In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa\'s plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.

Human adenovirus (HAdV) causes acute respiratory infections leading to mortality in children. This study analyzes the circulating respiratory HAdV genotypes in West Bengal, India during 2018-2022 among symptomatic patients. The overall positivity rate was 6.8%, out of which 26.4% were co-infected with other respiratory viruses. Children aged 2 to 5 years were mostly infected. Phylogenetic analysis revealed that the recombinant HAdV-B type 7/3, which has remarkable outbreak potential, predominantly circulated in this region followed by the non-recombinant HAdV-B type 3/3. Moreover, the amino acid sequences encoded by both the hexon and fiber genes of these two circulating strains possessed a few mutations that mostly diverged from the prototype strain, although the divergence was less pronounced in case of the amino acids encoded by the fiber gene of HAdV-B type 3/3. Overall, the results underscore the need for continuous surveillance of respiratory HAdV types to combat future possible epidemics.

The gene sequence data for apple mosaic virus (ApMV) in NCBI GenBank were analyzed to determine the phylogeny and population structure of the virus at a global level. The phylogenies of the movement protein (MP) and coat protein (CP) genes, encoded by RNA3, were shown to be identical and consisted of three lineages but did not closely correlate with those of P1 and P2, suggesting the presence of recombinant isolates. Recombination Detection Program (RDP v.4.56) detected significant recombination signal in the P1 region of K75R1 (KY883318) and Apple (HE574162) and the P2 region of Apple (HE574163) and CITH GD (MN822138). Observation on several diversity parameters suggested that the isolates in group 3 had higher divergence among them, compared to isolates in groups 1 and 2. The neutrality tests assigned positive values to P1, indicating that only this region experiencing balanced or contracting selection. Comparisons of the three phylogroups demonstrated high Fixation index (FST) values and confirmed genetic separation and the lack of gene flow among them. Additionally, ±500 bp of partial MP + \'intergenic region\' + partial CP coding regions of two Turkish isolates from apple and seven from hazelnut were sequenced and determined that their phylogenetic positions fell within group 1 and 3, respectively.

Marek\'s disease (MD) is a highly contagious, lymphoproliferative poultry disease caused by the oncogenic herpesvirus, serotype 1 Marek\'s disease virus (MDV-1), or Gallid herpesvirus 2 (GaHV-2). MDV strains have shown a continued evolution of virulence leading to immune failure, and MD cases continue to occur or surge. Meq, the major MDV-1 oncoprotein, induces T-cell neoplastic transformation through several mechanisms including inhibition of apoptosis, cell cycle regulation, and serum-anchorage independent growth. There is no current information on the MDV serotypes and pathotypes circulating in vaccinated commercial farms in Iran, where the birds are vaccinated at the hatchery with GaHV-2 and Meleagrid herpesvirus 1 (MeHV-1) vaccines. This study reports the molecular characterization of a GaHV-2 strain detected in 19 flocks of Iranian layer farms exhibiting MDV-1-like clinical signs and visceral lymphomas. Based on sequencing and phylogenetic analysis of the Meq gene, the Iranian GaHV-2 isolates could be divided into two separate clades regarding molecular features. The clade containing strains was closely related to Italian, Indian, and Hungarian virulent isolates, and the clade was related to American very virulent plus (vv+) isolates. For the first time, the MDV-1 virus was characterized by an outbreak in poultry flocks in Iran. Although MDV-1 strains obtained in Iran\'s present outbreak are presumably related to virulent (v) and vv+ pathotypes based on nucleotide, amino acid, and phylogenetic analysis of the viruses, they are not confirmed so far. Thus, it is highly recommended to perform further analyses to demonstrate the pathotype characteristics in vivo.
Caracterización molecular y análisis filogenético del virus de la enfermedad de Marek en Irán. La enfermedad de Marek (MD) es una enfermedad altamente contagiosa linfoproliferativa en la avicultura causada por el herpesvirus oncogénico, el virus de la enfermedad de Marek de serotipo 1 (MDV-1) o Gallid herpesvirus 2 (GaHV-2). Las cepas del virus de Marek han mostrado una evolución continua de virulencia que conduce a una falla inmunológica, y los casos de Marek continúan ocurriendo o aumentando. El gene Meq, codifica la principal oncoproteína de MDV-1, induce la transformación neoplásica de células T a través de varios mecanismos que incluyen la inhibición de la apoptosis, la regulación del ciclo celular y el crecimiento independiente del anclaje sérico. No hay información actual sobre los serotipos y patotipos del virus de Marek que circulan en las granjas comerciales vacunadas en Irán, donde las aves se vacunan en la planta de incubación con las vacunas GaHV-2 y Meleagrid herpesvirus 1 (MeHV-1). Este estudio reporta la caracterización molecular de una cepa del Gallid herpesvirus 2 detectada en 19 lotes de granjas de aves de postura iraníes que presentaron signos clínicos sugestivos del serotipo 1 del virus de la enfermedad de Marek y linfomas viscerales. Según la secuenciación y el análisis filogenético del gene Meq, los aislamientos iraníes de GaHV-2 podrían dividirse en dos clados separados con respecto a las características moleculares. El clado que contenía las cepas estaba estrechamente relacionado con los aislados virulentos de Italia, India y de Hungria y el clado estaba relacionado con los aislados americanos muy virulentos plus (vv+). Por primera vez, el serotipo 1 del virus de la enfermedad de Marek se caracterizó por un brote en parvadas avícolas en Irán. Aunque las cepas del virus de Marek, serotipo 1 obtenidas en el brote actual de Irán están presuntamente relacionadas con patotipos virulentos (v) y muy virulentos plus según el análisis de nucleótidos, aminoácidos y filogenético de los virus, hasta el momento no se han confirmado. Por lo tanto, se recomienda realizar más análisis para demostrar las características del patotipo in vivo.

Edwardsiella spp. is a gram-negative, facultatively anaerobic, intracellular bacteria threatening the aquaculture industry worldwide. Noticeably, E. tarda is now genotypically classified into three distinct groups (E. tarda, E. piscicida and E. anguillarum), but morphologically, it is unclear due to varying degrees of virulence in different fish hosts. Hence, to reclassify E. tarda, we investigated differences in genotypes, phenotypes and pathogenicity. We collected Edwardsiella isolates from five different counties of Taiwan between 2017 and 2021. At first, gyrB gene was amplified for a phylogenetic tree from 40 isolates from different fish and one reference isolate, BCRC10670, from the human. Thirty-nine strains clustered into E. anguillarum, 1 strain into E. piscicida and 1 strain into E. tarda from human strain. Second, all isolates were characterized using various phenotypic (API 20E biochemical profiles) and genotypic (pulsed-field gel electrophoresis [PFGE], and virulence-related gene detection). SpeI digestion revealed 10 pulsotypes and I-CeuI into 7 pulsotypes. Virulent genes (citC, gadB, katB, mukF and fimA) confirmed in 35, 31, 28, 37 and 38 isolates, respectively. Finally, in vivo challenge test in milkfish (Chanos chanos) indicated the highest mortality from E. anguillarum. Overall, results revealed unique features with Edwardsiella spp. genotypes and pathogenicity, which are relevant to the host and provide useful insights for future vaccine development.

In September 2017, an outbreak with high mortality, which showed the typical signs of ND, occurred among a flock of more than 2000 Eurasian collared doves in Konarak, southeast of Iran. A confirmed pigeon paramyxovirus type 1 strain was isolated from the brain tissues of the dead doves. The isolate, which was called Pigeon/Iran/Konarak/Barin/2017, was classified as a highly velogenic NDV. Complete genome sequencing and phylogenetic analysis showed that the isolate belonged to subgenotype XXI.2, which has never been reported from Iran before. The isolate had the highest homology (96.15%) with early 2010s Italian isolates. Further studies will be required to understand the diversity better.

OBJECTIVE: This study was carried out from January 2018 to March 2020 in Kolkata, eastern India to determine the prevalence rates and epidemiological patterns associated with the major viral agents of gastroenteritis among children ≤5 years of age. Molecular characterization of GARV, the predominant agent of viral gastroenteritis, was done to understand their genotype diversity.
RESULTS: 1284 of 3157 stool samples (~40%) from children (≤5 years) with acute gastroenteritis tested positive for one or more enteric viruses with positivity rates 25.11%, 8.74%, 6.62% and 6.11% for GARV, HAdV-F, AstV and NoV respectively. Co-infection was observed in 5.31% of cases. Associated clinical/meteorological variables like age, sex, symptoms, temperature and precipitation were assessed to find any correlation between these and enteric virus infection rates. >70% of viral gastroenteritis cases were observed in 6-24 months\' age group. GARV and AstV infection occurred mostly during cooler months while HAdV-F infection mostly occurred during warmer periods. No definite seasonality was observed for NoV infections. Clinical severity associated with GARV infection was higher compared to other enteric viruses. Genotyping of rotavirus positive samples revealed G3P[8] was the predominantly circulating GARV genotype throughout the study period.
CONCLUSIONS: GARV remained the predominant viral agent of acute gastroenteritis among children though its prevalence rates in this region declined significantly compared to the previous years (2010-2016). The prevalence of other enteric viruses was below 10%.
CONCLUSIONS: This study provides valuable insights regarding the current burden of viral gastroenteritis in Eastern India. The 2-year study in children will provide the baseline data for future surveillance studies in evaluating the impact of the introduced GARV vaccine on the overall prevalence of viral gastroenteritis.

Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.

Picobirnavirus (PBV) is an enteropathogen virus causing diarrhea as an opportunistic virus in its vertebrate host. There is no information about human or animal PBVs in Iran. The aim of the present study was the investigation of the epidemiology of bovine PBV in the broad geographical area of Iran. Four hundred and eighty-five stool samples of up to 1 month old diarrheic calves were collected from 14 provinces and were tested with polyacrylamide gel electrophoresis (PAGE), and reverse transcription polymerase chain reaction (RT-PCR). Five samples were positive in PAGE assay (1.00%) and all of them were amplified using GI specific primers in RT-PCR. Phylogenetic analysis of one of the amplicons (strain Nazaktabar-14) revealed a low relationship to bovine PBV sequences and more identity to PBV isolates from other hosts. The structural alignment of the deduced amino acids of the partially sequenced RdRp gene of the Nazaktabar-14 strain showed high conservation. Sequences obtained from other amplicons showed a high mutation rate and further analysis of one of them showed that, despite the potential of forming deleterious mutations, most of the point mutations occurred in the RdRp gene of PBVs may be a silent mutation. There is little information about the molecular epidemiology of bovine PBVs. This study was the first report on the occurrence of PBVs in Iran and the first study on the molecular epidemiology of bovine PBV in the Middle East, revealing its low frequency as a diarrhea causative agent.

Cordyceps species are notable medicinal fungi in China, which are pathogenic on insects and exhibit high biodiversity in tropical and subtropical regions. Recently, three new Cordyceps species, Cordycepschangchunensis and Cordycepsjingyuetanensis growing on pupae of Lepidoptera and Cordycepschangbaiensis growing on larvae of Lepidoptera, were found in Jilin Province, China and are described, based on morphological and ecological characteristics. These three new species are similar to the Cordycepsmilitaris group, but are distinctly distinguishable from the known species. Cordycepschangchunensis, characterised by its small and light yellow to orange stromata which is occasionally forked, covered with white mycelium at the base of stipe, globose to ovoid perithecia, is macroscopically similar to Cordycepsmilitaris. Cordycepschangbaiensis is clearly discriminated from other Cordyceps species by its white to orange and branched stromata, clavate to cylindrical fertile apical portion, immersed and globose to ovoid perithecia. Moreover, unbranched, clavate and orange to light red stromata, almond-shaped to ovoid and immersed perithecia separate Cordycepsjingyuetanensis from other Cordyceps species. nrITS, nrLSU and EF-1α sequences were undertaken and phylogenetic trees, based on Maximum Likelihood and Bayesian Inference analysis showed that the three new species clustered with Cordycepsmilitaris, but formed individual clades, as well as confirmed the results of our morphological study.