RESUMO
BACKGROUND: We previously reported the discovery of a novel, putative flavivirus designated T'Ho virus in Culex quinquefasciatus mosquitoes in the Yucatan Peninsula of Mexico. A 1358-nt region of the NS5 gene was amplified and sequenced but an isolate was not recovered. RESULTS: The complete genome of T'Ho virus was sequenced using a combination of unbiased high-throughput sequencing, 5' and 3' rapid amplification of cDNA ends, reverse transcription-polymerase chain reaction and Sanger sequencing. The genome contains a single open reading frame of 10,284 nt which is flanked by 5' and 3' untranslated regions of 97 and 556-nt, respectively. Genome sequence alignments revealed that T'Ho virus is most closely related to Rocio virus (67.4% nucleotide identity) and Ilheus virus (65.9%), both of which belong to the Ntaya group, followed by other Ntaya group viruses (58.8-63.3%) and Japanese encephalitis group viruses (62.0-63.7%). Phylogenetic inference is in agreement with these findings. CONCLUSIONS: This study furthers our understanding of flavivirus genetics, phylogeny and diagnostics. Because the two closest known relatives of T'Ho virus are human pathogens, T'Ho virus could be an unrecognized cause of human disease. It is therefore important that future studies investigate the public health significance of this virus.
Assuntos
Flavivirus/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma , Animais , Análise por Conglomerados , Culex , Flavivirus/isolamento & purificação , México , Fases de Leitura Aberta , Filogenia , Homologia de Sequência do Ácido NucleicoRESUMO
BACKGROUND: Baseline hematologic data are used by veterinarians and wildlife biologists to perform health assessments on target animal species. Hematologic measurements are influenced by various factors including geography. Baseline hematologic RIs have been established for domestic water buffaloes (Bubalus bubalis) from various countries in the Eastern Hemisphere, but these data are not readily available for the Western Hemisphere. OBJECTIVE: The aim of this study was to determine hematologic values for domestic water buffaloes from several commercial farms in southern Mexico. METHODS: Blood was collected from 126 healthy, postlactating females (3 to 10 years old) from the Murrah breed, and 10 hematologic variables were measured. RESULTS: Means, SDs, RIs, medians (MED), median absolute deviations (MAD), and other statistics were calculated for each hematologic variable. The MED (and MAD) for each variable are as follows: RBC count, 7.6 (1.1) × 1012 /L; hemoglobin, 116.0 (13.3) g/L; PCV, 41.5 (7.6) %; MCV, 56.8 (7.0) fL; MCH, 14.6 (1.6) pg; MCHC, 250.0 (35.6) g/L; RDW (SD), 29.7 (5.5) fL; RDW (CV), 18.2 (1.4) %; reticulocytes, 0.0 (0.0) %, and WBC count, 12.4 (1.3) × 109 /L. These values were compared to those previously reported for water buffaloes from several countries in the Eastern Hemisphere and, on most occasions, they differed significantly. CONCLUSIONS: Our data can be used by veterinarians and other personnel involved in buffalo production in Mexico during medical evaluations.
Assuntos
Búfalos/sangue , Animais , Contagem de Eritrócitos/veterinária , Índices de Eritrócitos/veterinária , Feminino , Hematócrito/veterinária , Hemoglobinas/análise , Contagem de Leucócitos/veterinária , México , Valores de ReferênciaRESUMO
Nucleotide sequencing was performed on part of the medium and large genome segments of 17 Cache Valley virus (CVV) isolates from the Yucatan Peninsula of Mexico. Alignment of these sequences to all other sequences in the Genbank database revealed that they have greatest nucleotide identity (97-98 %) with the equivalent regions of Tlacotalpan virus (TLAV), which is considered to be a variety of CVV. Next, cross-plaque reduction neutralization tests (PRNTs) were performed using sera from mice that had been inoculated with a representative isolate from the Yucatan Peninsula (CVV-478) or the prototype TLAV isolate (61-D-240). The PRNT titers exhibited a twofold difference in one direction and no difference in the other direction suggesting that CVV-478 and 61-D-240 belong to the same CVV subtype. In conclusion, we demonstrate that the CVV isolates from the Yucatan Peninsula of Mexico are genetically and antigenically similar to the prototype TLAV isolate.
Assuntos
Aedes/virologia , Vírus Bunyamwera/genética , Vírus Bunyamwera/imunologia , Animais , Vírus Bunyamwera/classificação , Vírus Bunyamwera/isolamento & purificação , Feminino , Soros Imunes/imunologia , México , Camundongos , Camundongos Endogâmicos BALB C , Testes de Neutralização , Filogenia , Análise de Sequência de DNA , Ensaio de Placa ViralRESUMO
We determined the complete nucleotide sequences of the small (S) and medium (M) RNA segments of an orthobunyavirus isolated from mosquitoes in the Yucatan Peninsula of Mexico. A 528-nt region of the large (L) RNA segment was also sequenced. The S RNA segment has greatest nucleotide identity to the homologous region of Cache Valley virus (CVV; 98%) followed by Potosi virus (POTV; 89%) and Northway virus (86%). The M RNA segment has 96% nucleotide identity to the homologous region of POTV, and less than 74% nucleotide identity to the homologous regions of all other orthobunyaviruses for which M segment sequence data are available. The L RNA segment has greatest nucleotide identity to the homologous region of POTV (98%) followed by CVV (82%) and Tensaw virus (77%). These data indicate that the virus, tentatively named Cholul virus (CHLV), is a novel reassortant that acquired its S RNA segment from CVV and its M and L RNA segments from POTV. Phylogenetic data support this conclusion.
Assuntos
Vírus Bunyamwera/classificação , Vírus Bunyamwera/genética , Vírus Bunyamwera/isolamento & purificação , Filogenia , Vírus Reordenados/classificação , Sequência de Aminoácidos , Animais , Sequência de Bases , Culicidae/virologia , México , Dados de Sequência Molecular , Vírus Reordenados/genética , Vírus Reordenados/isolamento & purificação , Recombinação Genética , Homologia de Sequência , Proteínas Virais/genéticaRESUMO
Previously, we reported a high prevalence of Culex flavivirus (CxFV) in Culex quinquefasciatus (Say) in the Yucatan Peninsula of Mexico. To determine whether other Culex spp. mosquitoes in this region are susceptible to natural CxFV infection, Cx. bahamensis (Dyar and Knab), Cx. coronator (Dyar and Knab), Cx. interrogator (Dyar and Knab), Cx. nigripalpus (Theobald) and Cx. opisthopus (Komp) in the Yucatan Peninsula of Mexico were tested for CxFV. Two pools of Cx. interrogator were positive. The envelope protein genes of these isolates and 16 isolates from Cx. quinquefasciatus were sequenced and shown to have > or =99.2% nucleotide identity. These data suggest that there is limited genetic diversity among CxFV isolates in the Yucatan Peninsula of Mexico.
Assuntos
Culex/virologia , Flavivirus/isolamento & purificação , Análise de Sequência de DNA , Animais , Culex/classificação , Flavivirus/genética , Variação Genética , Insetos Vetores/classificação , Insetos Vetores/virologia , México , Filogenia , Proteínas do Envelope Viral/genéticaRESUMO
A total of 191,244 mosquitoes from 24 species were collected in the Yucatan Peninsula of Mexico from January to December 2008, and tested for the presence of cytopathic virus by virus isolation in Vero cells. Eighteen virus isolates were obtained, all of which were orthobunyaviruses. These were identified by reverse transcription-polymerase chain reaction (RT-PCR) and nucleotide sequencing as Cache Valley virus (n=17) and South River virus (n=1). A subset (n=20,124) of Culex quinquefasciatus collected throughout the year was further tested by RT-PCR using flavivirus-specific primers. Flavivirus RNA was present in this mosquito species year-round. The overall flavivirus minimal infection rate, expressed as the number of positive mosquito pools per 1000 mosquitoes tested, was 7.7 and the monthly flavivirus minimal infection rates ranged from 4.3 to 16.6. Approximately one-third of the RT-PCR products were sequenced and all corresponded to Culex flavivirus, a recently discovered insect-specific flavivirus.
Assuntos
Culicidae/virologia , Flavivirus/isolamento & purificação , Orthobunyavirus/isolamento & purificação , Animais , Feminino , Flavivirus/genética , Masculino , México , Orthobunyavirus/genética , FilogeniaRESUMO
We determined the complete nucleotide sequences of the small (S) and medium (M) RNA genome segments of a Kairi virus (KRIV) isolate from the Yucatan Peninsula of Mexico. The S segment consists of 992 nucleotides, and the M segment consists of 4,619 nucleotides. Phylogenetic analyses were conducted on each genomic segment, and these data are discussed. A 526 nucleotide region of the large (L) segment was also sequenced. This is the first study to present sequence and phylogenetic data for a KRIV isolate from Latin America.
Assuntos
Orthobunyavirus/genética , RNA Viral/genética , Regiões 5' não Traduzidas/genética , Sequência de Bases , México , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Filogenia , RNA Viral/químicaRESUMO
As part of our ongoing surveillance efforts for West Nile virus (WNV) in the Yucatan Peninsula of Mexico, 96,687 mosquitoes collected from January through December 2007 were assayed by virus isolation in mammalian cells. Three mosquito pools caused cytopathic effect. Two isolates were orthobunyaviruses (Cache Valley virus and Kairi virus) and the identity of the third infectious agent was not determined. A subset of mosquitoes was also tested by reverse transcription-polymerase chain reaction (RT-PCR) using WNV-, flavivirus-, alphavirus-, and orthobunyavirus-specific primers. A total of 7,009 Culex quinquefasciatus in 210 pools were analyzed. Flavivirus RNA was detected in 146 (70%) pools, and all PCR products were sequenced. The nucleotide sequence of one PCR product was most closely related (71-73% identity) with homologous regions of several other flaviviruses, including WNV, St. Louis encephalitis virus, and Ilheus virus. These data suggest that a novel flavivirus (tentatively named T'Ho virus) is present in Mexico. The other 145 PCR products correspond to Culex flavivirus, an insect-specific flavivirus first isolated in Japan in 2003. Culex flavivirus was isolated in mosquito cells from approximately one in four homogenates tested. The genomic sequence of one isolate was determined. Surprisingly, heterogeneous sequences were identified at the distal end of the 5' untranslated region.
Assuntos
Culicidae/virologia , Flavivirus/isolamento & purificação , Insetos/virologia , RNA Viral/isolamento & purificação , Vírus do Nilo Ocidental/isolamento & purificação , Animais , Chlorocebus aethiops , Primers do DNA , Flavivirus/classificação , Flavivirus/genética , Genoma Viral , Humanos , México , Orthobunyavirus/classificação , Orthobunyavirus/genética , Orthobunyavirus/isolamento & purificação , Filogenia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Células Vero , Vírus do Nilo Ocidental/classificação , Vírus do Nilo Ocidental/genéticaRESUMO
Phylogeneticists have developed several statistical methods to infer recombination among molecular sequences that are evolutionarily related. Of these methods, Markov change-point models currently provide the most coherent framework. Yet, the Markov assumption is faulty in that the inferred relatedness of homologous sequences across regions divided by recombinant events is not independent, particularly for nonrecombinant sequences as they share the same history. To correct this limitation, we introduce a novel random tips (RT) model. The model springs from the idea that a recombinant sequence inherits its characters from an unknown number of ancestral full-length sequences, of which one only observes the incomplete portions. The RT model decomposes recombinant sequences into their ancestral portions and then augments each portion onto the data set as unique partially observed sequences. This data augmentation generates a random number of sequences related to each other through a single inferable tree with the same random number of tips. While intuitively pleasing, this single tree corrects the independence assumptions plaguing previous methods while permitting the detection of recombination. The single tree also allows for inference of the relative times of recombination events and generalizes to incorporate multiple recombinant sequences. This generalization answers important questions with which previous models struggle. For example, we demonstrate that a group of human immunodeficiency type 1 recombinant viruses from Argentina, previously thought to have the same recombinant history, actually consist of 2 groups: one, a clonal expansion of a reference sequence and another that predates the formation of the reference sequence. In another example, we demonstrate that 2 hepatitis B virus recombinant strains share similar splicing locations, suggesting a common descent of the 2 viruses. We implement and run both examples in a software package called StepBrothers, freely available to interested parties.
Assuntos
DNA Recombinante/classificação , DNA Viral/genética , Evolução Molecular , HIV-1/genética , Vírus da Hepatite B/genética , Argentina , Sequência de Bases , Teorema de Bayes , China , Biologia Computacional/métodos , DNA Recombinante/genética , DNA Viral/classificação , Humanos , Redes Neurais de Computação , Filogenia , Recombinação Genética , Análise de Sequência de DNA , Processos EstocásticosRESUMO
Background: most of the studies of HIV-1 infection in South America have been limited to Brazil and little is known about the viral variants that are causing disease else where in the continent. Aim: to determine the characteristics of the viral variants present in Chile as well as patterns of viral transmission. Material and methods: viral sequences were obtained from 21 HIV-1 infected people from Santiago, Chile who were infected either via sexual contact or intravenous drug use. Cloned sequences obtained from both the third variable and conserved regions of the envelope as well as the viral protease were evaluated. Results: we found only clade B subtype viruses in Santiago. An evaluation of the envelope gene revealed no evidence that the sequences were monophyletic by risk group. A number of the protease sequences were predicted to encode amino acid substitutions commonly found during selection for protease inhibitor resistance. Conclusions: the HIV-1 strains studied in Chile, belong to the subtype B. There is no molecular evidence of separate introductions of the virus into the different risk groups. A number of substitutions in the protease gene that may confer resistance to protease inhibitors were found in patients with no previous exposure to this class of drugs