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.

Evaluation of a commercial enzyme immunoassay for the detection of norovirus antigen in fecal samples from children with sporadic acute gastroenteritis.

The Ridascreen Norwalk-like virus enzyme immunoassay was compared with (RT)-PCR on 92 stool samples collected from children with sporadic acute gastroenteritis. Homogenization and pre-dilution of the whole stool sample resulted in high specificity (97.5%) and moderate sensitivity (60%). This assay may be useful to screen outbreaks for norovirus, but limited to detect the virus in sporadic cases of diarrhea.

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.

Calicivirus infection in human immunodeficiency virus seropositive children and adults.

BACKGROUND: The importance of enteric viral infections in HIV-related diarrhea is uncertain. Human caliciviruses have emerged as a leading cause of acute diarrhea worldwide. OBJECTIVES: To evaluate the importance of calicivirus infections in HIV-related diarrhea. Study design 151 fecal samples collected from children and adults infected with HIV, with and without diarrhea, were examined. In addition, 89 fecal samples from non HIV-infected children and adults were also tested. Samples were analyzed by RT-PCR using primer sets specific to Norovirus genogroup I or genogroup II as well as primers designed to react with both Noroviruses and Sapovirus genus. RESULTS: Viruses were detected with equal frequencies in stools from HIV infected and non-infected adults (12%). However, specimens from HIV infected children were more likely than those of HIV-negative children to have caliciviruses (51% versus 24%, P<0.05). Viral infections were not significantly associated with diarrhea neither in children nor in adults, regardless of HIV status. Viruses genetically related to the common Lordsdale virus (Norovirus genogroup II) and London/92 virus (Sapovirus) clusters were detected circulating among children. CONCLUSIONS: These results suggest that caliciviruses may be an important opportunistic pathogen in children infected with HIV.

Fluorimetric quantification of cell death in monolayer cultures and cell suspensions.

A fluorimetric assay using ethidium bromide (EB) was employed to quantify cell death in monolayer cell cultures (MA-104 cells) in situ and isolated cell suspensions (isolated colonic cells and Leishmania). Fluorescence of EB stained cells was measured with a photometer coupled to an inverted microscope for cell monolayers or in a spectrofluorometer for cell suspensions. Dead cells stained with trypan blue were fluorescent with EB in all preparations studied, but the latter gave an unequivocal signal. Staining with EB and fluorescein diacetate was mutually exclusive. The relationship between the number of EB fluorescent cells and the intensity of fluorescence measured in the microphotometer was linear for a large range of cell numbers (1-14000) from different types of preparations. Applicability of the method for measuring living and dead cells in two different time scales (minutes and hours) is shown using MA-104 cell monolayers infected with rotavirus and Leishmania suspensions treated with amphotericin B. The method is fast, simple, sensitive and reliable, enabling quantification of living and dead cells in monolayers and suspensions.

Identification of picobirnavirus, viruses with bisegmented double stranded RNA, in rabbit faeces.

Picobirnaviruses are a novel group of viruses recently found in the faeces of several species of vertebrates. Examination by polyacrylamide gel electrophoresis of rabbit faecal samples collected in one animal facility revealed the viruses in 23 (11 per cent) of 211 samples. Further analysis by electron microscopy and caesium chloride isopycnic centrifugation confirmed the presence of picobirnaviruses in the samples. The oral inoculation of three newly weaned rabbits with purified viruses resulted in the excretion of a virus with an electropherotype similar to the inoculum, by two of the three inoculated animals. Maximal viral shedding was detected 13 days after inoculation. No sign of diarrhoea was observed either in the inoculated animals or in the virus excreting animals surveyed. No antibody activity could be detected in the paired serum samples taken from the inoculated animals.

Infection with transfusion-transmitted virus (TTV) in humans and other primates in Venezuela.

Tranfusion-transmitted virus (TTV), a single-stranded circular DNA virus that chronically infects humans and other animals, displays a high degree of genetic diversity and was originally thought to be associated with hepatitis. The prevalences of TTV infection among different populations of humans and non-human primates from Venezuela have now been evaluated, using serum samples and three different detection tests. All three tests were PCR-based, one involving a hemi-nested PCR and primers based on the N22 open-reading-frame-1 region (N22-PCR), another employing 55 cycles with primers from the more conserved untranslated region (UTR-PCR), and the other using a hemi-nested PCR with primers from the same region (HUTR-PCR). The overall prevalences of human infection appeared much higher with the HUTR-PCR (52%) than with the N22-PCR (13%) or the UTR-PCR (5%). When the products amplified by N22-PCR from 28 human isolates of TTV were sequenced, only two genotypes of the virus were detected. The non-human sera tested came from primates kept in a zoo in north-western Venezuela. TTV DNA was detected, by HUTR-PCR, in both of the chimpanzee sera tested but not in any of the sera from the 11 New-World primates or the other 12 Old-World primates that were investigated. The results, particularly those of the HUTR-PCR, indicate that TTV infection is common in Venezuela, especially in populations, such as many Amerindian groups, who live under poor sanitary conditions. Although TTV infection may be relatively rare among non-human primates from the New World, this will have to be investigated further, using many more samples collected throughout the Americas.

Identification of viruses with bi- and trisegmented double-stranded RNA genome in faeces of children with gastroenteritis.

Polyacrylamide gel electrophoresis of nucleic acid extracted from faecal samples of diarrhoeic children revealed the presence of group A rotavirus in 50 (23.4%) samples and group C rotavirus in 1 (0.5%) sample out of 214 tested. One other sample showed the presence of three bands (with apparent length of 2.92, 2.37 and 1.32 kbp) which by enzymatic digestion analysis, were shown to consist of double-stranded RNA (dsRNA). The sample was shown by electron microscopy to contain virus particles with a diameter of 32-34 nm. On the basis of morphology and genomic characteristics, this virus closely resembles a virus hitherto described only in chickens by Leite et al. in 1990 and tentatively named "picotrirnavirus". From the same group of 214, one sample containing a "picobirnavirus" was also identified. Thus, small icosahedral viruses with either a bior trisegmented dsRNA genome appear to infect humans. However, their pathogenic potential remains to be established.

Comparative amino acid sequence analysis of the major outer capsid protein (VP7) of porcine rotaviruses with G3 and G5 serotype specificities isolated in Venezuela and Argentina.

Seven porcine group A rotavirus strains isolated in Venezuela were shown to be antigenically related to serotype G3 (five strains) or to serotype G5 (two strains), whereas two strains isolated in Argentina were classified as serotype G5. The serological classification of eight of these strains was confirmed by sequence analysis of the gene encoding the VP7 glycoprotein. A high degree of homology was observed among strains belonging to the same G serotype, although some variations in the serotype-specific regions were detected among different strains. Comparison with the published VP7 amino acid sequences of serotype G3 indicated that most porcine rotavirus strains are more closely related to each other and to human rotavirus strains than to rotavirus strains isolated from other species. Amino acid sequence comparison among serotype G5 porcine strains revealed that Venezuelan porcine isolates were more closely related to the American strain OSU, while the Argentinian strains had a higher similarity to the Australian strain TRF-41. This report confirms the worldwide distribution of these G serotypes among the porcine population.

The structure of the rotavirus inner capsid studied by electron microscopy of chemically disrupted particles.

The inner capsid structure of the OSU strain of porcine rotavirus was studied by electron microscopy of freeze-dried preparations and of negatively stained chemically disrupted virus particles. The analysis of the particles by the freeze-drying technique revealed a T:13 l (laevo) symmetry for the organization of the inner capsid. Treatment of single-capsid rotavirus particles with 30% formamide or 5 M-urea resulted in their degradation, giving rise to very similar products, corresponding to isolated vertices, edges and faces of the virus icosahedron. An analysis of such structures confirmed the triangulation number and handedness of the rotavirus inner capsid, and provided evidence for the open-mesh model, in which the five- and six-coordinated axes are represented by 'holes' formed by smaller trimeric morphological subunits.

Identification in porcine faeces of a novel virus with a bisegmented double stranded RNA genome.

Polyacrylamide gel electrophoresis of nucleic acids extracted from porcine faecal samples revealed in several samples the presence of two discrete bands. The bands were resistant to digestion with of DNase I and RNase T1, but not with RNase A in low salt conditions, indicating that they consisted of double stranded (ds) RNA. The two bands from different samples varied in sizes, in a range between 2.4-2.6 kbp and 1.7-1.9 kbp for the slow and fast moving band respectively. The bands cosedimented in CsCl gradients at an average density of 1.415 g/ml with icosahedral virus particles of a diameter of 34 nm and a triangulation number equal to 3. Aggregates of virus, which appeared to be immunocomplexes, were seen in one sample. From 244 faecal samples collected in one farm, 27 (11.1%) were found to contain the characteristic dsRNA pattern, with a higher prevalence in samples from animals 15 to 35 days old. The agent was equally distributed among samples from diarrhoeic or non-diarrhoeic animals. These results confirm the circulation among pigs of a novel virus, possibly of vertebrates, with a bisegmented double stranded RNA genome, similar to viruses previously described in humans, wild rats, guinea pigs, pigs, and chickens, for which the name "picobirnavirus" has been proposed.

Penetration and uncoating of rotaviruses in cultured cells.

Early steps of replication (penetration and uncoating) of the OSU strain of porcine rotavirus were studied in MA-104 cells. After adsorption of trypsin-treated viruses at 4 degrees, followed by a shifting of the temperature to 37 degrees, particles were seen within coated pits, coated vesicles, and secondary lysosomes, indicating that virus entry occurred by receptor-mediated endocytosis, and that uncoating (removal of the outer capsid) could occur by the effect of lysosomal enzymes. This latter aspect was studied using lysosomotropic drugs (chloroquine and ammonium chloride), which were found not to inhibit rotavirus replication, indicating that the low intralysosomal pH is not responsible for virus uncoating. The effect of Ca2+ concentration on intracellular rotavirus uncoating was investigated by treating cells with the calcium ionophore A23187, to increase the intracellular Ca2+ concentration during the early stages of virus replication. Under these conditions rotavirus uncoating did not occur, suggesting that the low Ca2+ concentration in the intracellular microenvironment may be responsible for rotavirus uncoating.

Prevalence of enteric viruses in human immunodeficiency virus seropositive patients in Venezuela.

The prevalence of enteric viruses associated with gastroenteritis was determined in 125 stool samples from patients infected with the human immunodeficiency virus (HIV), with or without diarrhea. Diagnostic assays included enzyme immunoassays for the identification of rotavirus, adenovirus, and Norwalk virus; polyacrylamide gel electrophoresis for atypical rotaviruses and picobirnaviruses and polymerase chain reaction for astrovirus. Enteric viruses were detected in 6.4% (8 of 125) of the stools collected: five (4.0%) samples positive for adenoviruses, and three (2.3%) samples positive for picobirnaviruses were detected. No rotavirus, astrovirus, or Norwalk virus were observed. Only one of the viruses identified (adenovirus) was found in a sample from a patient with diarrhea. Viruses were detected in 10% of the patients with AIDS, 14% of the symptomatic patients, and none of the asymptomatic persons. These results do not support a major role for enteric viruses in the diarrhea suffered by HIV-infected patients.

Effect of rotavirus infection on intracellular calcium homeostasis in cultured cells.

The effect of rotavirus infection on intracellular [Ca2+] was studied in a model system (MA-104 cells). In cells infected at high multiplicity with the OSU strain of rotavirus, production of infectious viruses was maximal at 6 hr postinfection. Cell death, as measured by incorporation of ethidium bromide, started at 6 hr and was complete at 15 hr postinfection. At 4 hr postinfection, intracellular [Ca2+], measured by quin2 fluorescence, was not modified, but Ca2+ permeability was increased. With progression of the infection, intracellular [Ca2+] and Ca2+ pools increased due to the failure of regulatory mechanisms to compensate increased Ca2+ entry. These effects were blocked by cycloheximide added up to 5 hr postinfection, but not by actinomycin D. Reduced extracellular [Ca2+] afforded protection of cell death induced by infection, under conditions at which production of infectious viruses was not affected. The cytopathic effect of rotavirus on host cells appears to be mediated by an increase in intracellular [Ca2+] induced by the synthesis of a viral product. The failure of ionic homeostasis of the enterocyte might be involved in the development of diarrhea.

Identification and type distribution of astroviruses among children with gastroenteritis in Colombia and Venezuela.

Astrovirus infections were detected by enzyme immunoassay in 12 (5%) of 251 stool samples from children with gastroenteritis from Bogota, Colombia. In addition, astroviruses were detected by reverse transcription-PCR in 3 (10%) of 29 stool samples negative for other enteric pathogens collected in Caracas, Venezuela, from children with gastroenteritis. Astrovirus type 1 was the most frequently detected virus.

Monoclonal antibodies to the VP6 of porcine subgroup I rotaviruses reactive with subgroup I and non-subgroup I non-subgroup II strains.

A panel of 10 monoclonal antibodies produced after immunization with two porcine subgroup I rotavirus strains (OSU and A46), and directed against the major inner capsid protein (VP6), fell into six patterns of reactivity when tested against a collection of human and animal group A rotavirus strains. Monoclonal antibodies of pattern I recognized all rotavirus strains. Antibodies of patterns 2 and 3 recognized all subgroup II strains and some, but not all, subgroup I strains. Pattern 4 antibodies identified all subgroup I strains and two strains (H2, equine; CC117, porcine) not reactive with reference subgroup monoclonal antibodies (strains non-I non-II). Pattern 5 antibody exhibited the same reactivity as pattern 4 except for not recognizing the non-I non-II equine strain. Pattern 6 antibodies reacted exclusively with subgroup I and non-I non-II rotaviruses of porcine origin. By competitive binding assays, monoclonal antibodies of patterns 4, 5 and 6 appeared to recognize a single antigenic site, which included at least three overlapping epitopes. In immunoblots all monoclonal antibodies, except one, recognized only the trimeric, but not the monomeric form of VP6.

Rotavirus infection alters Na+ and K+ homeostasis in MA-104 cells.

Infection of MA-104 cells with the OSU strain of rotavirus induced an increase in Na+ and a decrease in K+ intracellular concentrations, starting at 4 h post-infection. These changes were not related to an inhibition of the Na+/K+ pump since ouabain-sensitive 86Rb uptake was augmented in rotavirus-infected cells compared to control cells, whereas the [3H]ouabain binding and Na+/K+ ATPase activity in the cell homogenate were unaffected. Furosemide-sensitive 86Rb uptake (Na+/K+/2Cl- cotransport) was not modified by the infection. Passive 86Rb efflux and 22Na influx were augmented in infected cells suggesting an increase in the plasma membrane permeability. The increase in intracellular Na+ concentration might be responsible for the observed stimulation of the Na+/K+ pump. This effect was dependent upon the synthesis of viral proteins because it was abolished by addition of cycloheximide up to 4 h post-infection. Prevention of the increase in intracellular Na+ by the use of low Na(+)-containing media did not modify the pattern of protein synthesis. This suggests that changes in intracellular Na+ and K+ concentrations were not related to shutoff of cellular protein synthesis. Alterations of ion contents in the rotavirus-infected enterocytes might impair intestinal absorptive capacity before the appearance of histopathological lesions.

Enteric virus infections and diarrhea in healthy and human immunodeficiency virus-infected children.

Forty-three stool samples from 27 human immunodeficiency virus (HIV)-seropositive children and 38 samples from 38 HIV-negative children, collected during a 15-month period, were examined for enteric viruses. Diagnostic assays included enzyme immunoassays for rotavirus, adenovirus, and Norwalk virus; polyacrylamide gel electrophoresis for picobirnavirus and atypical rotavirus; and PCR for astrovirus and enterovirus. Specimens from HIV-positive children were more likely than those of HIV-negative children to have enterovirus (56 versus 21%; P < 0.0002) and astrovirus (12 versus 0%; P < 0.02), but not rotavirus (5 versus 8%; P > 0.5). No adenoviruses, picobirnaviruses, or Norwalk viruses were found. The rates of virus-associated diarrhea were similar among HIV-positive and HIV-negative children. Enteroviruses were excreted for up to 6 months in HIV-positive children; however, no evidence for prolonged excretion of poliovirus vaccine was observed. These results suggest that although infection with enterovirus and astrovirus may be frequent in HIV-infected children, enteric viruses are not associated with the diarrhea frequently suffered by these children.

Genetic mapping indicates that VP4 is the rotavirus cell attachment protein in vitro and in vivo.

To identify the rotavirus protein which mediates attachment to cells in culture, viral reassortants between the simian rotavirus strain RRV and the murine strains EHP and EW or between the simian strain SA-11 and the human strain DS-1 were isolated. These parental strains differ in the requirement for sialic acid to bind and infect cells in culture. Infectivity and binding assays with the parental and reassortant rotaviruses indicate that gene 4 encodes the rotavirus protein which mediates attachment to cells in culture for both sialic acid-dependent and -independent strains. Using ligated intestinal segments of newborn mice and reassortants obtained between the murine strain EW and RRV, we developed an in vivo infectivity assay. In this system, the infectivity of EW was not affected by prior treatment of the enterocytes with neuraminidase, while neuraminidase treatment reduced the infectivity of a reassortant carrying gene 4 from RRV on an EW background more than 80% relative to the controls. Thus, VP4 appears to function as the cell attachment protein in vivo as well as in vitro.

Cleavage of rotavirus VP4 in vivo.

The infectivity of rotavirus particles is dependent on proteolytic cleavage of the outer capsid protein, VP4, at a specific site. This cleavage event yields two fragments, identified as VP5* and VP8*. It has been hypothesized that the particle is more stable, but non-infectious, when VP4 is in the uncleaved state. Uncleaved VP4 and the resultant increased stability might be advantageous for the virus to resist environmental degradation until it infects a susceptible host. When VP4 is cleaved in the lumen of the host's gastrointestinal tract, the virus particle would become less stable but more infectious. To test this hypothesis, a series of experiments was undertaken to analyse the cleavage state of VP4 on virus shed by an infected host into the environment. Immunoblots of intestinal wash solutions derived from infant and adult BALB/c mice infected with a virulent cell culture-adapted variant of the EDIM virus (EW) or wild-type murine rotavirus EDIM-Cambridge were analysed. Virtually all of the VP4 in these samples was in the cleaved form. Moreover, cell culture titration of trypsin-treated and untreated intestinal contents from pups infected with EW indicated that excreted virus is fully activated prior to trypsin addition. It was also observed that trypsin-activated virus has no disadvantage in initiating infection in naive animals over virions containing an intact VP4. These studies indicate that VP4 is cleaved upon release from the intestinal cell and that virus shed into the environment does not have an intact VP4.