Identification of molecular characteristics of low pathogenic avian influenza (LPAI) H9N2 virus provides insights into the evolution of this subtype due to the modulation of genomic characteristics in co-circulation with another subtype. The present study aimed to analyze the molecular and phylogenetic characteristics of the current LPAI H9N2 virus in characteristics of internal proteins are crucial for the adaptations of AIVs viruses to a new host. Since H9N2 is indigenous among poultry, continuous monitoring of viral genetic changes is needed for risk assessment of potential transmissibility to human population and emergence of new reassortant virus. domestic poultry during the emergence of new highly pathogenic avian influenza (HPAI) H5N8 virus in Iran. To this end, deep sequencing of LPAI H9N2 virus was performed on Illumina MiSeq sequencing platform and the complete sequences of avian influenza viruses were obtained from GISAID EpiFlu database. Phylogenetic analysis of the surface and internal gene segments showed that the H9N2 2018 virus was closely related to Pakistani H9N2 isolates. HA cleavage site motif sequence of the Iranian isolate was 317KSSR GLF323. The A/chicken/Iran/1/2018 H9N2 strain carried the amino acid substitution (Q216L), which is a mutation correlated with a shift in the affinity of the HA from avian type sialic receptors to human type. Besides surface glycoproteins, molecular. Keywords: A/H9N2; molecular characterization; A/H5N8; co-circulation; A/H5N1; Illumina MiSeq.

Human immunodeficiency virus (HIV) is a pathogen that infects blood cells, using CD4 molecule and two cell receptors CCR5 and CXCR4. The other major actor is gp120/gp41 viral protein complex, which interacts with receptors. Here, the presence of synonymous mutations associated with HIV-1 tropism and the related RNA secondary-structure in HIV-1 infected patients was evaluated. The analysis includes gp120-sequences from 340 HIV-1 subtype-B infected patients, all retrieved from Los Alamos database and with phenotypic HIV tropism determination based on recombinant-virus entry-assay. Frequencies of all nucleotide substitutions were calculated. Mfold and RNAfold algorithms were used to predict RNA secondary-structure of HIV-1. Nineteen codons in V2/C2, V3 and C3 domains were found to be closely related to CCR5 and CXCR4. Additionally, in X4-sequences, gp120 gca303gcu and gua222guc synonymous mutations are positively related to the gp120 S11R and T8A/I codons in V3 protein domain. Furthermore, gua222guc increases stability of the viral RNA secondary-structure. Probably, it would not be surprising if a novel escape viral strategy therapy will be related to the gp120 synonymous mutations. Moreover, in relation to the pivotal role played by gp120 in polyvalent vaccine approaches, the impact of gp120 synonymous mutations may play an important role in HIV entry into the cell. Keywords: gp120; tropism; v3; s11r; evolution; vaccine.

This study was focused on the detection, characterization and virulence of a new baculovirus isolate from the larvae of cabbage looper, Trichoplusia ni (Hubner) (Lepidoptera: Noctuidae). T. ni is a polyphagous pest, and it has cosmopolitan distribution. An infected T. ni larvae was collected from a cabbage field in Turkey. Scanning electron microscopy studies showed the presence of typical occlusion bodies (OBs) with average size of 0.76 to 1.46µm in the collected larvae. Since the virions have single nucleocapsid within the envelopes, the isolate was named as Trichoplusia ni single nucleopolyhedrovirus Turkey isolate (TrniSNPV- TR). The total genome of the TrniSNPV-TR was determined as 122.9kb in size. Sequence analysis of the amplified late expression factor 8 (lef8), late expression factor 9 (lef9) and polyhedrin (polh) genes showed that the virus is a new isolate of nucleopolyhedroviruses and close to Trichoplusia ni SNPV isolates mentioned in the literature. However, this is the first study for the detection and characterization of a baculovirus from T. ni in Eurasian region. Insecticidal activities of the TrniSNPV-TR isolate (106OBs/ml-1) against neonate, 3rd and 5th instar larvae of T. ni and Helicoverpa armigera showed 98%-91%, 91%-87% and 65%-60% mortalities, respectively, within 14 days. LC50 of TrniSNPV-TR was determined as 2×103-9×103, 3×104-7×104 and 1×105-2×105OBs/ml on neonate, 3rd and 5th instar larvae, respectively. All these results showed that, TrniSNPV-TR has good potential to be utilized as a bio-pesticide against T. ni larvae in the future. Keywords: baculovirus; nucleopolyhedrovirus; Trichoplusia ni; TrniSNPV-TR; biological control.

The genome sequence of a novel RNA virus, Trichosanthes associated rhabdovirus 1 (TrARV1), was identified in a transcriptome dataset isolated from a root sample of Trichosanthes kirilowii, which is a flowering plant belonging to the family Cucurbitaceae. The fruits, seeds, and root tubers of T. kirilowii have been used clinically in traditional Chinese medicine. The TrARV1 genome sequence was predicted to have six open reading frames (ORFs) encoding five canonical structural proteins of the family Rhabdoviridae (N ORF for nucleocapsid, P ORF for phosphoprotein, M ORF for matrix protein, G ORF for glycoprotein, and L ORF for polymerase), and an accessory protein. Sequence comparisons and phylogenetic analyses based on L and N proteins confirmed that TrARV1 is a novel member of the genus Cytorhabdovirus of the family Rhabdoviridae. TrARV1 is most closely related to Wuhan insect virus 5 and persimmon virus A. The putative cis-regulatory elements involved in transcription termination and polyadenylation, commonly found in the gene junction regions of rhabdoviruses, were also identified in the TrARV1 genome having the consensus sequence 3'- ACUAAAUUAUUUUGAUCUUU-5'. The genome sequence of TrARV1 may be useful to study the evolution and molecular biology of cytorhabdoviruses. Keywords: Trichosanthes associated rhabdovirus 1; Cytorhabdovirus; Rhabdoviridae; Trichosanthes kirilowii.

Andrias davidianus ranavirus 1R (ADRV-1R), a core gene of the family Iridoviridae, is predicted to encode a viral transcription factor (vTF) since the protein contains a virus late transcription factor-3 like (VLTF3 like) domain. However, its characteristics and function are still unclear. In this study, the transcription and expression of ADRV-1R were investigated in Chinese giant salamander thymus cells (GSTCs). ADRV-1R transcription starts 6 hours post-infection (hpi), while the protein expression starts 8 hpi. Drug inhibition assay showed that the transcripts are inhibited by cycloheximide (CHX), a de novo protein synthesis inhibitor, indicating that ADRV-1R is a viral delayed-early (DE) gene. Subcellular localization showed that ADRV-1R is distributed in the cell nucleus and cytoplasm. The effect of ADRV-1R overexpression on cell proliferation and virus titer was analyzed. ADRV-1R overexpression significantly promoted the cell proliferation starting at day 2. Flow cytometry analysis further indicated that the protein promotes the GSTC cell cycle progression from G1 phase into S phase (G1/S transition). Moreover, ADRV-1R overexperession significantly increased ADRV titer in GSTCs. The virus titer was 6.3-6.9-fold higher at 36 hpi and further after than the control GSTC lines. These data showed that ADRV-1R is a delayed-early protein promoting cell proliferation and virus titers. Keywords: ranavirus; Andrias davidianus ranavirus; core gene; cell cycle; cell proliferations.

In this report, an H12N2 influenza A virus was identified from a fecal sample in the falcated teal, Anas falcata, located in the Dongting Lake wetland. This is the first report of H12N2 IAV detected from wild birds in China. Phylogenetic analysis showed that all eight segments of this H12N2 virus clustered in the Eurasian lineage. This strain was also shown to be closely related to those from duck-origin, goose origin and wild bird origin. This suggested a transmission of influenza A virus along the East Asian-Australian flyway. In addition, these results implied an interaction between wild birds and domestic poultry and established the need of a long-term and systematic surveillance of wild bird populations. Keywords: influenza A virus; H12N2 subtype; Dongting Lake wetland; wild birds; phylogenetic analysis.

Mitochondria are multitasking organelles that play a central role in energy production, survival and primary host defense against viral infections. Therefore, viruses target mitochondria dynamics and functions to benefit their replication and morphogenetic processes. We endeavor to understand the role of mitochondria during infection of ectromelia virus (ECTV), hence our investigations on mitochondria-related genes in non-immune (L929 fibroblasts) and immune (RAW 264.7 macrophages) cells. Our results show that during later stages of infection, ECTV significantly decreases the expression of mitochondria-related genes regulating many aspects of mitochondrial physiology and functions, including mitochondrial transport, small molecule transport, membrane polarization and potential, targeting proteins to mitochondria, inner membrane translocation, and apoptosis. Such down-regulation is cell-specific, since macrophages exhibited a more profound down-regulation of mitochondria-related genes compared to infected L929 fibroblasts. Only L929 cells exhibited up-regulation of two important genes responsible for oxidative phosphorylation and subsequent ATP production: Slc25a23 and Slc25a31. Changes in the expression of mitochondria-related genes are accompanied by altered mitochondria morphology and distribution in both types of cells. In depth Ingenuity Pathway Analysis (IPA) identified the "Sirtuin Signaling Pathway" as the most significant top canonical pathway associated with ECTV infection in both analyzed cell types. Taken together, down-regulation of mitochondria-related genes observed especially in macrophages indicates dysfunctional mitochondria, possibly contributing to energy collapse and induction of intrinsic pathway of apoptosis. Meanwhile, alteration of the expression of several mitochondria-related genes in fibroblasts without apoptosis induction may represent poxviral strategy to control cellular energy metabolism for efficient replication. Keywords: ectromelia virus; mitochondria; fibroblasts; macrophages.

A novel disease, of unknown origin, causing a deadly pneumonia of human patients was reported in December 2019 in Wuhan, Hubei province of China. Later called coronavirus disease (COVID-19), it rapidly spread across China and worldwide. Intensive research revealed that the etiological agent of the global COVID-19 pandemic was a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome contains typical coronavirus genes but the receptor binding domain (RBD) in the S protein is highly specific. The site for furin-like protease cleavage of the S protein into S1 and S2 subunits is also unique. Further analyses suggested that SARS-CoV-2 is of zoonotic origin. The analysis of the SARS-CoV-2 genome, especially the S gene, shows that natural evolutionary process between a bat-CoV and a pangolin-CoV or other animal coronavirus could have been important in creating SARS-CoV-2, with transmission of novel virus to the human population. On the other hand, new analyses indicate that SARS-CoV-2 is not a recombinant virus. Keywords: COVID-19; SARS-CoV-2; genome; bat coronavirus; pangolin coronavirus.

Middle East respiratory syndrome coronavirus (MERS-CoV) is an RNA virus that causes severe respiratory disease. Since it was identified in 2012, approximately 2500 MERS cases with high mortality have been confirmed in 27 countries. Although most cases have occurred in the Middle East, an outbreak in South Korea in 2015 showed that MERS could be a global threat via human-to-human transmission. There is no licensed vaccine against MERS. Thus, early detection is the best way to limit the spread of this fatal disease. In this review, we focus on transmission, the infection process, and scientific efforts in vaccine development and diagnostics for MERS-CoV. Keywords: Middle East respiratory syndrome coronavirus; epidemiology; virology; vaccine; diagnostics.

We investigated the experimental infection of two highly pathogenic avian influenza H5N1 viruses isolated from crow (A/crow/Assam/142119/2008) and chicken (A/chicken/Sikkim/151466/2009) in house crows (Corvus splendens). Both viruses caused infection in crows, where four out of six and three out of six crows succumbed to H5N1 infection within 11 days post challenge by crow and chicken viruses, respectively. The major clinical signs in crows were wing paralysis, circling and torticollis. The virus shedding detected from swabs was not persistent in both crow nor chicken viruses. Both viruses were isolated more frequently from oral swabs than from cloacal swabs. Both virus strains were isolated from brain, lungs, heart, liver, pancreas, spleen, large intestines of crows that succumbed to H5N1 infection. The surviving birds seroconverted in response to H5N1 virus infection. Microscopically, both viruses caused coagulative necrosis in pancreas and kidneys. Brain showed gliosis and neuronal degeneration. This experimental study highlights that crows could be infected with H5N1 viruses from different hosts with minor differences in pathogenicity. Therefore, it is imperative to carry out surveillance of highly pathogenic avian influenza H5N1 virus in synanthropic birds along with biosecurity measures to mitigate the H5N1 spread in poultry population. Keywords: chicken virus; crow virus; highly pathogenic avian influenza; house crows.