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.

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.

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.

[Riboprobes: an alternative in the detection of viral sequences]. / Las ribosondas: una alternativa en la detección de secuencias virales.

The use of riboprobes for the detection of RNA viral sequences is analyzed. Subgenomic fragments of cDNA from poliovirus type 2, dengue virus type 4 and human immunodeficiency virus type 1, were inserted downstream SP6 and/or T7 promoters in the transcription vectors pGEM-4z or pSP64. RNAs obtained by in vitro transcription in the presence of UTP infinity (32P) were used as probes for the detection of RNA viral sequences from infected cell lines in slot and Northern blot assays. The poliovirus riboprobe (P2-221) was able to detect specific viral sequences; thus, it could be used for the detection of the virus in serum, as well as in residual waters. The human immunodeficiency virus riboprobe (HIV-378), detected viral sequences poly A+RNA from infected cells; thus it can be used as a confirmatory test or as a tool in basic research. Finally, the dengue virus riboprobes (D4-2819 and D4-1134) detected specifically dengue 4 virus; however the sensitivity of the detection could be significantly improved amplifying viral sequences by the polymerase chain reaction (PCR) prior to probe hybridization.