Senecavirus A (SVA) the only member of the Senecavirus genus within the Picornaviridae family, is an emerging pathogen causing swine idiopathic vesicular disease and epidemic transient neonatal losses. Here, SVA strain (CH-HNKZ-2017) was isolated from a swine farm exhibiting vesicular disease in Henan Province of Central China. A phylogenetic analysis based on complete genome sequence indicated that CH-HNKZ-2017 was closely related to US-15-40381IA, indica- ting that a new SVA isolate had emerged in China.

In Cameroon, oil palm ( Elaeis guineensis Jacq.) is of economic importance. However, it is affected by vascular wilt presumed to be caused by Fusarium oxysporum f. sp. elaeidis (FOE). Accurate species identification requires molecular-based comparisons. The aim of this work was to molecularly identify Fusarium species associated with diseased oil palms and to determine the pathogenicity of selected isolates. Fungal samples of diseased palms were collected from the canopies and the soil of five oil palm estates of the Cameroon Development Corporation and characterized by sequencing and comparing the translation elongation factor 1a gene. The results revealed the presence of FOE from approximately 80% of the isolates. Cameroonian isolate within FOE clade 1 exhibited the greatest variability grouping with isolates from Suriname, Brazil and Democratic Republic of Congo. Other isolates found in FOE clade 2 formed a unique group which was comprised solely of isolates originating from Cameroon. Twenty-two isolates were chosen for pathogenicity tests. After a short time, 14 isolates were found to be pathogenic to oil palm seedlings. This study revealed the pathogenicity of FOE isolates from Cameroon and demonstrated that FOE in Africa is more diverse than previously reported, including a lineage not previously observed outside of Cameroon. Comparisons between all isolates will ultimately aid to devise appropriate control mechanisms and better pathogen detection methods.

Conventionally, Porcine sapelovirus (PSV) has been considered to comprise a single geno- type, PSV-1; however, a potentially novel member of PSV was recently discovered. In the present study, we propose a genotype definition of PSV based on phylogenetic and genetic analyses of the polyprotein, P1, and VP1 genes of available PSV sequences. Two genotypes, with pro- posed names PSV-1 and PSV-2, were identified. Moreover, the cut-off values (number of diffe- rences per site between amino acid sequences) for the definition of genotypes were established to be 0.1115 (polyprotein), 0.176 (P1), and 0.272 (VP1). The findings of this study are expected to enrich knowledge of PSV classification.

Canine parvovirus (CPV) causes acute gastroenteritis in domestic dogs, cats, and several wild carnivore species. In this study, the full-length VP2 gene of 36 CPV isolates from dogs and cats infected between 2016 and 2017 in Beijing was sequenced and analyzed. The results showed that, in dogs, the new CPV-2a strain was the predominant variant (n = 18; 50%), followed by the new CPV-2b (n = 6; 16.7%) and CPV-2c (n = 3; 8.3%) strains, whereas, among cats, the predominant strain was still CPV-2 (n = 9; 25%). One new CPV-2a strain, 20170320-BJ-11, and two CPV-2c strains, 20160810-BJ-81 and 20170322-BJ-26, were isolated and used to perform experimental infections. Multiple organs of beagles that died tested PCR positive for CPV, and characteristic histopathological lesions were observed in organs, including the liver, spleen, lungs, kidneys, small intestines, and lymph nodes. Experimental infections showed that the isolates from the epidemic caused high morbidity in beagles, indicating their virulence in animals and suggesting the need to further monitor evolution of CPV in China.

The purpose of the study was to analyze a part of the nucleotide sequences of ystB gene Y. enterocolitica strains isolated from wild animals. The material for the study consists of 30 Y. enterocolitica biotype 1A strains obtained from different wild animal species and belonging to different genotypes. Phylogenetic analysis of ystB nucleotide sequences belonging to four regular genotypes G1, G2, G3, G4 and to five groups of variations V1, V2, V3, V4, V5 revealed significant differences of Y. enterocolitica strains isolated from wild animals. The most phylogenetically distant were strains belonging to V5.

The present report describes the new occurrence of Tomato mosaic virus (ToMV) in cabbage, bean and Malva neglecta plants in Iran. In this study, sequence analyses of a partial RNA dependent RNA polymerases (RdRp) and complete movement protein (MP) and the coat protein (CP) nucleotide sequences of three new ToMV isolates collected from major crop fields in Iran revealed low genetic variation of RdRp gene compared to the CP and MP genes. The different topologies of the phylogenetic trees constructed, using available open reading frame (ORF1), ORF2 and ORF3 sequences from ToMV isolates, indicated different evolutionary constraints in these genomic regions. Statistical analysis also revealed that with the exception of CP other tested ToMV genes were under negative selection and the RdRp gene was under the strongest constraints. According to the phylogenetic tree it can be inferred from the nucleotide sequences of the complete CP and MP genes, that isolates from Iran and Egypt formed separate groups, irrespective of host origin. However, isolates clustered into groups with correlation to geographic origin but not the host. Analysis of the Ks *, Z* and Snn values also indicated genetic differentiation between ToMV populations. The Tajima’s D, Fu and Li’s statistical values were significantly negative for the RdRp gene of the Asian population which suggests the sudden expansion of ToMV in Asia. Taken together, the results indicate that negative selection and genetic drift were important evolutionary factors driving the genetic diversification of ToMV.

Passion fruit is an important fruit crop grown in parts of southern and north-eastern states of India. Leaf curl symptoms typical to begomovirus infection were observed on passion fruit plants at three locations of Madikeri District, Karnataka State, India. The disease incidence ranged from 10–20% in all the locations. In order to determine if the begomovirus was associated with leaf curl disease of passion fruit, 20 infected samples collected from different locations were subjected to PCR analysis using primers specific to begomovirus. This resulted in an expected PCR product of ~1.2 kb. Sequence analysis of these products revealed that they have more than 98% similarity among them and have similarity with other begomoviruses. Complete genome sequencing of begomovirus associated with one sample (PF1 collected from CHES, Madikeri) was done using RCA. Further, sequencing of betasatellite and alphasatellite was done after PCR amplification using specific primers. Complete DNA-A sequence of PF-isolate with other begomoviruses revealed that it shared nucleotide (nt) identity of 87.8 to 88.8% with Ageratum enation virus. This indicated the association of a novel begomovirus with leaf curl disease of passion fruit in India, for which we propose the name, Passion fruit leaf curl virus (PFLCuV) [IN-Kar-18]. PFLCuV associated betasatellite shared 98.3% sequence identity with Tomato leaf curl Bangladesh betasatellite, while alphasatellite had 95.7% sequence identity with Cotton leaf curl Multan alphasatellite. Recombinant analysis indicated a major component of PFLCuV DNA-A may have originated from a recombination of earlier reported begomoviruses. Recombination as well as GC plot analysis showed that the recombination occurred in the genome regions having low GC content regions of PFLCuV. However, there is no evidence of recombination in alphasatellite and betasatellite associated with leaf curl disease of passion fruit. This is the first record of a novel begomovirus and satellites associated with leaf curl disease of passion fruit from India.

Bacteria from the Simkaniaceae family are intracellular parasites belonging to the Chlamydiales order, detected in surface waters, drinking water, chlorine water, and in wastewater. Its main representative, Simkania negevensis, is pathogenic to humans and animals, especially fishes, as it principally causes respiratory tract diseases. Bacteria from this family are also capable of surviving and existing in free-living amoebas, omnipresent in the natural environment, which makes them an additional risk for human and animal health. The aim of the present study was to search for representatives of this family in freshwaters from the Odra River and two municipal lakes (Rusałka and Goplana). Out of 100 water samples analysed, the sequence of bacteria of Simkaniaceae family was found just in 1 percent, because phylogenetic analysis revealed that the obtained OdraWCh30 sequence shows 93% similarity to Simkania negevensis strain Z as well as 87% similarity to Candidatus Syngnamydia salmonis isolate Ho-2008 and Candidatus Syngnamydia salmonis isolate VS10102006 and 84-85% similarity to endosymbiont of Xenoturbella westbladi, Simkaniaceae bacterium clone SM081012-5s and Candidatus Syngnamydia venezia strain Pi3-2. This is the first case of detecting sequence of bacteria of Simkaniaceae family in the aquatic environment in Poland.

Canine distemper virus (CDV) infects wild and domestic Canidae worldwide. The hemag- glutinin (H) gene has the highest genetic variation in the genome of this virus. Thus, the H gene is commonly used for lineage identification and genetic analyses. In order to study the genetic characteristics and pathogenicity of CDV strains prevalent in China, 132 samples were collected from domestic dogs with suspected CDV infection, 58 samples were confirmed to be positive, and the H gene was successfully amplified from 15 samples. The epidemic strain was identified as type Asia-1 and the novel mutations, A51T, V58I, R179K and D262N, were detected in this strain. Isolated strains, BJ16B53, BJ16B14, and BJ17B8, were used for an animal infection experiment in raccoon dogs. BJ16B53 and BJ16B14 were found to cause clinical symptoms, death, and exten- sive lesions in various organs. These results are expected to facilitate the development of effective strategies to monitor and control CDV infection in China.

The present review aims to improve the scope and coverage of the phylogenetic matrices currently in use, as well as explore some aspects of the relationships among Paleogene penguins, using two key skeletal elements, the humerus and tarsometatarsus. These bones are extremely important for phylogenetic analyses based on fossils because they are commonly found solid specimens, often selected as holo− and paratypes of fossil taxa. The resulting dataset includes 25 new characters, making a total of 75 characters, along with eight previously uncoded taxa for a total of 48. The incorporation and analysis of this corrected subset of morphological characters raise some interesting questions considering the relationships among Paleogene penguins, particularly regarding the possible existence of two separate clades including Palaeeudyptes and Paraptenodytes , the monophyly of Platydyptes and Paraptenodytes , and the position of Anthropornis . Additionally, Notodyptes wimani is here recovered in the same collapsed node as Archaeospheniscus and not within Delphinornis, as in former analyses.

Lisianthus ( Eustoma grandiflorum) has become a major flowering plant in Okinawa, the southernmost prefecture of Japan. Its cultivation area has increased steadily with each passing year for two decades. Simultaneously, many types of lisianthus diseases related to damping-off symptoms have also increased dramatically. To create a strategy for preventing the disease, disease symptoms and pathogenic organisms of primary problematic disease with seasonal variation in the emergence were investigated. The symptoms were diagnosed as Fusarium stem rot (Kukigusare-byo) and the pathogen of the disease was identified as Fusarium avenaceum based on multigene sequences analyses. Indeed, the PCR result of the isolated strain in this study was the same as that isolated from lisianthus plants with Fusarium stem rot in Hokkaido Prefecture. Furthermore, the pathogen is clustered separately from the other F. avenaceum strains isolated from lisianthus in the USA. Diseased lisianthus plants spread throughout greenhouses even though several fungicides were applied. Additionally, they appeared from November to January and increased to 0.3% of the total number. Fusarium stem rot was found in 43.8% of the total number of farms from 2020–2021 in Okinawa Main Island.

Function of duck (Anas platyrhynchos) major histocompatibility complex class I (Anpl-MHC I) molecules in binding peptides is through the peptide binding groove (PBG), which is thought to be influenced by the high polymorphism of α1 and α2 domains. However, little is known about the polymorphism of Anpl-MHC I peptide binding domain (PBD), especially in the domestic duck. Here, we analyzed the polymorphism of forty-eight Anpl-MHC I α1 and α2 domains from domestic duck breeds previously reported. All sequences were analyzed through multiple sequence alignment and a phylogenetic tree was constructed. The coefficient of variance of the peptide binding domains (PBDs) from WS, CV, JD, and SX duck breeds was estimated based on the Wu-Kabat variability index, followed by the location of the highly variable sites (HVSs) on reported crystal structure models. Analysis of α1 and α2 domains showed common features of classical MHC class I and high polymorphism, especially in α1 domain. The constructed phylogenetic tree showed that PBDs of domestic ducks did not segregate based on breeds and had a close phylogenetic relationship, even with wild ducks. In each breed, HVSs were mostly located in the PBG, suggesting that they might determine peptide-binding characteristics and subsequently influence peptide presentation and recognition. The combined results of sequence data and crystal structure provide novel valuable insights into the polymorphism and diversity of Anpl-MHC I PBDs that will facilitate further studies on disease resistance differences between duck breeds and the development of cytotoxic T-lymphocyte (CTL) epitope vaccines suited for preventing diseases in domestic ducks.

We determined the level of flavonoids, citric acid and ascorbic acid in hips of rose species from the Caninae section occurring in Poland. We performed phytochemical analyses of 75 samples representing 11 species: Rosaagrestis Savi, R. canina L., R. dumalis Bechst., R. glauca Pourret, R. inodora Fries, R. jundzillii Besser, R. rubiginosa L., R. sherardii Davies, R. tomentosa Sm., R. villosa L. and R. zalana Wiesb. Flavonoid content was determined spectrophotometrically, and organic acid concentrations by HPLC. The content of the studied compounds varied greatly. Interspecific differences in the amount of flavonoids and ascorbic acid were highly significant. The most common species, Rosa canina, showed low average content of vitamin C (0.51 g/100 g of dry matter) and flavonoids (41 mg/100 g DM) and high content of citric acid (3.48 g/100 g DM). Ascorbic acid was highest in R. villosa hips (avg. 2.25 g/100 g DM), flavonoids were highest in R. rubiginosa (72 mg/100 g DM), and citric acid was highest in R. tomentosa (4.34 g/100 g DM). Flavonoid level correlated negatively with the amount of citric acid (r=-0.47, p<0.001). Cluster analysis of rose species based on the content of the investigated compounds confirmed the validity of the division of sect. Caninae into three subsections: Rubiginosae, Vestitae and Rubrifoliae. The phytochemical variation of these roses reflects their probable phylogenetic relationships as determined from morphology.

Despite the considerable progress that has recently been made in medicine, the treatment of viral infections is still a problem remaining to be solved. This especially concerns infections caused by newly emerging patogenes such as: human immunodeficiency virus, hepatitis C virus or SARS-coronavirus. There are several lines of evidence that the unusual genetic polymorphism of these viruses is responsible for the observed therapeutic difficulties. In order to determine whether some parameters describing a very complex and variable viral population can be used as prognostic factors during antiviral treatment computational methods were applied. To this end, the structure of the viral population and virus evolution in the organisms of two patients suffering from chronic hepatitis C were analyzed. Here we demonstrated that phylogenetic trees and Hamming distances best reflect the differences between virus populations present in the organisms of patients who responded positively and negatively to the applied therapy. Interestingly, the obtained results suggest that based on the elaborated method of virus population analysis one can predict the final outcome of the treatment even before it has started.