The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.

The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.

No Evidence of Dengue Virus Infections in Several Species of Bats Captured in Central and Southern Mexico.

Bats are reservoirs for viruses with zoonotic potential in the Americas, and scattered evidence exists suggesting that bats may act as reservoirs for dengue virus (DENV). To explore further the role of bats as part of DENV sylvatic cycles, 240 bats of 18 species were captured in 2 states of Mexico with contrasting ecological characteristics but concurrent DENV activity in humans. RT-PCR analysis of RNA extracted from liver or spleen tissue from de bats failed to show evidence for the presence of DENV nucleic acids in these organs. In addition, plasma assayed by plaque reduction neutralization test showed no evidence of neutralizing anti-DENV antibodies. These results suggest that American bats may not be reservoirs or amplification host for DENV infection.

Frequency of the thermolabile variant C677T in the MTHFR gene and lack of association with neural tube defects in the State of Yucatan, Mexico.

The C677T variant in the MTHFR gene is considered to be an associated risk factor for neural tube defects. However, the association has not been found in some ethnic groups. In order to assess the association between neural tube defects and the C677T variant, we determined the frequency of this variant in the MTHFR gene in the State of Yucatan, Mexico, where neural tube defects are highly prevalent. The study was performed on 65 subjects with spine bifida, 60 of their mothers and 110 control subjects. The presence of the C677T variant was determined by amplification and digestion with HinF1 of each subject's DNA. Genotypic and allelic frequencies were calculated for all groups. We did not observe any statistically significant difference in the genotypic or allelic frequencies between cases and controls for any of the groups studied (p > 0.05), suggesting that the thermolabile variant C677T is not an associated risk factor neither for the development of neural tube defects nor for mothers to have affected offspring in the population from Yucatan. Interestingly, the frequency of the C677T variant (54%) obtained in the Yucatan population is one of the highest reported (p < 0.01) and confirmed the high frequency of this allele throughout Mexico.

Identification of a putative coreceptor on Vero cells that participates in dengue 4 virus infection.

Dengue virus infects target cells by attaching to a cell surface receptor through the envelope (E) glycoprotein, located on the surface of the viral membrane. On Vero and BHK cells, heparan sulfate (HS) moieties of proteoglycans are the receptors for dengue virus; however, additional proteins have also been described as putative dengue virus receptors on C6/36, HL60, and BM cells. HS can also act as a receptor for other types of viruses or as an attachment molecule for viruses that require additional host cell molecules to allow viral penetration. In this study we searched for molecules other than HS that could participate in dengue virus infection of Vero cells. Labeled dengue 4 virus bound with high affinity to two molecules of 74 and 44 kDa. Binding of dengue virus to the 74-kDa molecule was susceptible to protease and sodium periodate treatment and resistant to heparinase treatments. Lectins such as concanavalin A and wheat germ agglutinin prevented dengue virus binding to both the 74- and the 44-kDa protein in overlay assays, while phytohemagglutinin P did not affect binding, suggesting that carbohydrate residues (alpha-mannose or N-acetylglucosamine) are important in virus binding to host cells. Protease susceptibility, biotin labeling, and immunofluorescence with a polyclonal antibody raised against the 74-kDa protein consistently identified the protein on the surfaces of Vero cells. Moreover, the antibody against the 74-kDa protein was able to inhibit dengue virus infection. These data suggest that HS might serve as a primary receptor, probably concentrating virus particles on the surfaces of Vero cells, and then other molecules, such as the 74-kDa protein, might participate as coreceptors in viral penetration. The 74-kDa protein possibly constitutes part of a putative receptor complex for dengue virus infection of Vero cells.

Interaction of cellular proteins with the 5' end of Norwalk virus genomic RNA.

The lack of a susceptible cell line and an animal model for Norwalk virus (NV) infection has prompted the development of alternative strategies to generate in vitro RNAs that approximate the authentic viral genome. This approach has allowed the study of viral RNA replication and gene expression. In this study, using mobility shift and cross-linking assays, we detected several cellular proteins from HeLa and CaCo-2 cell extracts that bind to, and form stable complexes with, the first 110 nucleotides of the 5' end of NV genomic RNA, a region previously predicted to form a double stem-loop structure. These proteins had molecular weights similar to those of the HeLa cellular proteins that bind to the internal ribosomal entry site of poliovirus RNA. HeLa proteins La, PCBP-2, and PTB, which are important for poliovirus translation, and hnRNP L, which is possibly implicated in hepatitis C virus translation, interact with NV RNA. These protein-RNA interactions are likely to play a role in NV translation and/or replication.

Identification of two surface proteins from C6/36 cells that bind dengue type 4 virus.

Dengue viruses infect cells by attaching to a surface receptor, probably through the envelope (E) glycoprotein, located on the surface of the viral membrane. However, the identity of the dengue virus receptor in the mosquito and in mammalian host cells remains unknown. To identify and characterize the molecules responsible for binding dengue virus, overlay protein blot and binding assays were performed with labeled virus. Two glycoproteins of 40 and 45 kDa located on the surface of C6/36 cells bound dengue type 4 virus. Virus binding by total and membrane proteins obtained from trypsin-treated cells was inhibited, while neuraminidase treatment did not inhibit binding. Periodate treatment of cell proteins did not reduce virus binding, but it modified the molecular weight of the polypeptide detected by overlay assays. Preincubation of C6/36 cells with electroeluted 40- and 45-kDa proteins or with specific antibodies raised against these proteins inhibited virus binding. These results strongly suggest that the 40- and 45-kDa surface proteins are putative receptors or part of a receptor complex for dengue virus.

Attenuating mutations in the poliovirus 5' untranslated region alter its interaction with polypyrimidine tract-binding protein.

Mutations in the 5' untranslated regions (5'-UTRs) of all three serotypes of the Sabin vaccine strains are known to be major determinants of the attenuation phenotype. To further understand the functional basis of the attenuation phenotype caused by mutations in the 5'-UTR, we studied their effects on viral replication, translation, and the interaction of the viral RNA with cell proteins. A mutation at base 472 (C472U), which attenuates neurovirulence in primates and mice, was previously found to reduce viral replication and translation in neuroblastoma cells but not in HeLa cells. This mutation reduced cross-linking of the poliovirus 5'-UTR to polypyrimidine tract-binding protein (pPTB) in neuroblastoma cells but not in HeLa cells. These defects were absent in a neurovirulent virus with C at nucleotide 472. When C472U and an additional mutation, G482A, were introduced into the 5'-UTR, the resulting virus was more attenuated, had a replication and translation defect in both HeLa cells and neuroblastoma cells, and cross-linked poorly to pPTB from both cell types. A neurovirulent revertant of this virus (carrying U472C, G482A, and C529U) no longer had a replication defect in HeLa and SH-SY5Y cell lines and cross-linked with pPTB to wild-type levels. The results suggest that the attenuating effects of the mutation C472U may result from an impaired interaction of the 5'-UTR with pPTB in neural cells, which reduces viral translation and replication. Introduction of a second mutation, G482A, into the 5'-UTR extends this defect to HeLa cells.

Recognition of synthetic oligopeptides from nonstructural proteins NS1 and NS3 of dengue-4 virus by sera from dengue virus-infected children.

The nonstructural proteins NS1 and NS3 from dengue virus are involved in the immune response during natural infection in humans. To analyze the immunogeneity of some epitopes present in NS1 and NS3 proteins from dengue virus type-4, six oligopeptides were synthesized; five from NS1 (NS1.1, NS1.2, NS1.3, NS1.4, and NS1.5) and one from NS3 (NS3.1). Peptides NS1.1, NS1.2, NS1.3, NS1.5, and NS3.1 were recognized by sera from dengue virus-infected children, suggesting that they represent exposed epitopes during natural dengue virus infection.

Differences in the UV-crosslinking patterns of the poliovirus 5'-untranslated region with cell proteins from poliovirus-susceptible and -resistant tissues.

The restricted tissue tropism observed in poliovirus infection is not governed solely by the expression of the poliovirus receptor (PVR) gene, but might be controlled at stages beyond virus entry, such as translation, replication, or assembly. Translation of poliovirus RNA by a cap-independent mechanism requires interactions of the 5'-untranslated region (5'UTR) with cell proteins. To determine whether the patterns of these interacting proteins differ in HeLa cells and permissive and nonpermissive tissues, UV-crosslinking assays using the poliovirus 5'UTR and tissue extracts from PVR transgenic mice were performed. The results indicate a correlation between the presence of a 97-kDa UV-crosslinked protein and permissivity to poliovirus infection. Acquired poliovirus susceptibility in in vitro-cultured kidney cells also correlates with the presence of a 97-kDa crosslinked band. The interaction of the 97-kDa protein from HeLa cells and mouse brain with the poliovirus 5'UTR is stable and specific. Whether the 97-kDa protein plays a role in poliovirus translation and tissue susceptibility remains to be determined.

G542X mutation in Mexican cystic fibrosis patients.

We analyzed the frequency of the G542X mutation in a sample of 76 Mexican cystic fibrosis patients and the genotype-phenotype correlation. The mutation was screened using PCR-mediated site-directed mutagenesis, and was present on 7.2% of the CF chromosomes. This frequency is significantly higher than the worldwide frequency according to the Cystic Fibrosis Genetic Analysis Consortium (3.4%, p < 0.01), and similar to that reported in Spain (8%), which is in accordance with the ethnic origin of the Mexican population. All patients carrying G542X on at least one allele had mild to moderate pulmonary disease. In patients with hepatobiliary involvement, the frequency of G542X chromosomes was higher than the frequency of the mutation in all the Mexican CF chromosomes.

Nuclear proteins bind to poliovirus 5' untranslated region.

Poliovirus induces a shut-off of messenger RNA (mRNA) translation by the proteolysis of a 220 kDa protein from the eukaryotic initiation factor eIF-4F, and by the phosphorylation of eIF-2. The absence of eIF-4F inhibits the initiation of translation dependent on cap structure recognition. Poliovirus RNA lacks cap structure and translates by a cap-independent mechanism which requires internal ribosomal entry. The poliovirus 5' untranslated region (5'UTR) contains the structural elements for cap-independent translation called internal ribosomal entry site (IRES element). Several cellular proteins have been described interacting with different segments from poliovirus 5'UTR. We have studied the specific interaction between 57/60, 52, and 35 kDa cellular proteins with poliovirus nt 275 to 636 and full length 5'UTR. By Western blot assay the 57/60 protein was identified as a pyrimidine tract binding protein (PTB), and the 52 kDa protein as a La-autoantigen. La and PTB are nuclear proteins involved in RNA polymerase III transcription termination and splicing, respectively.

Cell proteins bind to a linear polypyrimidine-rich sequence within the 5'-untranslated region of rhinovirus 14 RNA.

Members of the picornavirus family initiate translation of their RNA genomes by a cap-independent mechanism in which ribosomes bind to an internal site in the 5' untranslated region (5'-UTR). This unique process requires an internal ribosome entry site (IRES), a highly structured RNA whose function is mediated in part by interactions with cell proteins. The IRES element of human rhinovirus 2 (HRV-2) extends from nucleotide (nt) 10 to between nt 544 and 568 and has been shown to interact with two cell proteins, pyrimidine tract-binding protein (pPTB) and p97. To map the specific regions of HRV-14 RNA that bind cell proteins, mobility shift, UV cross-linking and Western immunoblot analyses were performed. The results indicate that an RNA sequence from nt 538 to 591 interacts with pPTB and La, two proteins previously shown to functionally interact with the IRES elements of several picornaviruses. Two additional proteins, p97 and p68, were also cross-linked to nt 538 to 591 RNA. These four proteins interact with a putatively unstructured portion of the 5'-UTR that contains a polypyrimidine tract and has been shown to be present at the 3' border of sequences that are essential for IRES function of HRV-2. These protein-RNA interactions are likely to play a role in internal initiation of translation.

Cell proteins bind to multiple sites within the 5' untranslated region of poliovirus RNA.

The 5' noncoding region of poliovirus RNA contains sequences necessary for translation and replication. These functions are probably carried out by recognition of poliovirus RNA by cellular and/or viral proteins. Using a mobility-shift electrophoresis assay and 1,10-phenanthroline/Cu+ footprinting, we demonstrate specific binding of cytoplasmic factors with a sequence from nucleotides 510-629 within the 5' untranslated region (UTR). Complex formation was also observed with a second sequence (nucleotides 97-182) within the 5' UTR. These two regions of the 5' UTR appear to be recognized by distinct cell factors as determined by competition analysis and the effects of ionic strength on complex formation. However, both complexes contain eukaryotic initiation factor 2 alpha, as revealed by their reaction with specific antibody.