Protein-encoding Regions Research Articles

Transgene‐mediated suppression of dengue viruses in the salivary glands of the yellow fever mosquito, Aedes aegypti

Controlled sex-, stage- and tissue-specific expression of antipathogen effector molecules is important for genetic engineering strategies to control mosquito-borne diseases. Adult female salivary glands are involved in pathogen transmission to human hosts and are target sites for expression of antipathogen effector molecules. The Aedes aegypti 30K a and 30K b genes are expressed exclusively in adult female salivary glands and are transcribed divergently from start sites separated by 263 nucleotides. The intergenic, 5'- and 3'-end untranslated regions of both genes are sufficient to express simultaneously two different transgene products in the distal-lateral lobes of the female salivary glands. An antidengue effector gene, membranes no protein (Mnp), driven by the 30K b promoter, expresses an inverted-repeat RNA with sequences derived from the premembrane protein-encoding region of the dengue virus serotype 2 genome and reduces significantly the prevalence and mean intensities of viral infection in mosquito salivary glands and saliva.

Characterization of a Putative Ancestor of Coxsackievirus B5

Like other RNA viruses, coxsackievirus B5 (CVB5) exists as circulating heterogeneous populations of genetic variants. In this study, we present the reconstruction and characterization of a probable ancestral virion of CVB5. Phylogenetic analyses based on capsid protein-encoding regions (the VP1 gene of 41 clinical isolates and the entire P1 region of eight clinical isolates) of CVB5 revealed two major cocirculating lineages. Ancestral capsid sequences were inferred from sequences of these contemporary CVB5 isolates by using maximum likelihood methods. By using Bayesian phylodynamic analysis, the inferred VP1 ancestral sequence dated back to 1854 (1807 to 1898). In order to study the properties of the putative ancestral capsid, the entire ancestral P1 sequence was synthesized de novo and inserted into the replicative backbone of an infectious CVB5 cDNA clone. Characterization of the recombinant virus in cell culture showed that fully functional infectious virus particles were assembled and that these viruses displayed properties similar to those of modern isolates in terms of receptor preferences, plaque phenotypes, growth characteristics, and cell tropism. This is the first report describing the resurrection and characterization of a picornavirus with a putative ancestral capsid. Our approach, including a phylogenetics-based reconstruction of viral predecessors, could serve as a starting point for experimental studies of viral evolution and might also provide an alternative strategy for the development of vaccines.

Genetic polymorphism of CYP2U1, a cytochrome P450 involved in fatty acids hydroxylation

The human cytochrome P450 2U1 (CYP2U1) has been described as a novel extrahepatic P450. CYP2U1 is a highly conserved gene mainly expressed in brain and thymus, but also at lower levels in kidney, lung or heart. This selective tissue distribution suggests important endogenous functions, in particular in the conversion of arachidonic acid into two bioactive compounds, the 19- and 20-HETE. To investigate the extent of CYP2U1 genetic polymorphism in 70 French individuals, a screening for sequence variations in the 5′-flanking and protein encoding regions was performed using PCR-SSCP and sequencing strategies. Four polymorphisms were identified and correspond to −204C>A and –241T>C in the 5′-flanking region, −37G>A in the 5′-untranslated region, and IVS2-17T>C in the intron 2. The most frequent mutations, –241T>C (59.7%) and IVS2-17T>C (66.0%), did not seem to alter CYP2U1 lung expression. These results suggest that CYP2U1 exhibits few genetic variations and support a probable role in endogenous processes.

Strategy Reveals Rare Disease Genes

FOR DECADES, THE GENETIC CAUSE OF a rare and fatal X chromosome– linked syndrome characterized by talipes equinovarus, atrial septal defect, Robin sequence, and persistent left superior vena cava (TARP) eluded clinicians and scientists. But a new genefinding strategy enabled scientists from the National Human Genome Research Institute (NHGRI) to discover the gene for TARP and to offer carrier testing to affected families (Johnston JJ et al. Am J Hum Genet. 2010;86[5]:743-748). The discovery was the latest in a string of successes for scientists using next-generation sequencing or massively parallel sequencing of the genome’s protein-encoding regions and old-fashioned clinical investigation to zero in on the genetic causes of rare disorders that had evaded detection by more traditional methods. “It’s a really rapidpath todiagnosis and understanding that was either impossible or extremely difficult and expensive to do previously,” said Leslie G. Biesecker, chief of NHGRI’s Genetic Disease Research Branch. The technique is likely to accelerate the identification of the genetic basis of a multitude of rare disorders. “There are thousands and thousands of cases where families are struggling with these very serious disorders and they don’t have answers to their most basic questions,” Biesecker said. The new technology allows sequencing of billions of base pairs of DNA fragments in the time it took the old technology to sequence millions. To further expedite the process, Biesecker and colleagues sequenced DNA samples from 2 large families that have multiple affected members. They sequenced only the protein-encoding regions of the X chromosome, which they believed were most likely to house the variant, and used their clinical understanding of TARP to filter through the results. For example,

Gene expression kinetics of the yellow head virus in experimentally infected Litopenaeus vannamei.

The yellow head virus (YHV) has been reported to be one of most pathogenic viruses for cultivated shrimp; however, serious problems have only been reported in farms in south and southeastern Asian. Recently, a YHV strain was detected in Litopenaeus vannamei cultivated in Mexican farms that lacked virus‐associated mortalities or epizooties, and the animals were apparently healthy. The identity of the virus was confirmed by sequencing replicative and structural protein‐encoding regions and comparing with homologous virus sequences. Phylogenic relationships and genetic distances were also determined and, although some differences were observed, an influence on virulence was uncertain. In addition, the expression levels of several transcripts (3CLPRO, POL, GP64 and GP116) were evaluated by quantitative real‐time polymerase chain reaction during an experimental infection. Although the transcript showed varying kinetics, viral genes were expressed in infected L. vannamei, demonstrating the replicative capability of this YHV strain.

Genomic analysis of multiple Roseophage SIO1 strains

Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near-shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re-sequenced and re-annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near-shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein-encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein-coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1-like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and approximately 50 km).

Phylogenetic analysis of the Pacific cutthroat trout ( Oncorhynchusclarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: A closer look at the highly fragmented inland species

The genus Oncorhynchus includes Pacific salmon and trout (anadromous and land-locked) species of the western United States and Mexico. All species and subspecies in this group are threatened, endangered, sensitive, or species of conservation concern in portions of their native ranges. To examine the relationships of the species within Oncorhynchus we sequenced a 768 bp fragment of the protein-encoding ND4 mtDNA region. We included all six recognized subspecies of O. clarki (cutthroat trout), O. gilae gilae (Gila trout) and O. g. apache (Apache trout). Gene trees from likelihood and Bayesian phylogenetic analyses revealed that Salvelinus was the sister group to Oncorhynchus, and as expected based on previous studies, O. clarki was sister to a clade that consisted of O. mykiss plus O. g. gilae and O. g. apache. Within the cutthroat clade ( O. clarki), the coastal form O. c. clarki was basal with the Rio Grande cutthroat ( O. c. virginalis) most derived. Divergence dating based on a fossil calibration molecular clock showed the oldest clade (mean node age) was O. masou ssp., which diverged roughly 7.6 MYA. Highest probability density intervals for divergence of O. masou overlapped with divergence (6.3 MYA) of Pacific salmon clades (( O. gorbuscha + O. nerka) and ( O. tshawytscha + O. kisutch)). The Pacific trout clade (( O. mykiss + O. gilae ssp.) + ( O. clarki ssp.)) diverged from the Pacific salmon around 6.3 MYA, with most of the diversification within the O. clarki clade occurring in the last 1 MY.

Protein function prediction – the power of multiplicity

Advances in experimental and computational methods have quietly ushered in a new era in protein function annotation. This 'age of multiplicity' is marked by the notion that only the use of multiple tools, multiple evidence and considering the multiple aspects of function can give us the broad picture that 21st century biology will need to link and alter micro- and macroscopic phenotypes. It might also help us to undo past mistakes by removing errors from our databases and prevent us from producing more. On the downside, multiplicity is often confusing. We therefore systematically review methods and resources for automated protein function prediction, looking at individual (biochemical) and contextual (network) functions, respectively.

Mage-b vaccine delivered by recombinant Listeria monocytogenes is highly effective against breast cancer metastases

New therapies are needed that target breast cancer metastases. In previous studies, we have shown that vaccination with pcDNA3.1-Mage-b DNA vaccine is effective against breast cancer metastases. In the study presented here, we have further enhanced the efficacy of Mage-b vaccination through the improved delivery of the vaccine using recombinant Listeria monocytogenes (LM). Three overlapping fragments of Mage-b as well as the complete protein-encoding region of Mage-b have been expressed as a fusion protein with a truncated non-cytolytic form of listeriolysin O (LLO) in recombinant LM. These different Mage-b vaccine strains were preventively tested for their efficacy against breast cancer metastases in a syngeneic mouse tumour model 4T1. The LM-LLO-Mage-b/2nd, expressing position 311–660 of the cDNA of Mage-b, was the most effective vaccine strain against metastases in the 4T1 mouse breast tumour model. Vaccination with LM-LLO-Mage-b/2nd dramatically reduced the number of metastases by 96% compared with the saline group and by 88% compared with the vector control group (LM-LLO), and this correlated with strong Mage-b-specific CD8 T-cell responses in the spleen, after restimulation with Mage-b. However, no effect of LM-LLO-Mage-b/2nd was observed on 4T1 primary tumours, which may be the result of a complete absence of Mage-b-specific immune responses in the draining lymph nodes. Vaccination with LM-LLO-Mage-b/2nd could be an excellent follow-up after removal of the primary tumour, to eliminate metastases and residual tumour cells.

Genetic Alteration of Keap1 Confers Constitutive Nrf2 Activation and Resistance to Chemotherapy in Gallbladder Cancer

Biliary tract cancer (BTC) is a highly malignant tumor, and identification of effective therapeutic targets to improve prognosis is urgently required. Oncogenic activation of survival genes is important for cancer cells to overcome oxidative stresses induced by their microenvironments that include chronic inflammation or exposure to anticancer drugs. We attempted to examine whether deregulation of Nrf2, a master transcriptional factor of various cytoprotective genes against oxidative stress, plays a role in the carcinogenesis of BTC. We screened genetic alteration of Keap1, a negative regulator of Nrf2, in BTC including tumors originated from gallbladder and extra- and intrahepatic bile ducts. Functional analysis of cancer-related mutant Keap1 in Nrf2 repression and the association between Nrf2 activation and resistance to 5-fluorouracil (5-FU) were investigated. Recurrent (in 1/11 cell lines and 6/53 primary tumors) Keap1 gene alterations were observed in BTC and were especially frequent (4/13, 30.7%) in gallbladder cancer (GBC). These alterations led to a considerable loss of Nrf2 repression activity, caused constitutive activation of Nrf2, and promoted cell proliferation. Down-regulation of Nrf2 activity by either Keap1 complementation or Nrf2 short interference RNA increased sensitivity to 5-FU in Keap1-altered BTC cells. Keap1 mutation occurs frequently in GBC. Aberrant Nrf2 activation provoked by Keap1 alteration is one of the molecular mechanisms for chemotherapeutic resistance in GBC and will be a novel therapeutic target as an enhancer of sensitivity to 5-FU-based regimens.

Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes

Simple sequence repeats (SSRs) are omnipresent in prokaryotes and eukaryotes, and are found anywhere in the genome in both protein encoding and noncoding regions. In present study the whole genome sequences of seven chromosomes (Shigella flexneri 2a str301 and 2457T, Shigella sonnei, Escherichia coli k12, Mycobacterium tuberculosis, Mycobacterium leprae and Staphylococcus saprophyticus) have downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs and also to determine difference between the tandem repeats in real genome and randomness genome (using sequence shuffling tool) of the organisms included in this study. The data obtained in the present study show that: (i) tandem repeats are widely distributed throughout the genomes; (ii) SSRs are differentially distributed among coding and noncoding regions in investigated Shigella genomes; (iii) total frequency of SSRs in noncoding regions are higher than coding regions; (iv) in all investigated chromosomes ratio of Trinucleotide SSRs in real genomes are much higher than randomness genomes and Di nucleotide SSRs are lower; (v) Ratio of total and mononucleotide SSRs in real genome is higher than randomness genomes in E. coli K12, S. flexneri str 301 and S. saprophyticus, while it is lower in S. flexneri str 2457T, S.sonnei and M. tuberculosis and it is approximately same in M. leprae; (vi) frequency of codon repetitions are vary considerably depending on the type of encoded amino acids.

Detection of a novel circovirus in mute swans ( Cygnus olor) by using nested broad-spectrum PCR

Circoviruses are the causative agents of acute and chronic diseases in several animal species. Clinical symptoms of circovirus infections range from depression and diarrhoea to immunosuppression and feather disorders in birds. Eleven different members of the genus Circovirus are known so far, which infect pigs and birds in a species-specific manner. Here, a nested PCR was developed for the detection of a broad range of different circoviruses in clinical samples. Using this assay, a novel circovirus was detected in mute swans ( Cygnus olor) found dead in Germany in 2006. Sequence analysis of the swan circovirus (SwCV) genome, amplified by multiply primed rolling-circle amplification and PCR, indicates that SwCV is a distinct virus most closely related to the goose circovirus (73.2% genome sequence similarity). Sequence variations between SwCV genomes derived from two different individuals were high (15.5% divergence) and mainly confined to the capsid protein-encoding region. By PCR testing of 32 samples derived from swans found dead in two different regions of Germany, detection rates of 20.0 and 77.3% were determined, thus indicating a high incidence of SwCV infection. The clinical significance of SwCV infection, however, needs to be investigated further.

The thousand‐dollar genome

On May 31 this year, James Watson received the DNA sequence of his full genome in a ceremony at the Baylor College of Medicine in Houston (TX, USA). It marked the end of a two‐month project by 454 Life Sciences, a biotech company in Branford (CT, USA) specializing in DNA sequencing, which generated the raw data from a blood sample given by Watson. Baylor College then verified whether the sequence encompassed the entire genome and, on July 6, Watson posted his genome—excluding a portion including the ApoE gene, which he had asked to be redacted—online at the GenBank database maintained by the US National Center for Biology Information (Bethesda, MD, USA). Watson, the co‐discoverer of the double helical structure of DNA and the father of the Human Genome Project, must have expected to be the first person to make his genome publicly available. He was not. Nine days earlier, on June 27, J. Craig Venter, the inventor of the ‘shot‐gun’ sequencing strategy, who once acknowledged a love–hate relationship with his former boss Watson, had posted his own complete genome online prior to a publication (Levy et al , 2007). There was no official race between Venter and Watson to be the first. The timing of the publications of their genomes was the result of two unrelated projects. But what is the rationale for making the genome data of noted geneticists publicly available in the first place? Is it pure scientific research or genetic exhibitionism? Or has science finally embraced celebrity culture? The media hoopla surrounding the sequencing of Watson's genome has already had some commentators worrying that genome sequencing could become the next must‐have for the rich and privileged (Check, 2007). However, beyond the publicity, it is only a matter of time until genome sequencing will be affordable for most …

Construction of an infectious cDNA clone for a Brazilian prototype strain of dengue virus type 1: Characterization of a temperature-sensitive mutation in NS1

To help understand the mechanism of pathogenesis of dengue virus (DV), we set out to create an infectious cDNA of the Brazilian prototype strain of DV serotype 1 (DV1-BR/90). PCR-amplified fragments of DV1-BR/90 cDNA were readily assembled into a subgenomic cDNA that could be used to produce replicating RNAs (replicons), lacking the structural protein-encoding regions of the genome. However, assembly of a cDNA capable of producing infectious virus was only possible using a bacterial artificial chromosome plasmid, indicating that DV1 sequences were especially difficult to propagate in E. coli. While characterizing our cDNA we discovered a fortuitous temperature-sensitive mutation in the NS1 encoding region. Using our infectious cDNA and a renilla luciferase-expressing replicon we were able to demonstrate that this mutation produced a defect in RNA replication at 37 °C, demonstrating that the DV1 NS1 protein plays an essential role in RNA replication.

Compartmentalization of the gut viral reservoir in HIV-1 infected patients

BackgroundRecently there has been an increasing interest and appreciation for the gut as both a viral reservoir as well as an important host-pathogen interface in human immunodefiency virus type 1 (HIV-1) infection. The gut associated lymphoid tissue (GALT) is the largest lymphoid organ infected by HIV-1. In this study we examined if different HIV-1 quasispecies are found in different parts of the gut of HIV-1 infected individuals.ResultsGut biopsies (esophagus, stomach, duodenum and colorectum) were obtained from eight HIV-1 infected preHAART (highly active antiretroviral therapy) patients. HIV-1 Nef and Reverse transcriptase (RT) encoding sequences were obtained through nested PCR amplification from DNA isolated from the gut biopsy tissues. The PCR fragments were cloned and sequenced. The resulting sequences were subjected to various phylogenetic analyses. Expression of the nef gene and viral RNA in the different gut tissues was determined using real-time RT-PCR. Phylogenetic analysis of the Nef protein-encoding region revealed compartmentalization of viral replication in the gut within patients. Viral diversity in both the Nef and RT encoding region varied in different parts of the gut. Moreover, increased nef gene expression (p < 0.05) and higher levels of viral genome were observed in the colorectum (p < 0.05). These differences could reflect an adaptation of HIV-1 to the various tissues.ConclusionOur results indicated that different HIV-1 quasispecies populate different parts of the gut, and that viral replication in the gut is compartmentalized. These observations underscore the importance of the gut as a host-pathogen interface in HIV-1 infection.

Complete nucleotide sequence of genotype 4 hepatitis C viruses isolated from patients co-infected with human immunodeficiency virus type 1

The hepatitis C virus (HCV) genotype 4 is spreading among southern European intravenous drug users, who are frequently co-infected with human immunodeficiency virus type 1 (HIV-1). Response to interferon (IFN) α-based therapies in HIV-1 positive patients co-infected with HCV genotype 4 is poor, similar to that obtained for HCV genotype 1 and much lower than for HCV genotypes 2 and 3. The lack of sequence data related to HCV of genotype 4 prompted us to sequence the complete genome of two genotype 4 variants isolated from two HIV-1 co-infected patients (24 and 25). Our aim was to investigate the evolutionary relationships of the former variants with other genotypes and/or genotype 4 subtypes. Sequence alignments and phylogenetic analysis from genomic regions 5′NC, core-E1 and NS5B revealed that the variants isolated from patients 24 and 25 (both subtyped 4c/4d by INNO-LIPA II HCV) belong to subtypes 4d and 4a, respectively. When looking at the complete genome sequence one of the variants showed a new genotype 4 subtype. Interestingly, sequence length differences in the interferon sensitivity determining region coding regions were observed when compared with sequences from other genotypes. Similarly, when the catalytic efficiency of the NS3/4 protease from patients 24 and 25 samples were determined, they displayed 70.6 ± 7.7 and 23.5 ± 3.4%, respectively, of the activity shown by genotype 1 NS3/4 proteases. Overall, pairwise comparison and phylogenetic analysis of nucleotide sequences of the complete genome or the different protein-encoding regions showed that genotype 4 sequences were more closely related to genotype 1 sequences. The description of new HCV genome variants may help our understanding of the HCV biology as well as the role of different genotypes in HCV treatment and therapy response.

Comparison of 3′-End Encoding Regions of Turkey Coronavirus Isolates from Indiana, North Carolina, and Minnesota with Chicken Infectious Bronchitis Coronavirus Strains

Objective: To analyze the 3′-end structural protein-encoding region of turkey coronavirus (TCoV) isolates associated with outbreaks of acute enteritis in Indiana, North Carolina, or Minnesota. Methods: Four isolates of TCoV were sequenced over the entire 3′-end structural protein-encoding region and compared phylogenetically along with the corresponding sequences of infectious bronchitis virus (IBV) strains. Results: The sequence similarity between TCoV and IBV was lower than that among TCoV isolates or that among IBV strains. The variation of sequences between TCoV and IBV was mainly contributed by the S protein gene. The sequence similarity of S gene between TCoV and IBV was lower than that among TCoV isolates or that among IBV strains. The phylogenetic tree based on the S protein region was similar to that based on the entire 3′-end structural protein-encoding region with TCoV isolates and IBV strains grouped in two separate clusters. The phylogenetic tree based on other genes had a very different topology with TCoV isolates randomly forming groups with different IBV strains. Conclusions: These results suggested that TCoV probably shared the same origin with that of IBV and acquired sequences of S gene for turkey intestine tropism during the process of evolution in a separate environment.

Evaluation of a structural polymorphism in the ankyrin repeat and kinase domain containing 1 (ANKK1) gene and the activation of executive attention networks

The specificity of genetic effects on brain activation is a central issue in understanding how molecular actions at the synapse relate to anatomic patterns of brain activity. In an effort to understand the basis for the specificity of gene-associated brain activity, we explore a well-studied genetic polymorphism, TaqIA, which lies downstream of the DRD2 gene in the protein-encoding region of a neighboring gene, ANKK1, which is not expressed in the brain. We utilize the attention network test and find that carriers of the A1 allele show gene-associated functional activation in an anatomically specific, dopamine-rich region of the brain comprising the anterior cingulate gyrus, a finding partially consistent with prior data from functional imaging genetics. A review of the patterns of expression for ANKK1 and DRD2 and the extent of linkage disequilibrium between the two genes sheds light on additional criteria for the selection of candidate genes in imaging-genetic studies.

Classification and Structure of Echovirus 5′-UTR Sequences

Enteroviruses are classified into two genetic clusters on the basis of 5'-UTR and all echoviruses (ECV) are classified together with coxsackie B viruses (CBV), coxsackie A viruses (CAV) types 2-10, 12, 14 and 16, and enteroviruses (EV) 68, 69, 71 and 73. During the present study, 5'-UTR-derived sequences constituting the largest part of the Internal Ribosome Entry Site (IRES) of ECVs were studied with respect to their possible secondary structures, which were predicted following the phenomenon of "covariance", i.e. the existence of evolutionary pressure in favour of structural conservation in the light of nucleotide sequence variability. In this and previous studies, no correlation between overall 5'-UTR identity and the currently recognised Human Enterovirus species was found, implying that notwithstanding their divergent protein-encoding regions, these species are free to exchange 5'-UTRs by recombination. Secondary structure features which are known to be highly conserved amongst enteroviruses and specifically the GNRA tetraloop in secondary structure domain IV, involved in long-term tertiary interactions and loop B in secondary structure domain V with an as yet unknown function were also conserved in ECVs. In contrast, the C(NANCCA)G motif, which is considered to be important in virus transcription and translation, was not conserved in all ECVs and sequence patterns observed in other enterovirus groups and rhinoviruses were recorded.

Comparative Genomics of Foot-and-Mouth Disease Virus

Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5' and 3' untranslated regions (UTR), as was tolerance for insertions/deletions in the 5' UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L(pro), 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.