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The emergence of the SARS-CoV-2 Variant of Concern (VOC), Omicron, has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed sometimes in Latin American countries in the circulation of the different lineages of the Omicron VOC. Once the sub-lineages were introduced in the country, community transmission was responsible for generating a characteristic distribution of them, with a predominance of sub-lineages not necessarily similar to the one observed in travelers or neighboring countries.

The emergence of the SARS-CoV-2 Variant of Concern (VOC) Omicron has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela, by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed in Latin American countries in the circulation of the different lineages of the Omicron VOC.

By the end of 2021, the Omicron variant of concern (VOC) emerges in South Africa. This variant caused immediate concern, due to the explosive increase in cases associated with it and the large number of mutations it exhibits. In this study, the restriction sites that allow detecting the mutations K417N and N440K in the Spike gene are described. This analysis allows us to propose a rapid method for the identification of cases infected with the Omicron variant. We show that the proposed methodology can contribute to provide more information on the prevalence and rapid detection of cases of this new VOC.

Introducción: El agente etiológico responsable de COVID-19, SARSCoV-2, es un virus ARN perteneciente a la familia Coronaviridae. Durante la replicación, los componentes virales interactúan con la maquinaria celular induciendo alteraciones en la fisiología celular, lo que contribuye a la patogénesis del virus. Método: Revisión bibliográfica en NCBI/Pubmed sobre estrés celular y SARS-CoV-2 Hallazgos de interpretación: Como respuesta a la infección, en la célula hospedadora se activan vías de señalización, cuyo principal objetivo es recuperar la homeostasis y de no lograrlo, inducir a la activación de la muerte celular. Entre las vías de señalización mejor caracterizadas, destacan las rutas de estrés celular como el estrés oxidativo, la UPR (Respuesta a proteínas no plegadas), y la autofagia, las cuales son evolutivamente bien conservadas y además están interconectadas entre sí. Hay fuerte evidencia teórica y experimental de diversas interacciones de algunos componentes de estas rutas con distintas proteínas virales de los coronavirus, y ya se han adelantado algunos estudios con SARS-CoV-2. En esta revisión, resaltamos algunas de las rutas celulares-virus que se han caracterizado hasta el momento. Reflexiones finales: Aún queda mucho por entender de estas rutas y su relación con las infecciones virales; esto pudiera constituir un importante blanco para la investigación y desarrollo de terapias antivirales.

La infección generada por el SARS-CoV-2 ha causado más de 200 millones de casos y de 4,5 millones de muertes en todo el mundo. El SARS-CoV-2 ha ido acumulando mutaciones que permiten clasificarlo en diferentes linajes. Algunos de esos linajes han sido denominados variantes por la OMS: bajo vigilancia (VUM), de interés (VOI) o de preocupación (VOC). Metodología. Se han descrito diferentes estrategias para la vigilancia genómica de estas variantes del SARS-CoV-2 en cada país. En Venezuela las estrategias incluyen la amplificación de un fragmento de la espiga, PCR-RFLP y secuenciación del genoma completo viral, lo que nos ha permitido monitorear la introducción de VOCs y VOIs al país. Resultados. Para octubre de 2021, en Venezuela se han descrito la circulación de tres VOCs, Alpha, Gamma y Delta, y las dos VOIs (Lambda y Mu). Globalmente, la variante Delta predomina en prácticamente en todos los continentes salvo algunos países de Latinoamérica, aunque se estima que pronto prevalecerá también en la región. Discusión. La circulación de variantes en los países es un proceso muy dinámico y Venezuela no escapa de esta realidad; por ello es importante seguir la vigilancia genómica de este virus.

Variants of Concern or Interest of SARS-CoV-2 (VOC or VOI), the coronavirus responsible for COVID-19, have emerged in several countries. Mutations in the amino acid 452 of the Spike protein are particularly important and associated with some of these variants: L452R, present in Delta VOC, and L452Q, present in Lambda VOI. These mutations have been associated with both increased infectivity and evasion of protective immune response. A search on GISAID to detect the number of sequences harboring the L452R mutation and the frequency of Delta VOC among them, showed that since August 2021, most of these sequences belong to the Delta VOC. Restriction enzyme analysis is proposed as a rapid method to detect L452R. A small amplicon from the Spike gene was digested with MspI. A 100% concordance was observed between digestion and sequencing results. The mutation L452Q can also be detected by restriction analysis, allowing the identification of putative Lambda VOIs. The proposed methodology, which allows screening of a great number of samples, could provide a faster information on the prevalence of Delta VOC cases.

Variants of Concern of SARS-CoV-2 (VOCs), the new coronavirus responsible for COVID-19, have emerged in several countries. Mutations in the amino acid 484 of the Spike protein are particularly important and associated with some of these variants: E484K or E484Q. These mutations have been associated with evasion to neutralizing antibodies. Restriction enzyme analysis is proposed as a rapid method to detect these mutations. A search on GISAID was performed in April 2021 to detect the frequency of these two mutations in the sequence available and their association with other lineages. E484K, present in some VOCs, has emerged in several other lineages and is frequently found in recent viral isolates. A small amplicon from the Spike gene was digested with two enzymes: HpyAV, and MseI. The use of these two enzymes allows the detection of mutations at position 484, and to differentiate between these three conditions: non-mutated, and the presence of E484K or E484Q. A 100% correlation was observed with sequencing results. The proposed methodology, which allows for the screening of a great number of samples, will probably help to provide more information on the prevalence and epidemiology of these mutations worldwide, to select the candidates for whole-genome sequencing.

Hepatitis B virus (HBV) chronic infection is responsible for almost 900.000 deaths each year, due to cirrhosis or hepatocellular carcinoma (HCC). Ten HBV genotypes have been described (A-J). HBV genotype F and H circulate in America. HBV genotypes have been further classified in subgenotypes. There is a strong correlation between the genetic admixture of the American continent and the frequency of genotypes F or H: a high frequency of these genotypes is found in countries with a population with a higher ratio of Amerindian to African genetic admixture. The frequency of occult HBV infection in Amerindian communities from Latin America seems to be higher than the one found in other HBV-infected groups, but its association with American genotypes is unknown. There is growing evidence that some genotypes might be associated with a faster evolution to HCC. In particular, HBV genotype F has been implicated in a frequent and rapid progression to HCC. However, HBV genotype H has been associated to a less severe progression of disease. This study reviews the diversity and frequency of autochthonous HBV variants in the Americas and evaluates their association to severe progression of disease. Although no significant differences were found in the methylation pattern between different genotypes and subgenotypes of the American types, basal core promoter mutations might be more frequent in some subgenotypes, such as F1b and F2, than in other American subgenotypes or genotype H. F1b and probably F2 may be associated with a severe presentation of liver disease as opposed to a more benign course for subgenotype F4 and genotype H. Thus, preliminary evidence suggests that not all of the American variants are associated with a rapid progression to HCC.

By the end of 2021, the SARS-CoV-2 Variant of Concern (VOC) Delta was predominant in most of the world. At the end of November, the Omicron variant was first detected in South Africa. This variant was immediately classified as VOC, due to the explosive increase of cases in South Africa, and the great number of mutations exhibited by this new lineage. Since then, Omicron VOC displaced Delta one in almost every country. Venezuela implemented in May 2021 molecular testing of all the passengers arriving at Venezuelan airports.In this study, we analyzed the presence of variants of SARS-CoV-2 in those positive samples, by sequencing a small fragment of the Spike genomic region.The Omicron variant was found in passengers arriving to Venezuela from the beginning of December. Complete genome analysis confirmed the presence of the Omicron VOC. The detection of this VOC coincided with an unprecedented increase in the frequency of passengers with positive nucleic acid testing.Genomic surveillance of samples for international travelers returning to Venezuela allowed us to rapidly detect the introduction of the Omicron variant in the country.

Objective: Hepatitis C virus (HCV) infection is a public health problem and a major cause of chronic hepatitis. This virus exhibits a great genetic variability, with 8 genotypes and numerous subtypes. The aim of this study was to evaluate the fluctuations of HCV subtypes during 2 decades in Venezuela. Methods: HCV genotypes were determined by direct sequencing of the 5ʹ-noncoding region in 392 isolates circulating in patients attended during the years 2014–2015. HCV subtype assignment was confirmed in a subset of samples (n = 24) by partial sequencing of the NS5B region. The genotype distribution was compared with the one observed in a previous study of patients followed up during the years 1994–1996 and 2005–2006. Results: Some variation was observed in the HCV genotype distribution over these 20 years. HCV genotype 1b prevalence was reduced significantly from 1994–1995 to 2004–2005, as previously described, and then remained constant. During the last 10 years, a significant decrease of HCV subtype 2b (36/237 in 2005–2006 vs. 24/392 in 2014–2015, p < 0.001) was observed. Patients infected with HCV G2acj were significantly older than the ones infected with G1 (53 vs. 47 years, p = 0.004), and male sex was significantly more prevalent among G3a-infected patients compared to the other ones (71 vs. 47%, p = 0.047). Conclusions: Fluctuations in HCV subtype distribution have been observed over 2 decades in Venezuela. Different major mode of transmission and susceptibility to the available HCV treatment during each period might be playing a role in the observed fluctuations in HCV subtype distribution.

Introduction: Variants of Concern of SARS-CoV-2 (VOCs), the new coronavirus responsible for COVID-19, have emerged in several countries. Two mutations in the gene coding for the Spike protein of the viral genome are particularly important and associated with some of these variants: E484K and N501Y. Restriction enzyme analysis is proposed as a rapid method to detect these two mutations. Methodology: A search on GISAID was performed in April 2021 to detect the frequency of these two mutations in the sequence available and their association with other lineages. A small amplicon from the Spike gene was digested with two enzymes: HpyAV, which allows detecting E484K mutation, and MseI, for detecting the N501Y one. Results: The mutations E484K and N501Y, associated with VOCs, have emerged in several other lineages, particularly E484K. A 100% correlation was observed with sequencing results. Conclusions: The proposed methodology, which allows screening a great number of samples, will probably help to provide more information on the prevalence and epidemiology of these mutations worldwide, to select the candidates for whole-genome sequencing.

SARS-CoV-2 is the new coronavirus responsible for COVID-19 disease. The first two cases of COVID-19 were detected in Venezuela on March 13, 2020. The aim of this study was the genetic characterization of Venezuelan SARS-CoV-2 isolates. A total of 7 full SARS-CoV-2 genome sequences were obtained by Sanger sequencing, from patients of different regions of Venezuela, mainly from the beginning of the epidemic. Ten out of 11 isolates (6 complete genomes and 4 partial spike genomic regions) belonged to lineage B, bearing the D614G mutation in the Spike protein. Isolates from the first outbreak that occurred in the Margarita Island harbored an in-frame deletion in its sequence, without amino acids 83–85 of the NSP1 of the ORF1. The search for deletions in 48,635 sequences showed that the NSP1 gene exhibit the highest frequency of deletions along the whole genome. Structural analysis suggests a change in the N-terminal domain with the presence of this deletion. In contrast, isolates circulating later in this island lacked the deletion, suggesting new introductions to the island after this first outbreak. In conclusion, a high diversity of SARS-CoV-2 isolates were found circulating in Venezuela, with predominance of the D614G mutation. The first small outbreak in Margarita Island seemed to be associated with a strain carrying a small deletion in the NSP1 protein, but these isolates do not seem to be responsible for the larger outbreak which started in July.

Introducción. El virus de la hepatitis C (HCV) presenta una gran variabilidad genética, con siete genotipos y numerosos subtipos. La determinación del tipo viral ha sido fundamental para la escogencia y la duración del tratamiento antiviral adecuado. En Venezuela, el genotipo 2 del HCV es relativamente diverso, siendo particularmente prevalente el subtipo 2j.Objetivo. Evaluar el desempeño de las metodologías para la determinación del genotipo del HCV, particularmente para la identificación del subtipo 2j.Materiales y métodos. Se determinaron el genotipo y el subtipo del HCV mediante la técnica de hibridación inversa LiPA (Line Probe Assay) y secuenciación de las regiones genómicas 5’NC y NS5B del virus.Resultados. En 65 muestras analizadas, la metodología basada en la amplificación de la región 5’NC mostró mayor sensibilidad (100 %), en comparación con la técnica LiPA (91 %) y la secuenciación de la región NS5B (77 %). La determinación de genotipo, tomando como método de referencia la secuenciación de NS5B, mostró un alto grado de concordancia para la secuenciación de la región 5´NC y la hibridación inversa LiPA, con 100 % en la asignación de genotipos, comparado con 70 % y 66 % para los subtipos, respectivamente. La secuenciación de la región NS5B permitió identificar los subtipos 2j y 2s, los cuales no fueron detectados por las otras metodologías. No se observó un patrón característico para las muestras subtipo 2j en la hibridación inversa LiPA.Conclusión. Aunque es la metodología con menor sensibilidad, la secuenciación de la región NS5B es una herramienta poderosa para la correcta discriminación de los distintos subtipos circulantes del HCV, lo cual reviste importancia epidemiológica.

In less than two years since SARS-CoV-2 emerged, the new coronavirus responsible for COVID-19, has accumulated a great number of mutations. Many of these mutations are located in the Spike protein and some of them confer to the virus higher transmissibility or partial resistance to antibody mediated neutralization. Viral variants with such confirmed abilities are designated by WHO as Variants of Concern (VOCs). The aim of this study was to monitor the introduction of variants and VOCs in Venezuela. A small fragment of the viral genome was sequenced for the detection of the most relevant mutations found in VOCs. This approach allowed the detection of Gamma VOC. Its presence was confirmed by complete genome sequencing. The Gamma VOC was detected in Venezuela since January 2021, and in March 2021 was predominant in the East and Central side of the country, representing more than 95% of cases sequenced in all the country in April-May 2021. In addition to the Gamma VOC, other isolates carrying the mutation E484K were also detected. The frequency of this mutation has been increasing worldwide, as shown in a survey of sequences carrying E484K mutation in GISAID, and was detected in Venezuela in many probable cases of reinfection. Complete genome sequencing of these cases allowed us to identify E484K mutation in association with Gamma VOC and other lineages. In conclusion, the strategy adopted in this study is suitable for genomic surveillance of variants for countries lacking robust genome sequencing capacities. In the period studied, Gamma VOC seems to have rapidly become the dominant variant throughout the country.

Prevalence and molecular epidemiology studies for hepatitis B (HBV) and C (HCV) virus are scarce in Warao Amerindians from Venezuela, where an epidemic of human immunodeficiency virus type 1 (HIV-1) has recently been documented. To carry out a molecular epidemiology analysis of hepatitis B (HBV) and C (HCV) virus in Warao individuals from the Delta Amacuro State of Venezuela. A total of 548 sera were tested for serological and molecular markers for HBV and HCV. The prevalence of active infection (presence of HBV surface antigen, HBsAg), exposure to HBV (presence of Antibody to HBV core antigen, anti-HBc) and anti-HCV, was 1.8%, 13% and 0% respectively. HBV exposure was significantly lower in men below 18 years old and also lower than rates previously reported in other Amerindian communities from Venezuela. Thirty one percent (31%, 25/80) of individuals without evidence of HBV infection exhibited anti-HBs titer ≥ 10U.I / ml, being significantly more frequent in individuals younger than 20 years. A higher HBV exposure was observed among HIV-1 positive individuals (33% vs 11%, p

The aim of this study was to evaluate the prevalence and genetic diversity of hepatitis B virus (HBV) and hepatitis C virus (HCV) in human immunodeficiency virus type 1 (HIV-1)-co-infected Venezuelan patients. The prevalence of HBV and HCV markers of infection in HIV-1 patients was 14 % for anti-hepatitis B core antigen, 3 % for hepatitis B surface antigen and 0.7 % for anti-HCV, respectively. HBV prevalence was higher than HCV, as expected for a country where sexual intercourse, not intravenous drug use, is the main mode of HIV-1 transmission. The HCV genotype distribution in HIV-1-co-infected patients was similar to that obtained in HCV-mono-infected patients, but genotype 1a was more frequent in HIV-1-infected patients. The HBV genotype distribution exhibited differences between mono-infected and HIV-1-co-infected individuals. HBV F3 was the most common subgenotype in both groups, followed by F1b in HIV-1 co-infection and F2 in HBV mono-infection. In addition, genotype G (single infection) was found in an HIV-1-co-infected individual. A high prevalence of occult HBV infection was detected in HIV-1-co-infected naive patients (18 %), with F2 being the most common genotype (75 %). To the best of our knowledge, these results correspond to the first description of frequency and molecular characterization of HBV and HCV in HIV-1 Venezuelan patients.

Introduction: Co-infection with GB virus C (GBV-C) in patients infected with human immunodeficiency virus 1 (HIV-1) has been associated with prolonged survival. The aim of this study was to evaluate the prevalence of GBV-C infection among HIV-1-infected patients in Venezuela, and to determine the effects of the co-infection on the levels of relevant cytokines. Methodology: Plasma samples were collected from 270 HIV-1-seronegative and 255 HIV-1-seropositive individuals. GBV-C infection was determined by RT-PCR of the NS5 region and genotyped by sequence analysis of the 5´UTR region. HIV-1 strains were characterized by sequence analysis of pol , vif , env , and nef genes. Selected cytokines were evaluated by ELISA. Results: Ninety-seven of 525 (18.5%) plasma samples tested positive for GBV-C RNA. A significantly higher prevalence of GBV-C was found among HIV-1 patients compared to HIV-1-seronegative individuals (67/255, 26% versus 30/270, 11%; p < 0.001). Statistical difference was observed in the viral load between HIV-1+GBV-C+ and HIV-1+GBV-C- (p = 0.014), although no differences in CD4 + cell counts were found between both groups. TNFα concentration was higher in HIV-1 + GBV-C - than in HIV-1 + GBV-C + patients (25.9 pg/mL versus 17.3 pg/mL; p = 0.02); RANTES expression levels were more variable in GBV-C co-infected patients and more frequently elevated in HIV-1 mono-infected patients compared to patients co-infected with GBV-C. Conclusions: The previously observed beneficial effect of co-infection with HIV-1 and GBV-C on disease progression is complex and might be due in part to a change in the cytokine environment. More studies are required to understand the interaction between both viruses.

Objectives: We previously reported HIV-1 infection in Warao Amerindians from Venezuela. The aim of this study was to evaluate the extent and the dynamic of HIV-1 dissemination in eight Warao communities. Design and Setting: HIV-1 infection was evaluated in 576 Warao Amerindians from the Orinoco Delta. Partial HIV-1 pol sequences were analyzed to reconstruct the spatiotemporal and demographic dynamics of the epidemic. Results: HIV-1 antibodies were present in 9.55% of Warao Amerindians, ranging from 0 to 22%. A significantly higher prevalence was found in men (15.6%) compared with women (2.6%), reaching up to 35% in men from one community. All but one isolates were classified as subtype B. Warao’s HIV-1 subtype-B epidemic resulted from a single viral introduction at around the early 2000s. After an initial phase of slow growth, the subtype B started to spread at a fast rate (0.8/year) following two major routes of migration within the communities. Conclusion: A dramatic high prevalence was documented in almost all the communities of Warao Amerindians from the Orinoco Delta tested for HIV-1 infection. This epidemic resulted from the dissemination of a single HIV-1 subtype B founder strain introduced about 10 years ago and its size is probably doubling every year, creating a situation that can be devastating for this vulnerable Amerindian group.

Globally, about 50% of liver cancer originates as a result of long term infection with hepatitis B virus (HBV), and some genotypes and mutations have been associated with an increased severity of infection. The aim of this study was to evaluate the genetic diversity of HBV in patients from Venezuela, with chronic infection, cirrhosis and hepatocellular carcinoma (HCC) and to compare the occurrence of mutations in all patient groups. Samples from patients with different pathologies of the liver, associated with HBV infection, were collected. The HBV S region was analyzed for genotype determination and, when available, the whole genome sequence was examined for mutations analysis. Genotype F was the most common genotype (87%). While the HBV subgenotype F3 was the most frequent genotype in the whole group of samples (44%), the subgenotype F2 predominated in HCC patients (56%). Mutations were more common in HCC and cirrhosis cases (p=0.01). The A1762T mutation was significantly associated with the advanced stage of liver disease (p=0.008). Additionally, mutations were more common in early stages of liver disease in HBV subgenotype F2-infected patients, and a significant association between this subgenotype and the emergence of T 1753C, A1762T, A1762T/G1764A (p=0.04) and C1773T (p=0.001) mutations in chronic patients was found, when compared to the HBV subgenotype F3. By comparing F2 with all other HBV subgenotypes, a positive association for the three basal core promoter (BCP) mutants (A1762T, A1762T/G1764A p=0.01, G1764A p=0.04) was found. These results suggest that the HBV subgenotype F2 might be associated to more severe forms of liver disease in comparison with the HBV subgenotype F3.

A B S T R A C T Background: This study investigated the distribution of human papillomavirus (HPV) types in invasive cervical cancer (ICC), cervical intraepithelial neoplasia 2 (CIN2) and cervical intraepithelial neoplasia 3 (CIN3) in Venezuela. Methods: Paraffin-embedded samples from 329 women from 29 medical centers of the 24 states of Venezuela were analyzed to determine the distribution of HPV types for ICC, CIN2, and CIN3, the prevalence of single and multiple infection, and the association of HPV types with severity of lesion, comparing CIN2 versus CIN3+ (CIN3 and ICC). The samples were analyzed with the polymerase chain reaction (PCR) followed by reverse hybridization for the identification of HPV types. Results: HPV was identified in 95/96 ICC specimens (98.9%), in 142/149 CIN3 (95.3%) and in 78/84 CIN2 samples (92.8%). The most common types for ICC and CIN3 were: HPV16, 18, 31, and 33, and for CIN2 were HPV16, 31, 51, 52, and 18. HPV single infection was found in 82.1% of ICC cases, in 79.4% of CIN2 cases, and in 77.4% of CIN3 cases. HPV16 was identified as a single infection more frequently in women with CIN3+ than in those with CIN2 (68.6% versus 46.7%, P = 0.002), and HPV16 or HPV18 types were more prevalent in CIN3+ than in CIN2 (73.4% versus 50%, P = 0.0006). Conclusion: this is the first study of the distribution of HPV types in ICC, CIN2, and CIN3 conducted throughout the territory of Venezuela. HPV16 and HPV18 were the most frequent HPV types identified in single and multiple infections in both ICC and CIN3 groups, and are associated with severity of lesion. The knowledge of the distribution of HPV types would allow organization of an HPV-DNA-based screening test, and consideration of the implementation of prophylactic vaccination in Venezuela.

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.

We previously reported a high prevalence of HIV-1 infection in Warao Amerindians from Venezuela due to the rapid spread of a single B subtype strain. In this study we evaluated the coreceptor use of the HIV-1 strains infecting this Amerindian community. Sequences of the HIV-1 V3 loop from 56 plasma samples were genotyped for coreceptor use. An extremely high frequency of CXCR4 strains was found among HIV-1-infecting Waraos (47/49, 96%), compared to HIV-1 strains infecting the non-Amerindian Venezuelan population (35/79, 44%, p 0.00001). Evolutionary analysis showed that a significant number of infections occurred between 1 and 12 months before collection and that a great proportion (50-70%) of HIV-1 transmissions occurred within the very early phase of infection (≤12 months). This is consistent with an initial infection dominated by an X4 strain or a very rapid selection of X4 variants after infection. This Amerindian population also exhibits the highest prevalence of tuberculosis in Venezuela, being synergistically bad prognostic factors for the evolution of morbidity and mortality in this vulnerable population.

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.

Surface antigen negative hepatitis B virus (HBV) infection was evaluated in Venezuela, by molecular characterization of blood samples positive for antibodies to core antigen (anti-HBc) and negative for surface antigen (HBsAg) in blood donors (residual infections). HBV DNA was found in 11/258 samples (4.3%), and was significantly associated with high levels of anti-HBc antibodies (>25 UI/ml, P < 0.05), while no correlation was found between the presence of HBV DNA and the levels of anti-HBs. Synonymous and non-synonymous mutations were found in the HBV surface region (but not vaccine escape mutants) and in the precore/core region (precore mutants in 2/7 samples and 33-45 bp deletions near the N-terminal core region in 4/19 samples). While HBV genotype F prevails among HBsAg positive samples from blood donors in Venezuela, residual infection isolates were mainly genotypes A and D. Phylogenetic analysis of viral surface and core region revealed discrepancies in genotype designation in 6/9 samples, suggesting the presence of mixed infection or recombination. In conclusion, HBV residual infection in Venezuela does not seem to be frequently observed in HBV genotype F. This type of infection is frequently associated with variants exhibiting mutations in the surface gene that might be affecting the correct recognition by commercial tests, with precore mutants and with core internal deletions. These variants do not seem to cause severe liver disease, and on the contrary, were found circulating at low viremia.

GB virus C or hepatitis G virus (GBV-C/HGV) is highly prevalent among population groups at risk of parenterally transmitted viral agents, but it has also a worldwide distribution in other non-risk population groups. GBV-C/HGV RNA and antibodies against its envelope protein (anti-E2 Abs) were found in 3/86 (3%) and 7/89 (8%) of biomedical science personnel (BSP), in 31/453 (7%) and 37/200 (19%) of blood donors (BD), and in 6/64 (9%) and 26/59 (44%) of hemodialysis patients (HD) from Caracas, Venezuela. A significant gradient of GBV-C/HGV exposure (anti-E2 Abs and/or GBV-C/HGV RNA) was found between BSP (lowest prevalence), BD, and HD (P < 0.001). GBV-C/HGV RNA and anti-E2 Abs were also found in 2/69 (2.9%) and 2/44 (4.5%) of individuals from a rural community, in 9/162 (5.5%) and 2/40 (5%) of West Amerindians, and in 14/56 (25%) and 4/53 (7.5%) of South Amerindians. Socioeconomic and cultural factors may have contributed to the relatively high risk of exposure to GBV-C/HGV in BD and Amerindians. Whereas GBV-C/HGV genotypes 1 (n = 1), 2 (n = 6), and 3 (n = 22) were present in Venezuela, only the Asiatic genotype 3 was found infecting Amerindians and rural populations (n = 16). Genotype assignment based on the 5' noncoding region of the GBV- C/HGV genome was corroborated in some isolates by genetic analysis of the E2 region. This report confirms the circulation of the Asiatic genotype of GBV-C/HGV among Amerindians, suggesting an old origin of GBV-C/HGV. This might be associated with the apparently low pathogenesis of this virus.

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. J. Med. Virol. 64:356–359, 2001. © 2001 Wiley-Liss, Inc.

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.

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.

Recently, a new virus related to flaviviruses, the hepatitis G virus (HGV), or GBV-C virus, was discovered as a putative blood-borne human pathogen. HGV RNA (NS5 region) was amplified by reverse transcription-nested PCR in the sera of 6 of 64 (9%) hemodialysis patients; 2 of 80 (2.5%) West Yukpa Amerindians, a population with a high rate of HBV infection but negative for HCV infection; and 1 patient with an acute episode of non-A, non-B, non-C hepatitis (NABCH). The patterns of single-strand conformation polymorphism of the amplified products were unique among different specimens and similar on follow-up for hemodialysis patients. All patients tested remained HGV RNA positive 1 and 2 years later, without major sequence variation, except for the NABCH patient, for whom a double infection and an apparent clearance of the original dominant variant was observed after 2 years. The sequences of the NS5 amplified products demonstrated 85 to 90% identity with other reported HGV sequences.

Background Occult hepatitis B infection (OBI) is characterized by the presence of hepatitis B virus (HBV) DNA in the absence of HBsAg in the serum of patients. The aim of this study was to characterize HBV infection among a Piaroa community, an Amerindian group which exhibits significant evidence of exposure to HBV but relatively low presence of HBsAg, and to explore the presence of OBI in this population. Results Of 150 sera, with 17% anti-HBc and 1.3% HBsAg prevalence, 70 were tested for the presence of HBV DNA. From these, 25 (36%) were found positive for HBV DNA by PCR in the core region. Two of these 25 sera were HBsAg positive, indicating an overt infection. Of the remaining 68 sera tested, 23 exhibited OBI. Of these, 13 were HBV DNA out of 25 anti-HBc positive (52%) and 10 HBV DNA positive, out of 43 anti-HBc negative (23%), with a statistical significance of p = 0.03. Viral DNA and HBsAg were present intermittently in follow up sera of 13 individuals. Sequence analysis in the core region of the amplified DNA products showed that all the strains belonged to HBV genotype F3. The OBI isolates displayed 96-100% nucleotide identity between them. One isolate exhibited the co-circulation of a wild type variant with a variant with a premature stop codon at the core protein, and a variant exhibiting a deletion of 28 amino acids. Conclusions The frequency of OBI found in this Amerindian group warrants further studies in other communities exhibiting different degrees of HBV exposure.

Hepatitis B virus (HBV) and hepatitis C virus (HCV) infections are the principal risk factor associated to end-stage liver diseases in the world. A study was carried out on end-stage liver disease cases admitted to an important hepatology unit in Medellin, the second largest city in Colombia. From 131 patients recruited in this prospective study, 71% of cases were diagnosed as cirrhosis, 12.2% as HCC, and 16.8% as cirrhosis and HCC. Regarding the risk factors of these patients, alcohol consumption was the most frequent (37.4%), followed by viral etiology (17.6%). Blood and/or hepatic tissue samples from patients with serological markers for HCV or HBV infection were characterized; on the basis of the phylogenetic analysis of HCV 5′ UTR and HBV S gene, isolates belonged to HCV/1 and HBV/F3, respectively. These results confirm the presence of strains associated with poor clinical outcome, in patients with liver disease in Colombia; additionally, HBV basal core promoter double mutant was identified in HCC cases. Here we show the first study of cirrhosis and/or HCC in Colombian and HBV and HCV molecular characterization of these patients. Viral aetiology was not the main risk factor in this cohort but alcohol consumption. COL0024159

Background: Changes in hepatitis C virus (HCV) genotype distribution with time have been reported in several countries. Goals: To explore eventual changes in HCV genotype distribution in Venezuela over a 10 years period. Study: HCV genotype was determined by direct sequencing of the 5' noncoding region, in 236 isolates circulating in patients treated during years 2005 to 2006. Genotype distribution was compared with the one observed in 43 patients followed during years 1994 to 1996. Results: The prevalence HCV genotype 1 and 2 was 70% and 26%, respectively, in patients followed during years 1994 to 1996. The frequency of genotype 2 was significantly increased to 41% (P = 0.04) in patients treated during years 2005 to 2006. A significant reduction in HCV genotype 1b prevalence (48% to 27%, P = 0.01) was also observed after this 10 years period, whereas the prevalence of HCV genotype 1 a did not change over time (22% vs. 27%, NS). Transfusion was more significantly associated with infection with HCV genotype 1b than with other genotypes (52% vs. 20%, P = 0.002). Conclusions: HCV subtype 1b seems to have been displaced by HCV genotype 2 in a relatively short period, without increase in the frequency of genotype 3. The low frequency of HCV genotype 3 in Venezuela might be due to the fact that intravenous drug use in Venezuela is less common than in other countries. The implementation of anti-HCV testing in blood banks since 1994 in Venezuela, might have contributed to the reduction in the frequency HCV genotype 1b infection.

Hepatitis C virus genotypes in Venezuela were analyzed by restriction fragment length polymorphism in the 5' noncoding region. The absence of BstUI digestion was found to be a useful marker for genotype 2 specimens. From 122 serum samples, 66, 20, and 2.5% were classified as genotypes 1, 2, and 3, respectively; 0.8% were classified as genotype 4; and 10% appeared to be mixed infections.

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.