Detection of HEV genome on wastewater samples collected on first sampling.

<p>Representative results of the positive samples amplified by RT-nested PCR targeting the ORF2/3 region (137bp). MW: Molecular Weight. 1. Girardota village 2. San Pedro de Los Milagros 3. Venecia 4.Granada 5.Arboletes 6. Cisneros 7. Nutibara village 8. Frontino 9. Puerto Berrío 10. Zaragoza. (-) negative control (+) positive control. 2% agarose gel electrophoresis stained with ethidium bromide.</p

Geographic location of Antioquia state and the municipalities/villages included in the study.

<p>Geographic location of Antioquia state and the municipalities/villages included in the study.</p

Water treatment systems of the municipalities of Antioquia State included in the study

<p>Water treatment systems of the municipalities of Antioquia State included in the study</p

Genetic diversity of hepatitis C virus and resistance associated substitutions to direct-acting antiviral treatment in Colombia

Hepatitis C virus (HCV) infection is one of the leading risk factors for end-stage liver disease development worldwide. This RNA virus displays high genetic diversity with 8 genotypes and 96 subgenotypes with heterogeneous geographical distribution around the world. In this study, we carried out an active case finding of individuals with a history of transfusion events before 1996 in three cities in Colombia. Then, the characterization of the HCV genotypes, subgenotypes, and resistance associate substitutions (RAS) was performed in samples positives for antibodies anti-HCV + from this study population. In addition, samples from PWID and patients with end-stage liver disease submitted to liver transplantation were included in the phylogenetic and RAS analysis. The 5′UTR, NS5A, and NS5B regions of the HCV genome were amplified in serum or liver explants samples. After the edition, assembly, and alignment of the sequences, genotyping through phylogenetic analysis was performed using IQTREE V2.0.5 based on the maximum likelihood approach. The identification of RAS was carried out by alignments based on the reference sequence (GenBank NC_004102). Two hundred sixty individuals with blood transfusion events before 1996 were recruited. The seroprevalence of antibodies anti-HCV was 2.69% in this population. The HCV genotypes 1, 2, and 4 and subgenotypes 1a, 1b, 2a, 4a and 4d were characterized in samples of the study populations. Three RAS (Q30R, C316N, and Y93H) were identified in samples obtained from 2 individuals who received blood transfusion before 1996 and without previous antiviral treatment and 6 samples obtained from patients with end-stage liver disease. Among the 20 samples analyzed, the HCV genotype 1, subgenotype 1b, was the most frequent (60%). We report the first characterization of HCV subgenotypes 4a and 4d and the first RAS identification in patients in Colombia.https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=00003185070000-0002-8093-0544https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000008981jose.usmec@campusucc.edu.cohttps://scholar.google.com.co/citations?user=cU2KyT4AAAAJ&hl=e

Sampling and viral concentration methodologies.

<p>Sampling and viral concentration methodologies.</p

HEV phylogenic tree based on a fragment of 99 pb ORF2/3 HEV region.

<p>Based on the Bayesian Information Criterion (BIC), the model chosen for the phylogenetic analysis was Tamura 3-parameter + gamma distribution. The tree was constructed using the Neighbor-Joining method with 1000 bootstrap replicates. Samples obtained in this study are shown with a black circle (●). Clades for genotypes 1, 2, 3 and 4 are indicated with brackets. The GenBank accession number, genotype and country of isolation identify viral strains. Ven_Res_1erMx, SanPedro_Res_1erMx and Cisneros_Res_1erMx corresponded to wastewater sample collected on the first sampling at Venecia, San Pedro de los Milagros and Cisneros municipalities, respectively.</p

An updated RT-qPCR assay for the simultaneous detection and quantification of chikungunya, dengue and zika viruses

The real-time reverse transcription-polymerase chain reaction (real-time RT-qPCR) has become a leading technique for the detection and quantification of arboviruses, including Chikungunya, Dengue, and Zika viruses. In this study, an updated real-time RT-qPCR assay was designed and evaluated together with a synthetic positive-control chimeric RNA for the simultaneous detection and quantification of Chikungunya, Dengue, and Zika viruses. Amplification assays were performed to verify the construct integrity and optimal reaction/thermal cycling conditions. The analytical sensitivity of the assay was determined for each virus in single and multiplex reactions, as well as the performance in the detection and viral load quantification of experimental samples. The real-time RT-qPCR assay presented here allowed for the simultaneous detection and quantification of Chikungunya, Dengue, and Zika viruses and could be applied in several studies where the accurate quantification of viral genomes is required.https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000318507https://orcid.org/0000-0002-8093-0544https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000008981jose.usmec@campusucc.edu.cohttps://scholar.google.com.co/citations?user=cU2KyT4AAAAJ&hl=e

Low Neutralizing Antibody Titers against the Mu Variant of SARS-CoV-2 in 31 BNT162b2 Vaccinated Individuals in Colombia

Global surveillance programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are showing the emergence of variants with mutations in the spike protein. Genomic and laboratory surveillance are important to determine if these variants may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies. Three of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated: Mu, a variant of interest; Gamma, a variant of concern; B.1.111, which lacks genetic markers associated with greater virulence. Microneutralization assays were performed by incubating 120 mean tissue culture infectious doses (TCID50) of each SARS-CoV-2 isolate with five two-fold serial dilutions of sera from 31 BNT162b2-vaccinated volunteers. The mean neutralization titer (MN50) was calculated by the Reed&ndash;Muench method. At the end of August, Mu represented 49% of coronavirus disease 2019 (COVID-19) cases in Colombia, followed by 25% of Gamma. In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162b2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma. This study shows the importance of continuing surveillance programs of emerging variants, as well as the need to evaluate the neutralizing antibody response induced by other vaccines

Complete Genome Sequence of a Colombian Zika Virus Strain Obtained from BALB/c Mouse Brain after Intraperitoneal Inoculation

A Zika virus (ZIKV) strain was isolated from an acute febrile patient during the Zika epidemics in Colombia. The strain was intraperitoneally inoculated into BALB/c mice, and 7 days postinoculation, neurological manifestations and ZIKV infection in the brain were demonstrated. The reported genome sequence is highly related to strains circulating in the Americas.https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000318507https://orcid.org/0000-0002-8093-0544https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000008981jose.usmec@[email protected]://scholar.google.com.co/citations?user=cU2KyT4AAAAJ&hl=e

First evidence of the Hepatitis E virus in environmental waters in Colombia

RESUMEN: Hepatitis E virus (HEV) is one of the main causes of acute viral hepatitis of enteric transmission. HEV has been detected in environmental samples in several countries from Europe and Asia, constituting a risk factor for waterborne infection. In Colombia, HEV has been identified in samples obtained from patients as well as from swine, but no environmental studies have been carried out. To determine if HEV is present in environmental waters, samples from the main source of drinking water plant and of wastewater system of eight municipalities and two villages of Antioquia state (North West Colombia), were collected between December 2012 and April 2014. The HEV genome was detected by RT-PCR in 23.3% (7/30) of the samples from the main source of drinking water plants and in 16.7% (5/30) from sewage. Viral concentrates obtained from three positive sewage samples were used to inoculate HepG2 cell cultures that were followed for one month; however, the viral genome was not detected in any cell culture. This study demonstrates the circulation of HEV in both source of drinking water plants and wastewater in Antioquia state, Colombia. The presence of HEV in environmental waters could be a risk for waterborne transmission in this population. The findings of the present study, together with the evidence of HEV circulation in human and swine in Colombia, should be consider by public health authorities for the development of surveillance programs and the inclusion of HEV infection diagnosis in the guidelines of viral hepatitis in the country. This is the first report of HEV in environmental samples in Colombia and the second one in Latin America