SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia.

Objectives: To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia.

Methods: A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument.

Results: Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.

PGE2 Produced by Exogenous MSCs Promotes Immunoregulation in ARDS Induced by Highly Pathogenic Influenza A through Activation of the Wnt-β-Catenin Signaling Pathway.

Acute respiratory distress syndrome is an acute respiratory failure caused by cytokine storms; highly pathogenic influenza A virus infection can induce cytokine storms. The innate immune response is vital in this cytokine storm, acting by activating the transcription factor NF-κB. Tissue injury releases a danger-associated molecular pattern that provides positive feedback for NF-κB activation.

Whole-genome sequence and genesis of an avian influenza virus H5N1 isolated from a healthy chicken in a live bird market in Indonesia: accumulation of mammalian adaptation markers in avian hosts.

Background: Influenza A viruses are a major pathogen that causes significant clinical and economic harm to many animals. In Indonesia, the highly pathogenic avian influenza (HPAI) H5N1 virus has been endemic in poultry since 2003 and has caused sporadic deadly infections in humans. The genetic bases that determine host range have not yet been fully elucidated.

Synthesis and assessment of copper-based nanoparticles as a surface coating agent for antiviral properties against SARS-CoV-2.

To halt the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), governments around the world have imposed policies, such as lockdowns, mandatory mask wearing, and social distancing. The application of disinfecting materials in shared public facilities can be an additional measure to control the spread of the virus. Copper is a prominent material with antibacterial and antiviral effects.

Initial study on TMPRSS2 p.Val160Met genetic variant in COVID-19 patients.

Background: Coronavirus disease 2019 (COVID-19) is a global health problem that causes millions of deaths worldwide. The clinical manifestation of COVID-19 widely varies from asymptomatic infection to severe pneumonia and systemic inflammatory disease. It is thought that host genetic variability may affect the host's response to the virus infection and thus cause severity of the disease.

Bone marrow-derived mesenchymal stem cells attenuate pulmonary inflammation and lung damage caused by highly pathogenic avian influenza A/H5N1 virus in BALB/c mice.

Background: The highly pathogenic avian influenza A/H5N1 virus is one of the causative agents of acute lung injury (ALI) with high mortality rate. Studies on therapeutic administration of bone marrow-derived mesenchymal stem cells (MSCs) in ALI caused by the viral infection have been limited in number and have shown conflicting results. The aim of the present investigation is to evaluate the therapeutic potential of MSC administration in A/H5N1-caused ALI, using a mouse model.

Comparison of Virulence and Lethality in Mice for Avian Influenza Viruses of Two A/H5N1 and One A/H3N6 Isolated from Poultry during Year 2013-2014 in Indonesia.

In Indonesia, the highly pathogenic avian influenza A/H5N1 virus has become endemic and has been linked with direct transmission to humans. From 2013 to 2014, we isolated avian influenza A/H5N1 and A/H3N6 viruses from poultry in Indonesia. This study aimed to reveal their pathogenicity in mammals using a mouse model.

Whole-Genome Sequence of an Avian Influenza A/H9N2 Virus Isolated from an Apparently Healthy Chicken at a Live-Poultry Market in Indonesia.

We isolated an avian influenza A/H9N2 virus from an apparently healthy chicken at a live-poultry market in January 2018. This is the first report of a whole-genome sequence of A/H9N2 virus in Indonesia. Phylogenetic analyses indicated that intrasubtype reassortment of genome segments is involved in the genesis of the A/H9N2 virus.

Functional growth inhibition of influenza A and B viruses by liquid and powder components of leaves from the subtropical plant Melia azedarach L.

We evaluated the anti-influenza-virus effects of Melia components and discuss the utility of these components. The effects of leaf components of Melia azedarach L. on viruses were examined, and plaque inhibition tests were performed.

Seroevidence for a High Prevalence of Subclinical Infection With Avian Influenza A(H5N1) Virus Among Workers in a Live-Poultry Market in Indonesia.

Background:  In Indonesia, highly pathogenic avian influenza A(H5N1) virus has become endemic in poultry and has caused sporadic deadly infections in human. Since 2012, we have conducted fixed-point surveillance of avian influenza viruses at a live-poultry market in East Java, Indonesia. In this study, we examined the seroprevalence of avian influenza A(H5N1) virus infection among market workers.

Neuraminidase-producing oral mitis group streptococci potentially contribute to influenza viral infection and reduction in antiviral efficacy of zanamivir.

Influenza is a serious respiratory disease among immunocompromised individuals, such as the elderly, and its prevention is an urgent social issue. Influenza viruses rely on neuraminidase (NA) activity to release progeny viruses from infected cells and spreading the infection. NA is, therefore, an important target of anti-influenza drugs.

Evaluation of anti-A/Udorn/307/1972 antibody specificity to influenza A/H3N2 viruses using an evanescent-field coupled waveguide-mode sensor.

Discrimination of closely related strains is a key issue, particularly for infectious diseases whose incidence fluctuates according to variations in the season and evolutionary changes. Among infectious diseases, influenza viral infections are a worldwide cause of pandemic disease and mortality. With the emergence of different influenza strains, it is vital to develop a method using antibodies that can differentiate between viral types and subtypes.

Observations of immuno-gold conjugates on influenza viruses using waveguide-mode sensors.

Gold nanoparticles were conjugated to an antibody (immuno-AuNP) against A/Udorn/307/1972 (H3N2) influenza virus to detect viruses on a sensing plate designed for an evanescent field-coupled waveguide-mode sensor. Experiments were conducted using human influenza A/H3N2 strains, and immuno-AuNP could detect 8×10(5) PFU/ml (40 pg/µl) intact A/Udorn/307/1972 and 120 pg/µl A/Brisbane/10/2007. Furthermore, increased signal magnitude was achieved in the presence of non-ionic detergent, as the virtual detection level was increased to 8×10(4) PFU/ml A/Udorn/307/1972.

Homology modeling study toward identifying structural properties in the HA2 B-loop that would influence the HA1 receptor-binding site.

Influenza hemagglutinin (HA) consists of a fibrous globular stem (HA2) inserted into the viral membrane supporting a globular head (HA1). HA1 receptor-binding has been hypothesized to be structurally correlated to the HA2 B-loop, however, this was never fully understood. Here, we elucidated the structural relationship between the HA2 B-loop and the HA1 receptor-binding site (RBS).

Direct targeting of proteins to lipid droplets demonstrated by time-lapse live cell imaging.

A protein that specifically targets lipid droplets (LDs) was created by connecting two domains of nonstructural protein 4B containing amphipathic helices from hepatitis C virus. We demonstrated its direct targeting and accumulation to the LD surface by time-lapse live cell imaging, comparable to those observed with adipose differentiation-related protein.

RNA binding properties of novel gene silencing pyrrole-imidazole polyamides.

Pyrrole-imidazole (PI) polyamides are a novel group of gene-silencing compounds, which bind to a minor groove of double stranded (ds)DNA in a sequence-specific manner. To explore the RNA binding properties of PI polyamides targeting rat transforming growth factor-β1 (TGF-β1 Polyamide) and influenza A virus (PA polyamide), we designed dsRNAs with an identical sequence to the target DNA and analyzed RNA binding properties of the polyamide. Biacore assay showed fast binding of TGF-β1 Polyamide to the dsRNA, whereas mismatch polyamide did not bind to the dsRNA.

A polyphenol-rich extract from Chaenomeles sinensis (Chinese quince) inhibits influenza A virus infection by preventing primary transcription in vitro.

Ethnopharmacological Relevance: The fruits of Chaenomeles sinensis Koehne (Chinese quince) are distributed throughout China and Japan. It has traditionally been known to have a therapeutic effect against respiratory symptoms caused by infectious diseases.

Aim Of The Study: The polyphenol-rich extract, CSD3, from Chaenomeles sinensis has previously been shown to neutralize influenza virus infectivity.

Isolation of human monoclonal antibodies to the envelope e2 protein of hepatitis C virus and their characterization.

We isolated and characterized two human monoclonal antibodies to the envelope E2 protein of hepatitis C virus (HCV). Lymphoblastoid cell lines stably producing antibodies were obtained by immortalizing peripheral blood mononuclear cells of a patient with chronic hepatitis C using Epstein-Barr virus. Screening for antibody-positive clones was carried out by immunofluorescence with Huh7 cells expressing the E2 protein of HCV strain H (genotype 1a) isolated from the same patient.

Bacterial neuraminidase rescues influenza virus replication from inhibition by a neuraminidase inhibitor.

Influenza virus neuraminidase (NA) cleaves terminal sialic acid residues on oligosaccharide chains that are receptors for virus binding, thus playing an important role in the release of virions from infected cells to promote the spread of cell-to-cell infection. In addition, NA plays a role at the initial stage of viral infection in the respiratory tract by degrading hemagglutination inhibitors in body fluid which competitively inhibit receptor binding of the virus. Current first line anti-influenza drugs are viral NA-specific inhibitors, which do not inhibit bacterial neuraminidases.

Surface functionalization chemistries on highly sensitive silica-based sensor chips.

The surfaces of silica-based sensor chips, designed for evanescent-field-coupled waveguide-mode sensors, were functionalized using various surface chemistries. The immobilization of molecular entities on the functionalized silica surfaces was monitored using various microscopic techniques (scanning electron, fluorescence, and atomic force microscopies). Further, gold nanoparticle-based signal enhancement analyses were performed with protein conjugation on different functionalized surfaces using a waveguide-mode sensor.

Identification of a novel compound with antiviral activity against influenza A virus depending on PA subunit of viral RNA polymerase.

Influenza viruses have developed resistance to current drugs, creating a need for new antiviral targets and new drugs to treat influenza virus infections. In this study, computational and experimental screening of an extensive compound library identified THC19, which was able to suppress influenza virus replication. This compound had no cytotoxic effects and did not disrupt cell cycle progression or induce apoptosis in MDCK cells as confirmed by WST-1 assays, flow cytometry analysis, and caspase-3 assays.

Flow cytometric assay using two fluorescent proteins for the function of the internal ribosome entry site of hepatitis C virus.

The initiation of translation in hepatitis C virus (HCV) occurs at the internal ribosome entry site (IRES) located at the 5'-end of its genomic RNA. To study the function of HCV IRES, we constructed a reporter plasmid that generates a bicistronic mRNA encoding two fluorescent proteins: cap-dependent DsRed2 and IRES-dependent Azami Green (AG). We introduced the plasmid into Huh7.

Development of a simple system for screening anti-hepatitis C virus drugs utilizing mutants capable of vigorous replication.

Replication of infectious hepatitis C virus in Huh7 cells, a human hepatocyte cell line, has become possible due to the unique properties of the JFH1 isolate. Developing reporter virus systems for a simple titration has been attempted by integrating heterologous reporter genes into the JFH1 genome, resulting in a big infectivity reduction that limits the usefulness of such reporter systems. To overcome this problem, JFH1-infected Huh7 cells were cultured continuously for 2 years to obtain Huh7-adapted JFH1 variants capable of yielding up to 1000-fold higher titers.

Anti-influenza virus principles from Muehlenbeckia hastulata.

Extracts of Chilean medicinal plants were evaluated in vitro for their activities against influenza virus proliferation in MDCK cells. The most potent extract obtained was from Muehlenbeckia hastulata (Polygonaceae), known as Quilo in Chile, from which three active principles were isolated and identified as pheophorbide a (1), hypericin (2) and protohypericin (3). Minimum inhibitory concentration (MIC) values of 42 ng/ml for compound 1, 2.