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International Journal of Infectious Diseases ; 122:401-404, 2022.
Article in English | Web of Science | ID: covidwho-2069126

ABSTRACT

Objectives: Considering the spread of new genetic variants and their impact on public health, it is impor-tant to have assays that are able to rapidly detect SARS-CoV-2 variants.Methods: We retrospectively examined 118 positive nasopharyngeal swabs, first characterized by the Sanger sequencing, using the Simplexa (R) SARS-CoV-2 Variants Direct assay, with the aim of evaluating the performance of the assay to detect N501Y, G496S, Q498R, Y505H, E484K, E484Q, E484A, and L452R mutations.Results: A total of 111/118 nasopharyngeal swabs were in complete agreement with the Sanger sequenc-ing, whereas the remaining seven samples were not amplified due to the low viral load. The evaluation of the ability of the assay to detect the E484Q mutation was performed using a viral isolate of the SARS-CoV-2 Kappa variant, showing concordance in 15/15 samples. Simplexa (R) SARS-CoV-2 Variant Direct assay was able to detect mutation pattern of Alpha, Beta, Gamma, Delta, and Omicron variants with 100% speci-ficity and 94% sensitivity, whereas 100% sensitivity and specificity for the Kappa variant was observed.Conclusion: The assay can be useful to obtain faster results, contributing to a prompt surveillance of SARS-CoV-2 variants;however, it requires to be confirmed by the Sanger method, especially in the case of pattern of mutations that are different from those expected and also requires updates as new variants emerge.(c) 2022 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

2.
J Hosp Infect ; 115: 51-58, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1379144

ABSTRACT

BACKGROUND: Occurrence of hepatitis C virus (HCV) infection is reduced by effective risk management procedures, but patient-to-patient transmission continues to be reported in healthcare settings. AIM: To report the use of phylogenetic analysis in the clinical risk management of an HCV outbreak among 128 thalassaemia outpatients followed at a thalassaemia centre of an Italian hospital. METHODS: Epidemiological investigation and root-cause analysis were performed. All patients with acute hepatitis and known chronic infection were tested for HCV RNA, HCV genotyping, and NS3, NS5A, and NS5B HCV genomic region sequencing. To identify transmission clusters, phylogenetic trees were built for each gene employing Bayesian methods. FINDINGS: All patients with acute hepatitis were infected with HCV genotype 1b. Root-cause analysis, including a lookback procedure, excluded blood donors as the source of HCV transmission. The phylogenetic analysis, conducted on seven patients with acute infection and eight patients with chronic infection, highlighted four transmission clusters including at least one patient with chronic and one patient with acute HCV infection. All patients in the same cluster received a blood transfusion during the same day. Two patients with acute hepatitis spontaneously cleared HCV within four weeks and nine patients received ledipasvir plus sofosbuvir for six weeks, all achieving a sustained virological response. CONCLUSION: Combined use of root-cause analysis and molecular epidemiology was effective in ascertaining the origin of the HCV outbreak. Antiviral therapy avoided the chronic progression of the infection and further spread in care units and in the family environment.


Subject(s)
Hepatitis C , Thalassemia , Antiviral Agents/therapeutic use , Bayes Theorem , Disease Outbreaks , Genotype , Hepacivirus/genetics , Hepatitis C/epidemiology , Humans , Italy/epidemiology , Phylogeny , Risk Management , Thalassemia/complications , Thalassemia/epidemiology , Thalassemia/therapy
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