SARS-CoV-2 host tropism: An in silico analysis of the main cellular factors.

Recent reports have shown that small and big felines could be infected by SARS-CoV-2, while other animals, like swines and mice, are apparently not susceptible to this infection. These findings raise the question of the role of cell factors associated with early stages of the viral infection in host selectivity. The cellular receptor for SARS-CoV-2 is the Angiotensin Converting Enzyme (ACE2). Transmembrane protease serine 2 (TMPRSS2) has been shown to prime the viral spike for its interaction with its receptor. GRP78 has also been proposed as a possible co-receptor. In this study, we used several bioinformatics approaches to bring clues in the interaction of ACE2, TMPRSS2, and GRP78 with SARS-CoV-2. We selected several mammalian hosts that could play a key role in viral spread by acting as secondary hosts (cats, dogs, pigs, mice, and ferrets) and evaluated their predicted permissiveness by in silico analysis. Results showed that ionic pairs (salt bridges, N-O pair, and long-range interactions) produced between ACE2 and the viral spike has an essential function in the host interaction. On the other hand, TMPRSS2 and GRP78 are proteins with high homology in all the evaluated hosts. Thus, these proteins do not seem to play a role in host selectivity, suggesting that other factors may play a role in the non-permissivity in some of these hosts. These proteins represent however interesting cell targets that could be explored in order to control the virus replication in humans and in the intermediary hosts.

Hepatitis E virus infection in Latin America: a review.

Data reported during recent years reveal the complex picture of the epidemiology of hepatitis E virus (HEV) infection in Latin America. Whereas in countries like Argentina and Brazil is almost identical to the characteristic of most countries from North America and Europe, HEV in the Caribbean and Mexico involves the water-borne, non-zoonotic viral genotypes responsible for epidemics in Asia and Africa. Nevertheless, Latin America has been considered a highly endemic region for hepatitis E in the scientific literature, a generalization that ignores the above complexity. In addition, reports from isolated Amerindian communities, which display well known, important and very specific epidemiological features for hepatitis B and D virus infections are neither taken into account when considering the epidemiology of hepatitis E in the region. This review updates compilation of the available information for the HEV infection, both among humans and other mammals, in Latin America, discusses the strengths and the weaknesses of our current knowledge, and identifies future areas of research.

Inhibition of hepatitis B virus and human immunodeficiency virus (HIV-1) replication by Warscewiczia coccinea (Vahl) Kl. (Rubiaceae) ethanol extract.

The primary objective of this study was to search for natural products capable of inhibiting hepatitis B virus (HBV) replication. The research design, methods and procedures included testing hydro-alcoholic extracts (n = 66) of 31 species from the Venezuelan Amazonian rain forest on the cell line HepG2 2.2.15, which constitutively produces HBV. The main outcomes and results were as follows: the species Euterpe precatoria, Jacaranda copaia, Jacaranda obtusifolia, Senna silvestris, Warscewiczia coccinea and Vochysia glaberrima exerted some degree of inhibition on HBV replication. The leaves of W. coccinea showed a significant antiviral activity: 80% inhibition with 100 µg mL⁻¹ of extract. This extract also exerted inhibition on covalently closed circular deoxyribonucleic acid (cccDNA) production and on HIV-1 replication in MT4 cells (more than 90% inhibition with 50 µg mL⁻¹ of extract). Initial fractionation using organic solvents of increasing polarity and water showed that the ethanol fraction was responsible for most of the antiviral inhibitory activities of both the viruses. It was concluded that Warscewiczia coccinea extract showed inhibition of HBV and HIV-1 replication. Bioassay-guided purification of this fraction may allow the isolation of an antiviral compound with inhibitory activity against both viruses.

Hepatitis A virus genetic diversity in Venezuela: exclusive circulation of subgenotype IA and evidence of quasispecies distribution in the isolates.

Hepatitis A virus (HAV) infection is highly prevalent in Latin America, including Venezuela. Subgenotype IA seems to circulate in an almost exclusive fashion, except in Brazil. The aim of this study was the molecular characterization of the HAV infection in Venezuela, in order to characterize the circulating strains and to analyze the presence of quasispecies in sporadic cases and an epidemic outbreak. A total of 125 (113 sera and 12 feces) samples positive for anti-HAV IgM from sporadic cases and epidemic outbreak, were submitted to hemi-nested RT-PCR for amplification of the VP1 N terminus or complete region of the HAV genome. Sequences obtained from 96 Venezuelan isolates were used for phylogenetic analysis. The quasispecies distribution was evaluated by cloning of HAV amplicons. Phylogenetic analysis of HAV sequences from Venezuela showed the exclusive circulation of subgenotype IA, but with co-circulation of two lineages, not found in other countries. The genetic variability found among Venezuelan strains was also analyzed by single-strand conformation polymorphism (SSCP). This technique allowed the detection of intra-strain variability, which was indeed related to the presence of quasispecies populations in the isolates. The quasispecies heterogeneity was higher in some isolates derived from sporadic cases compared to the one observed in the outbreak. The molecular characterization of HAV isolates from Venezuela showed the circulation of a unique subgenotype IA, but with the presence of diverse strains and quasispecies inside the viral populations.

Molecular characterization of sewage-borne pathogens and detection of sewage markers in an urban stream in Caracas, Venezuela.

Molecular characterization of two sewage-borne pathogens identified hepatitis A virus (HAV) subgenotype IA and Giardia duodenalis assemblages A and B as predominant genotypes circulating in an urban area of Venezuela. This study reveals epidemiological features of human pathogens of worldwide distribution and the efficacy of molecular methods for accurate assessment of sewage pollution.

Subgenotype diversity of hepatitis B virus American genotype F in Amerindians from Venezuela and the general population of Colombia.

The objective of this study was the evaluation of the genetic diversity found in HBV circulating among Venezuelan Amerindians and the general population in Colombia. Phylogenetic analysis of the S region in 194 isolates showed that genotype F is highly predominant in Colombia and Venezuela. This might be related to the genetic background of the population. F3 is the main subgenotype which circulates in both countries. Phylogenetic analysis of 61 complete genome sequences of HBV American genotypes confirms the presence of two genotypes F and H, and 4 F subgenotypes. In Venezuela, subgenotypes F1, F2, and F3 circulate in East and West Amerindians, while only F3 was found among South Amerindians. Japreira community derived from Yucpa Amerindians around 150 years ago. However, several Japreira HBV sequences were forming a clade that can be classified as subgenotype 2b, differing from Yucpa sequences that belong mainly to subgenotype F3. The apparent absence of correlation between the phylogenetic groupings of HBV isolates with the ethnical origin in aboriginal populations might be suggesting a recent origin of HBV American subgenotypes, or a genetic drift effect.

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.

Molecular epidemiology of hepatitis B virus in Afro-Venezuelan populations.

Hepatitis B virus (HBV) infection among Venezuelan populations of African origin was analyzed. These populations exhibited lower HBV prevalence than the one found in the African continent. Sequence analysis of 6 isolates showed that 3 belonged to genotype F, while the 3 others were HBV genotype A. HBV genotype A was more common in the Afro-Venezuelan groups than in the general Venezuelan population. This might reflect the introduction of genotype A during the slavery period. The absence of the African genotype E among these isolates supports the hypothesis of a recent origin for this HBV genotype. HBV genotype F has already been introduced to these relatively isolated communities.

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.

[Low impact of silent hepatitis B virus infection on the incidence of post-transfusion hepatitis in Venezuela]. / Bajo impacto de la infección silente por el virus de la hepatitis B en la incidencia de hepatitis postransfusional en Venezuela.

OBJECTIVE: Silent infection by hepatitis B virus (HBV) occurs in the absence of serological markers for the virus. This type of occult infection is generally chronic, asymptomatic, and associated with low levels of viral replication. This study determined the presence of HBV DNA in the sera of blood donors who were negative for serological markers that were tested during screening, with the goal of evaluating the impact of silent HBV infection in posttransfusion hepatitis B in Venezuela. METHODS: A total of 2,075 sera were tested in 53 serum pools of 25-50 donations (0.5-1.0 mL from each sample). The pools were subjected to ultracentrifugation prior to DNA extraction by the proteinase K, phenol/chloroform method. RESULTS: No HBV DNA was found in any of the pools by nested polymerase chain reaction, using primers for highly conserved regions of the genes that code for the surface antigen and for the viral capsid. Aminotransferase levels were normal in 98% of 200 sera that were tested. CONCLUSIONS: These results suggest that there is a low risk of acquiring posttransfusion hepatitis B in Venezuela.

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.

Hepatitis B virus DNA in blood samples positive for antibodies to core antigen and negative for surface antigen.

Anti-hepatitis B core antigen (HBcAg)-positive hepatitis B surface antigen (HBsAg)-negative plasma samples from blood donors were tested by nested PCR. DNA positivity was more significantly associated with high levels of anti-HBcAg than with low levels of anti-HBsAg antibodies. Analysis of a dilution of anti-HBcAg antibodies might result in a more rational exclusion of anti-HBcAg-positive HBsAg-negative samples, reducing the number of donations discarded and enabling more countries to incorporate anti-HBcAg testing.

Restricted isotypic antibody reactivity to hepatitis C virus synthetic peptides in immunocompromised patients.

An enzyme immunoassay based on three synthetic peptides from the core, NS4, and NS5 regions of hepatitis C virus allowed the detection of antibodies in 100% of immunocompetent infected patients and in 91% of immunocompromised patients (hemodialysis and hemophiliac patients). Immune impairment seemed to restrict the spectrum of antibody isotypes reacting to the core peptide.

Sequence heterogeneity within three different regions of the hepatitis G virus genome.

Two sets of primers derived from the 5'-terminal region and the NS5 region of the hepatitis G virus (HGV) genome were used to amplify PCR fragments from serum specimens obtained from different parts of the world. All PCR fragments from the 5'-terminal region (5'-PCR, n = 56) and from the NS5 region (NS5-PCR, n = 85) were sequenced and compared to corresponding published HGV sequences. The range of nucleotide sequence similarity varied from 74 and 78% to 100% for 5'-PCR and NS5-PCR fragments, respectively. Additionally, five overlapping PCR fragments comprising an approximately 2.0-kb structural region of the HGV genome were sequenced from each of five sera obtained from three United States residents. These sequences were compared to 20 published sequences comprising the same region of the HGV genome. Nucleotide and deduced amino acid sequences obtained from different individuals were homologous from 82.9 to 93. 6% and from 90.4 to 99.0%, respectively. Sequences obtained from follow-up specimens were almost identical. Comparative analysis of deduced amino acid sequences of the HGV structural proteins and hepatitis C virus (HCV) structural proteins combined with an analysis of predicted secondary structures and hydrophobic profiles allowed prediction of processing sites within the HGV structural proteins. A phylogenetic sequence analysis performed on the 2.0-kb structural region supports the existence of three previously identified HGV genetic groups. However, phylogenetic analysis performed on only small DNA fragments yielded inconsistent genetic grouping and failed to confirm the existence of genetic groups. Thus, in contrast to HCV where almost any region can be used for genotyping, only large or carefully selected genome fragments can be used to identify consistent HGV genetic groups.

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.

Norwalk virus infection in Venezuela.

The presence of antibodies against Norwalk virus (NV) was studied in sera from different Venezuelan populations, using an enzyme immuno-assay (EIA) based on recombinant NV protein. Antibodies to NV were found in 47%-53% of urban subjects from Caracas, 83% of rural subjects from the west of the country, and 73%-93% of Amerindian subjects. The prevalences found in the rural and Amerindian groups were significantly higher than that in the urban group. Although about 50% of the children studied were seropositive for NV by the age of 5 years, only four (0.4%) of 1120 faecal samples from children with diarrhoea which were tested for the presence of NV antigen by sandwich EIA were found positive. An increase of at least 4-fold in the titre of anti-NV IgA was found in three (5%) of 61 pairs of sera taken during and 1 month after an acute episode of diarrhoea not due to rotavirus. NV was therefore not a predominant aetiological cause of gastro-enteritis in young children in Venezuela between 1993 and 1995, although it can be the cause of diarrhoea in infants.

Turnover of hepatitis C virus genotypes in hemodialysis patients.

Hepatitis C virus (HCV) genotypes were determined in hemodialysis patients with a high prevalence and incidence of infection. A change of HCV genotype was observed in 6/14 follow-up samples analyzed 13 and 21 months later. The appearance and disappearance of HCV genotypes may be due to either genotype-specific intermittent viremic status or viral interference.