, where most Zika virus cases in Brazil have been reported, resulted in 11 whole and partial Zika virus genomes. Phylogenetic analyses revealed a well-supported Bahia-specific Zika virus lineage, which indicates sustained Zika virus circulation in Salvador, Bahia's capital city, since mid-2014.
Assuntos
Infecção por Zika virus/virologia , Zika virus/classificação , Adulto , Idoso , Brasil/epidemiologia , DNA Viral , Feminino , Genoma Viral , Humanos , Masculino , Tipagem Molecular , Filogenia , Análise de Sequência de DNA , Zika virus/genética , Infecção por Zika virus/epidemiologiaRESUMO
Metagenomic next-generation sequencing (mNGS) of samples from 15 patients with documented Zika virus (ZIKV) infection in Bahia, Brazil, from April 2015 to January 2016 identified coinfections with chikungunya virus (CHIKV) in 2 of 15 ZIKV-positive cases by PCR (13.3%). While generally nonspecific, the clinical presentation corresponding to these two CHIKV/ZIKV coinfections reflected infection by the virus present at a higher titer. Aside from CHIKV and ZIKV, coinfections of other viral pathogens were not detected. The mNGS approach is promising for differential diagnosis of acute febrile illness and identification of coinfections, although targeted arbovirus screening may be sufficient in the current ZIKV outbreak setting.
Assuntos
Febre de Chikungunya/epidemiologia , Vírus Chikungunya/isolamento & purificação , Coinfecção/epidemiologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Infecção por Zika virus/epidemiologia , Zika virus/isolamento & purificação , Adulto , Brasil/epidemiologia , Febre de Chikungunya/diagnóstico , Febre de Chikungunya/virologia , Vírus Chikungunya/genética , Coinfecção/diagnóstico , Coinfecção/virologia , Feminino , Humanos , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/métodos , Zika virus/genética , Infecção por Zika virus/diagnóstico , Infecção por Zika virus/virologiaRESUMO
A newly developed transcription-mediated amplification assay was used to detect chikungunya virus infection in 3 of 557 asymptomatic donors (0.54%) from Puerto Rico during the 2014-2015 Caribbean epidemic. Viral detection was confirmed by using PCR, microarray, and next-generation sequencing. Molecular clock analysis dated the emergence of the Puerto Rico strains to early 2013.
Assuntos
Doadores de Sangue/provisão & distribuição , Febre de Chikungunya/diagnóstico , Vírus Chikungunya/isolamento & purificação , Testes Genéticos/métodos , Genômica , Doadores de Sangue/estatística & dados numéricos , Febre de Chikungunya/epidemiologia , Febre de Chikungunya/genética , Vírus Chikungunya/genética , Vírus Chikungunya/imunologia , Vírus Chikungunya/patogenicidade , Testes Genéticos/estatística & dados numéricos , Humanos , Porto Rico/epidemiologiaRESUMO
Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.
Assuntos
Gastroenterite/diagnóstico , Gastroenterite/virologia , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Viroses/diagnóstico , Viroses/virologia , Vírus/classificação , Vírus/genética , Pré-Escolar , Gastroenterite/epidemiologia , Humanos , Lactente , Recém-Nascido , Análise de Sequência com Séries de Oligonucleotídeos/normas , Prevalência , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Sensibilidade e Especificidade , Viroses/epidemiologiaRESUMO
Polyomaviruses are small circular DNA viruses associated with chronic infections and tumors in both human and animal hosts. Using an unbiased deep sequencing approach, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. The â¼5.0 kB viral genome exhibits little overall homology (<46% amino acid identity) to known polyomaviruses, and, due to phylogenetic variation among its individual proteins, cannot be placed in any existing taxonomic group. PCR-based screening detected MXPyV in 28 of 834 (3.4%) fecal samples collected from California, Mexico, and Chile, and 1 of 136 (0.74%) of respiratory samples from Mexico, but not in blood or urine samples from immunocompromised patients. By quantitative PCR, the measured titers of MXPyV in human stool at 10% (weight/volume) were as high as 15,075 copies. No association was found between the presence of MXPyV and diarrhea, although girls were more likely to shed MXPyV in the stool than boys (p=0.012). In one child, viral shedding was observed in two stools obtained 91 days apart, raising the possibility of chronic infection by MXPyV. A multiple sequence alignment revealed that MXPyV is a closely related variant of the recently reported MWPyV and HPyV10 polyomaviruses. Further studies will be important to determine the association, if any, of MXPyV with disease in humans.
Assuntos
Diarreia/epidemiologia , Diarreia/virologia , Filogenia , Polyomavirus/genética , Sequência de Bases , Teorema de Bayes , California/epidemiologia , Criança , Chile/epidemiologia , Fezes/virologia , Feminino , Genoma Viral/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , México/epidemiologia , Análise em Microsséries , Modelos Genéticos , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Polyomavirus/isolamento & purificação , Prevalência , Alinhamento de Sequência , Fatores Sexuais , Eliminação de Partículas Virais/genéticaRESUMO
OBJECTIVE: To assess the utility of a panviral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections (RTIs). STUDY DESIGN: The Virochip was compared with conventional direct fluorescent antibody (DFA)- and polymerase chain reaction (PCR)-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. RESULTS: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity, 85% to 90%; specificity, >/=99%; positive predictive value, 94% to 96%; negative predictive value, 97% to 98%) in the detection of respiratory syncytial virus, influenza A, and rhinoviruses/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. CONCLUSIONS: Given its favorable sensitivity and specificity profile and expanded spectrum for detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric RTIs.