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.

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.

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.

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.

The seroprevalences of anti-hantavirus IgG antibodies among selected Venezuelan populations.

In Venezuela, the isolation of hantaviruses from rodents and the detection, in 1999, of a clinically confirmed human case of hantavirus infection led to increased interest in these viruses. In an attempt to estimate the problem posed by such viruses in Venezuela, ELISA based on purified, recombinant, nucleoprotein were used to check 1380 human serum samples for the presence of IgG antibodies to hantavirus. The ELISA results, as confirmed by indirect immunofluorescence and Western-blot assays, indicated that 23 (1.7%) of the serum samples contained antibodies to hantaviruses. Seroprevalences were similar among all age-groups and for both genders and were no higher among rural populations with a relatively high risk of exposure to rodents than among the overall study population. Although the numbers of samples involved were small, the seroprevalence among the subjects who were residents of Carabobo state was much higher than the overall value (10.3% v. 1.7%; P < 0.01). Human infection with hantavirus appears uncommon but widely distributed in Venezuela.

Hepatitis delta virus genotypes I and III circulate associated with hepatitis B virus genotype F In Venezuela.

The genotypes of hepatitis B (HBV) and delta (HDV) viruses circulating among Venezuelan Amerindian populations, where these viruses are endemic, were determined by sequencing of PCR amplified products from HBsAg positive sera. HDV genotype I (n = 7, 6 from West Amerindians), and III (n = 5, 4 from South Amerindians), were found. Only one HDV genotype I isolate was associated with HBV genotype D, 4 HDV genotype I and 2 HDV genotype III infected individuals were co-infected with HBV genotype F. The failure to detect the South American HDV genotype III in West Amerindians might be related to the outbreak of fulminant hepatitis with high mortality rate occurred between 1979 and 1982, probably affecting more the Amerindians infected with HDV genotype III. These results suggest the circulation of HDV genotype I among Amerindians, probably introduced through European immigrations, and that this HDV genotype is able to replicate in association with HBV genotype F.

Prevalence of infection with hepatitis C virus in Venezuela, as assessed with an immuno-assay based on synthetic peptides.

Information on infection with hepatitis C virus (HCV) in South America is scarce. The seroprevalences of antibodies to HCV among urban, rural and Amerindian populations from Venezuela, and the genotypes of the HCV isolates recovered, were therefore determined. A total of 2592 sera were tested with an immuno-assay which was developed in-house and based on synthetic peptides. Each reactive sample was then re-tested, using other enzyme immuno-assays and a reverse-transcription, nested PCR, and any sample confirmed positive (in any test) was considered HCV-positive. Genotypes were determined by analysis of RFLP. Overall, 39 (1.5%) of the samples were found HCV positive. The results of the immuno-assays indicated that the seroprevalence of HCV markers among the Amerindians investigated (23/1082, or 2.1%) was significantly higher than that among the other subjects (16/1510, or 1.1%; P = 0.02). No such difference was observed in the numbers of subjects confirmed positive by PCR, however (6/1082 v. 10/1510), and some of the anti-HCV reactivity observed among Amerindians may have been the result of cross-reactivity with parasitic infections. The relative low prevalence of active HCV infection (16/2582, or 0.6%) and the HCV genotypes observed (mainly genotype 1) are in agreement with the results of previous studies indicating that HCV is not autochthonous to South America. However, it is clear that the virus may now be found even in isolated Amerindian populations. The in-house, synthetic-peptide-based immuno-assay seems to be a valuable tool for epidemiological studies.

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.

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.

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.

Identification of mutations in the rotavirus protein VP4 that alter sialic-acid-dependent infection.

To explore further the role of VP4 as the rotavirus cell attachment protein, VP7 monoreassortants derived from the sialic-acid-dependent simian strain RRV and from the sialic-acid-independent human strains D, DS-1 and ST-3 were tested for susceptibility of infectivity of neuraminidase-treated MA-104 cells. Infectivity of RRV x D VP7 and RRV x ST-3 VP7 monoreassortants decreased when sialic acid was removed from the cell surface. However, of three separate RRV x DS-1 VP7 monoreassortants tested, only one was sialic-acid-dependent. Sequence analysis showed that both sialic-acid-independent strains contained a single amino acid change, Lys to Arg, at position 187. In addition, sialic-acid-independent infectivity was seen in one of 14 RRV VP4 neutralization escape mutants tested, and this strain was found to have a Gly to Glu change at amino acid position 150. These results indicate that positions 150 and 187 of VP4 play an important role in early rotavirus-cell interactions.

Productive penetration of rotavirus in cultured cells induces coentry of the translation inhibitor alpha-sarcin.

Internalization of rotavirus in MA104 cells was found to induce coentry of alpha-sarcin, a toxin that inhibits translation in cell-free systems and to which cells are normally impermeable. Entry of the toxin, measured by inhibition of protein synthesis at early times after infection, correlated with virus penetration leading to expression of infectivity, since toxin entry (1) was induced only by trypsin-treated triple-layered virions, to a degree dependent on the toxin and the virus concentration; (2) correlated with the degree of permissivity of different cell lines to rotavirus infection; (3) was inhibited to a similar extent as infectivity by treatment of cells with neuraminidase; and (4) was inhibited by pre- or postadsorption incubation of the virus with neutralizing monoclonal antibodies to VP7 and VP4 (VP8*). Neither the virus infectivity nor the toxin coentry was significantly affected by treatment of cells with bafilomycin A1, an inhibitor of the vacuolar proton ATPase, indicating that both events are independent of the endosomal acid pH. Virus-like particles (VLP), composed of rotavirus proteins 2/6/7/4, but not 2/6/7 or 2/6, were able to induce toxin entry as efficiently as virions. Use of genetically modified VLP in combination with the toxin coentry assay, which measures entry through a productive pathway, should allow identification of the regions of the outer capsid proteins essential for rotavirus penetration.

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.

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.

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.

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.

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.

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.

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.