A real-time RT-PCR for detection of clade 1 and 2 H5N1 Influenza A virus using Locked Nucleic Acid (LNA) TaqMan probes

<p>Abstract</p> <p>Background</p> <p>The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants.</p> <p>Results</p> <p>We developed a single real-time RT-PCR assay for detection of both clades of H5N1 viruses, directly from clinical specimens, using locked nucleic acid TaqMan probes. Primers and probe used in this assay were designed based on a highly conserved region in the <it>HA </it>gene of H5N1 viruses. The analytical sensitivity of the assay was < 0.5 PFU and 10 - 100 ssDNA plasmid copies. A total of 106 clinical samples (58 from patients infected with clade 1, 2.1 or 2.3 H5N1 viruses and 48 from uninfected or seasonal influenza A virus-infected individuals) were tested by the assay. The assay showed 97% concordance with initial diagnostics for H5 influenza virus infection with a specificity of 100%.</p> <p>Conclusions</p> <p>This assay is a useful tool for diagnosis of H5N1 virus infections in regions where different genetic clades are co-circulating.</p

Deteksi Resistensi Oseltamivir Influenza A (H1N1pdm09) dari Pasien Infeksi Saluran Pernafasan Akut Berat di Indonesia tahun 2014

Influenza viruses are classified into subtypes based on two surface antigens known as hemagglutinin (HA) and neuraminidase (NA). Antigenic changes of influenza virus can cause resistance to antiviral drugs which is already limited in variation. Resistance to the drugs used recently are due to antigenic drift by point mutation in a single amino acid at position 275 (H275Y). The purpose of this research is to identify the presence of influenza virus A (H1N1pdm09) that were resistant to oseltamivir from cases of severe acute respiratory infection (SARI)in Indonesia in 2014 by using a rapid detection test. Detection of oseltamivir resistance in NA gene is to identify the single nucleotide polimorphism (SNP) at position 275 (H275Y) using the real-time RT-PCR method from clinical specimens SARI case. A total of 870 specimens from six sentinel hospitals were collected and 15 of them positive H1N1pdm09. Of the 15 clinical specimens, H1N1pdm09 virus strains that have mutations H275Y were not found. Based on this finding, it can be concluded that during the year 2014, there is no influenza virus A (H1N1pdm09) resistant to oseltamivir from SARI cases specimen in six sentinel hospitals in Indonesia

Detection of neuraminidase inhibitor-resistant influenza A (H1N1)pdm09 viruses obtained from influenza surveillance in Indonesia

Background: Influenza antiviral resistance has been shown to occur in many countries and is commonly found in influenza A(H1N1)pdm09 and A(H3N2). In this study, we monitored and investigated the neuraminidase inhibitor resistance of influenza A(H1N1)pdm09 viruses through the influenza surveillance system in Indonesia. Methods: A total of 4752 clinical specimens were collected from patients with influenza-like illness and severe acute respiratory infection during the year 2016. An allelic discrimination assay was conducted by a single base substitution or a single-nucleotide polymorphism that is specific to the H275 wild-type and Y275 mutant. Sequencing was performed to confirm the H275Y mutations, and we analysed the phylogenetic relationship. Results: The first occurrence of oseltamivir-resistant influenza A(H1N1)pdm09 was observed in the samples from the influenza-like illness surveillance. Two H275Y oseltamivir-resistant viruses (0.74%) out of 272 influenza A(H1N1)pdm09 positives were found. Both of them were collected from untreated patients. Conclusion: The number of oseltamivir-resistant influenza A(H1N1)pdm09 viruses in Indonesia is very low. However, it is necessary to continue with active surveillance for oseltamivir resistance in severe and mild cases

Linkage disequilibrium suggests genomic stability in Omicron clades of SARS-CoV-2 from the ASEAN countries

After more than 2 years of pandemic caused by SARS-CoV2, COVID-19 is still a national concern in many countries worldwide. One of the key investigations is to understand the factors contributing to the evolutionary dynamics of SARS-CoV2 as a pathogen. Currently, almost all countries have lifted border control orders and have allowed inter-country travel with minimal restrictions. This provides better resolutions on genomic patterns and the evolution of circulating SARS-CoV-2 in each community with the influence of imported strains. In this report, we surveyed genomes of SARS-CoV-2 strains circulating in the Association of Southeast Asian Nations (ASEAN) countries. This project serves as a collaborative effort from the ASEAN Member States that had participated in the programme ‘Strengthening Laboratory Capacity on COVID-19 Bio Genomic for ASEAN Countries