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Apple and citrus are perennial tree fruit crops that are vital for nutritional security and agricultural economy and to achieve the Sustainable Development Goals of the United Nations. Apple scab and fire blight, along with Huanglongbing, canker, and tristeza virus, stand out as their most notorious diseases and annually destabilize fruit supply. An environmentally sound approach to managing these diseases is improving tree resistance through breeding and biotechnology. Perennial fruit tree germplasm collections are distributed globally and offer untapped potential as sources of resistance. However, long juvenility, specific pollination and flowering habits, and extensive outcrossing hinder apple and citrus breeding. Advances in breeding approaches include trans- and cis-genesis, genome editing, and rapid-cycle breeding, which, in addition to conventional crossbreeding, can all facilitate accelerated integration of resistance into elite germplasm. In addition, the global pool of available sources of resistance can be characterized by the existing genetic mapping and gene expression studies for accurate discovery of associated loci, genes, and markers to efficiently include these sources in breeding efforts. We discuss and propose a multitude of approaches to overcome the challenges of breeding for resistance in woody perennials and outline a technical path to reduce the time required for the ultimate deployment of disease-resistant cultivars. [ABSTRACT FROM AUTHOR]

Heterophyiasis is a highly endemic disease in the Nile Delta, Egypt, where people consume raw or undercooked Oreochromis niloticus and Mugil cephalus. Birds and rats play a crucial role in fish-borne zoonotic trematode transmission since they serve as natural and experimental hosts. This study aimed to update the epidemiological information, morphological description, molecular identification and gene expression of two distinct heterophyid metacercariae in Giza, Wadi Al-Rayan, and Lake Manzala, Egypt, whereas various heterophyid infections could be expected. The present Centrocestus formosanus, Heterophyes heterophyes, and Heterophyes nocens with accession numbers OR947651.1, OR947700.1, and OR947719.1, respectively, matched with those recorded in the GenBank. Findings of the current investigation indicated that various cytokines like IL-1β, MHC-II, and TNF-α rapidly elevated in the infected pigeon's intestines. Additionally, the infection expanded due to the parasite's ejection from the host and the host's clinical affliction, which induced humoral immune responses. Interestingly, investigation of other trematode species is in extreme demand in terms of zoonoses. We suggest controlling snails, managing migratory birds, and examining and frying fishes to the point when the encysted metacercariae is destroyed. [ABSTRACT FROM AUTHOR]

Newcastle disease (ND) is caused by virulent strains of avian paramyxovirus type 1, also known as Newcastle disease virus (NDV). Despite vaccination, the frequency of reported outbreaks in Ethiopia has increased. From January to June 2022, an active outbreak investigation was conducted in six commercial chicken farms across areas of central Ethiopia to identify the circulating NDV strains. Thirty pooled tissue specimens were collected from chickens suspected of being infected with NDV. A questionnaire survey of farm owners and veterinarians was also carried out to collect information on the farms and the outbreak status. NDV was isolated using specific-pathogen-free (SPF)-embryonated chicken eggs and detected using haemagglutination and the reverse transcriptase–polymerase chain reaction (RT–PCR). The genotype and virulence of field NDV isolates were determined using phylogenetic analysis of fusion (F) protein gene sequences and the mean death time (MDT) test in SPF-embryonated chicken eggs. The questionnaire results revealed that ND caused morbidity (23.1%), mortality (16.3%), case fatality (70.8%), and significant economic losses. Eleven of thirty tissue specimens tested positive for NDV using haemagglutination and RT–PCR. The MDT testing and sequence analysis revealed the presence of virulent NDV classified as genotype VII of class II velogenic pathotype and distinct from locally used vaccine strains (genotype II). The amino acid sequences of the current virulent NDV fusion protein cleavage site motif revealed 112RRQKR↓F117, unlike the locally used avirulent vaccine strains (112GRQGR↓L117). The epidemiological data, MDT results, cleavage site sequence, and phylogenetic analysis all indicated that the present NDV isolates were virulent. The four NDV sequences were deposited in GenBank with accession numbers F gene (PP726912-15) and M gene (PP726916-19). The genetic difference between avirulent vaccine strains and circulating virulent NDV could explain the low level of protection provided by locally used vaccines. Further studies are needed to better understand the circulating NDV genotypes in different production systems. [ABSTRACT FROM AUTHOR]

Simple Summary: Porcine parvovirus 7 (PPV7) infection or co-infections with other pathogens have been documented in aborted pig fetuses and in sows that experienced reproductive failure, which has led to concern about the viral infection. Therefore, it is important to investigate the prevalence and genetic characterization of PPV7. In this study, we reported the prevalence and genetic characteristics of PPV7 circulating in swine in Hunan, China. These results will be of interest to those working in virus evolutionary dynamics analysis and would be helpful to provide the impetus and basis to further elucidate the pathogenesis of PPV7. Porcine parvovirus 7 (PPV7) was first discovered in swine in 2016, and PPV7 infection has been detected in aborted pig fetuses and in sows that experienced reproductive failure. The objective of this study was to report the prevalence and genetic characterization of PPV7 in Hunan, China. Seventy of the four hundred and twenty-two (16.6%) serum, semen, and tissue samples collected from pigs were positive for PPV7. One complete PPV7 strain and eighteen complete cap gene sequences were obtained; nucleotide and amino acid identity among the nineteen Cap sequences were 88.1–99.4% and 88.1–100%, respectively. They shared identity with previously discovered sequences ranging from 86.6 to 98.9% and 83.7 to 99.8% at the nucleotide- and amino acid-level, respectively. The phylogenetic tree analysis exhibited that PPV7 strains had two major groups based on the presence or absence of five amino acid (181–185) insertions on the Cap protein. Analysis of the Cap protein demonstrated that PPV7 Cap had significant variability, implying that PPV7 evolved at high substitution rates. Substantial variations of that PPV7 Cap may enable the emergence of newly mutated capsid profiles due to its viral adaptation to host responses. Furthermore, antigenic alteration owing to PPV7 Cap protein amino acid mutations at immune epitopes may enable viruses to escape from the host's immune system. This study determined the prevalence and genetic characteristics of PPV7 circulating in swine in Hunan, China, and provided the impetus and basis to further investigate the pathogenicity and epidemiology of PPV7. [ABSTRACT FROM AUTHOR]

Background: Canine circovirus (CanineCV) is a single-stranded circular DNA virus that infects domestic and wild canids in many countries. CanineCV is associated with gastroenteritis and diarrhea, respiratory disease, and generalized vasculitis leading to a fatal event. The Capsid protein (Cap) is a structural protein of the virus which has high genetic variability and plays a role in the canine immune response. In this study, we cloned the full-length CanineCV Capsid gene (Cap). In-silico analyses were used to explore the genomic and amino acid variability and natural selection acting on the Cap gene. The immune relevance for T-cell and B-cell epitopes was predicted by the immunoinformatic approach. Results: According to the Cap gene, our results showed that CanineCV was separated into five phylogenetic groups. The obtained CanineCV strain from this study was grouped with the previously discovered Thai strain (MG737385), as supported by a haplotype network. Entropy analyses revealed high nucleotide and amino acid variability of the Capsid region. Selection pressure analysis revealed four codons at positions 24, 50, 103, and 111 in the Cap protein evolved under diversifying selection. Prediction of B-cell epitopes exhibited four consensus sequences based on physiochemical properties, and eleven peptide sequences were predicted as T-cell epitopes. In addition, the positive selection sites were located within T-cell and B-cell epitopes, suggesting the role of the host immune system as a driving force in virus evolution. Conclusions: Our study provides knowledge of CanineCV genetic diversity, virus evolution, and potential epitopes for host cell immune response. [ABSTRACT FROM AUTHOR]

Bovine papular stomatitis virus (BPSV) is a parapoxvirus that infects cattle, causing skin lesions on the udder and mouth. There have been few studies on the prevalence and molecular characteristics of BPSV in Iraq. Here, we describe the prevalence, phylogenetic analysis, and clinico-epidemiological features of BPSV in cattle in Al-Qadisiyah, Iraq. A total of 264 animals were examined for teat and oral lesions, and BPSV was detected by PCR in 79.9% (211/264) of cattle and calves with skin lesions. The lesions included ulcers, papules, and scabby proliferative areas. The BPSV strains from Iraq clustered phylogenetically with BPSV strains detected in the USA. Further studies are needed to explore the evolution and epidemiology of this virus in the region. [ABSTRACT FROM AUTHOR]

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes. [ABSTRACT FROM AUTHOR]

Background and Aim: Ducks worldwide are infected with duck circovirus (DuCV), which causes feather abnormality, emaciation, and poor growth performance. DuCV is similar to other circoviruses that induce immunosuppression due to the occurrence of the bursae of Fabricius (BF) and spleen atrophies. In Thailand, retarded ducks with feather losses were submitted for disease investigation. The ducks presented low body weight gain, had small BF and spleens, and were consistent with duck-infected DuCV. Our study investigated the possibility of DuCV infection in duck flocks in Thailand. We also analyzed the genetic characteristics of the virus. Materials and Methods: BF and spleen samples were collected from affected meat and layer ducks from six farms thought to have been infected with DuCV. These tissues were then subjected to histopathological examination and molecular identification using conventional polymerase chain reaction and nucleotide sequencing. To identify DuCV, phylogenetic trees were generated using MEGA version X software. Samples of tissues or swabs were collected to determine whether coinfections with bacteria and viruses existed. Results: Phylogenetic analysis using the entire genome (1995–1996 bp) and cap gene (762 bp) revealed that the DuCV isolates circulating in Thailand belonged to DuCV genotype I, which was further subdivided into two sub-genotypes: sub-genotype I b and an unclassified sub-genotype based on reference sub-genotypes. Thai isolates have variations in 10 amino acid residues in the capsid protein. Ducks infected with Thai DuCV were also coinfected with Riemerella anatipestifer, Escherichia coli, Pasteurella multocida, duck viral enteritis, and duck Tembusu virus, which is consistent with previous DuCV infection studies. Conclusion: Six DuCVs from ducks who were previously found to have feather loss, were underweight, had growth retardation, and had poor body condition were identified in this study as belonging to genotype Ⅰ and constituting at least two sub-genotypes. Due to the immunosuppressive effects of DuCV, coinfection of bacterial and viral pathogens was typically observed in Thai DuCV-infected ducks.

Abstract Heterophyiasis is a highly endemic disease in the Nile Delta, Egypt, where people consume raw or undercooked Oreochromis niloticus and Mugil cephalus. Birds and rats play a crucial role in fish-borne zoonotic trematode transmission since they serve as natural and experimental hosts. This study aimed to update the epidemiological information, morphological description, molecular identification and gene expression of two distinct heterophyid metacercariae in Giza, Wadi Al-Rayan, and Lake Manzala, Egypt, whereas various heterophyid infections could be expected. The present Centrocestus formosanus, Heterophyes heterophyes, and Heterophyes nocens with accession numbers OR947651.1, OR947700.1, and OR947719.1, respectively, matched with those recorded in the GenBank. Findings of the current investigation indicated that various cytokines like IL-1β, MHC-II, and TNF-α rapidly elevated in the infected pigeon’s intestines. Additionally, the infection expanded due to the parasite’s ejection from the host and the host’s clinical affliction, which induced humoral immune responses. Interestingly, investigation of other trematode species is in extreme demand in terms of zoonoses. We suggest controlling snails, managing migratory birds, and examining and frying fishes to the point when the encysted metacercariae is destroyed.

Abstract Background Canine circovirus (CanineCV) is a single-stranded circular DNA virus that infects domestic and wild canids in many countries. CanineCV is associated with gastroenteritis and diarrhea, respiratory disease, and generalized vasculitis leading to a fatal event. The Capsid protein (Cap) is a structural protein of the virus which has high genetic variability and plays a role in the canine immune response. In this study, we cloned the full-length CanineCV Capsid gene (Cap). In-silico analyses were used to explore the genomic and amino acid variability and natural selection acting on the Cap gene. The immune relevance for T-cell and B-cell epitopes was predicted by the immunoinformatic approach. Results According to the Cap gene, our results showed that CanineCV was separated into five phylogenetic groups. The obtained CanineCV strain from this study was grouped with the previously discovered Thai strain (MG737385), as supported by a haplotype network. Entropy analyses revealed high nucleotide and amino acid variability of the Capsid region. Selection pressure analysis revealed four codons at positions 24, 50, 103, and 111 in the Cap protein evolved under diversifying selection. Prediction of B-cell epitopes exhibited four consensus sequences based on physiochemical properties, and eleven peptide sequences were predicted as T-cell epitopes. In addition, the positive selection sites were located within T-cell and B-cell epitopes, suggesting the role of the host immune system as a driving force in virus evolution. Conclusions Our study provides knowledge of CanineCV genetic diversity, virus evolution, and potential epitopes for host cell immune response.

Nile tilapia Oreochromis niloticus is one of the most important fishery resources and a valuable fish species for aquaculture programmes. It is found in almost all waters and is widely dispersed. Several natural populations of this species have been impacted by genetic pollution despite their significant economic relevance. Understanding population structure is a crucial first step in protecting this species in its native habitats as well as in choosing which wild stocks to use in hatchery initiatives. To demonstrate the genetic-population structure of this species, genetic differences among three geographically secluded populations of O. niloticus were investigated utilizing mitochondrial DNA cytochrome b gene sequences. The results were used to estimate the levels of genetic variability within and among the populations. The 56 cyt b (821 bp) sequences analysis revealed 21 haplotypes, with a nucleotide diversity of 0.0510 and a haplotype diversity of 0.881. In each of the populations, seven (7) singleton variable sites and 19 informative-parsimony sites, genetic diversity could be identified and few population haplotypes were found, indicating a minor genetic distinction between them. For the purpose of conservation and/or Nile tilapia breeding programmes, this information would assist in choosing the fish populations that maintain greater genetic variation in O. niloticus.

Abstract Background Bovine coronavirus (BCoV) is implicated in severe diarrhea in calves and contributes to the bovine respiratory disease complex; it shares a close relationship with human coronavirus. Similar to other coronaviruses, remarkable variability was found in the genome and biology of the BCoV. In 2022, samples of feces were collected from a cattle farm. A virus was isolated from 7-day-old newborn calves. In this study, we present the genetic characteristics of a new BCoV isolate. The complete genomic, spike protein, and nucleocapsid protein gene sequences of the BCoV strain, along with those of other coronaviruses, were obtained from the GenBank database. Genetic analysis was conducted using MEGA7.0 and the Neighbor-Joining (NJ) method. The reference strains’ related genes were retrieved from GenBank for comparison and analysis using DNAMAN. Results The phylogenetic tree and whole genome consistency analysis showed that it belonged to the GIIb subgroup, which is epidemic in Asia and America, and was quite similar to the Chinese strains in the same cluster. Significantly, the S gene was highly consistent with QH1 (MH810151.1) isolated from yak. This suggests that the strain may have originated from interspecies transmission involving mutations of wild strains. The N gene was conserved and showed high sequence identity with the epidemic strains in China and the USA. Conclusions Genetic characterization suggests that the isolated strain could be a new mutant from a wild-type lineage, which is in the same cluster as most Chinese epidemic strains but on a new branch.

Abstract Background Hepatozoon canis is a protozoan parasite transmitted to dogs through ingesting the arthropod vector (hard ticks), which contains mature protozoal oocysts harboring infectious sporozoites. Aims This study aims to evaluate the blood parameters, biochemical assays and histopathological appraisal of infected police dogs with Hepatozoon canis, from kennels in the police academy of Egypt during 2020–2021. Methods Red blood cells count, hemoglobin, hematocrit, blood platelets and white blood cells count from collected blood samples were analyzed, and serum albumin, creatinine, urea, aspartate aminotransferase and alanine aminotransferase were analyzed from serum samples. Polymerase chain reaction amplified the 18S ribosomal RNAgene of the Hepatozoon species for genetic analysis, and the deoxyribonucleic acid products were sequenced and added to GenBank. Results The present study resulted in 5% of the police dog population being infested with Rhipicephalus sanguineus. This study registered the sequences of the Hepatozoon canis 18S ribosomal RNAgene in Egypt for the first time in Genbank (MW362244.1–MW362245.1). The biochemical assay revealed that the parasite severely affected the protein, significantly increasing serum albumin in positive polymerase chain reaction testing dogs. Conclusion A thorough inspection discovered that 100 police dogs had clinical symptoms like fever, emaciation and anemia, while the other 200 were healthy and had no evident clinical indicators.

Rotavirus A (RVA) causes gastroenteritis in humans and animals. The zoonotic potential of RVA has been reported and raises major concerns, especially in animal-human interface settings. The study aimed to characterize and investigate the genetic diversity among RVAs in dogs and cats in Thailand. We collected 572 rectal swab samples from dogs and cats in Bangkok animal hospitals from January 2020 to June 2021. The one-step RT-PCR assay detected RVAs in 1.92% (11/572) of the samples, with 2.75% (8/290) in dogs and 1.06% (3/282) in cats. Two canine RVA and one feline RVA were subjected to whole genome sequencing. Our results showed that all three viruses were identified as RVA genotype G3P[3]. The genetic constellation of RVAs is unique for different species. For canine RVAs is G3-P [3]-I3-R3-C3-M3-A9-N2-T3-E3-H6, while Feline RVA is G3-P [3]-I8-R3-C3-M3-A9-N3-T3-E3-H6. Notably, both canine and feline RVAs contained the AU-1 genetic constellation with multiple reassortments. The results of phylogenetic, genetic, and bootscan analyses showed that canine RVAs may have reassorted from dog, human, and cat RVAs. While feline RVA was closely related to RVAs in humans, bats, and simians. This study provided genetic characteristics and diversity of RVAs in dogs and cats and suggested possible multiple reassortments, suggesting the zoonotic potential of the viruses. Thus, public health awareness should be raised regarding the zoonotic potential of RVAs in dogs and cats. Further studies on RVAs on a larger scale in dogs and cats in Thailand are needed. [ABSTRACT FROM AUTHOR]

Simple Summary: Indigenous goats are important in the daily lives of people in East Africa because they adapt well to various climatic conditions. However, there is little information about these breeds both locally and internationally. This review discusses how these goats are raised, their physical and genetic characteristics, and diversity. It shows that there is no proper way by which these breeds are identified as most of them appear to be similar, hence they are named based on the region or tribe they are raised in. This review also points out several challenges like mixed breeding, lack of records, animal health problems, poor grazing fields, and basic care practices. To overcome these issues, it suggests the adoption of a participatory approach across goat value chains and the use of modern genomic tools in selection to improve goat breeding. This approach aims to protect the unique genetic resources of East African indigenous goats and ensure their future conservation. Indigenous goats are important in the livelihoods of rural households in East African countries. This is due to their ability to produce and reproduce in different environments and climatic conditions. Even though these indigenous goats are important, there is little available information on the genetic characterization of these breeds in Africa and at the international level. This paper reviews the status of indigenous goats, highlighting their production systems, phenotypic and genetic characteristics, and genetic diversity, and proposes potential ways for sustainable improvement and conservation in East African countries. Most households use traditional production systems with various uncharacterized goat breeds and ecotypes, which are hence named after the tribe or locality in which they are found. Most of these goats are classified as small East African breeds, with significant variability in morphological features. Some of the challenges to goat production in this region are indiscriminate crossbreeding, lack of pedigree records, parasites and disease incidences, low-quality pastures, and low levels of management. There is a need for a collaborative approach amongst the actors in goat breeding value chains as well as integrating modern genomic tools into breeding programs to enhance selection. This will ensure the resilience and sustainability of these unique indigenous goat populations in East Africa [ABSTRACT FROM AUTHOR]

In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights. [ABSTRACT FROM AUTHOR]

Tembusu virus (TMUV) is an important infectious disease, causing economic losses in duck production. Since the first report of TMUV infection in Vietnam in 2020, the disease has persisted and affected poultry production in the country. This study conducted epidemiological and genetic characterization of the viral strains circulating in north Vietnam based on 130 pooled tissue samples collected in six provinces/cities during 2021. The TMUV genome was examined using conventional PCR. The results indicated that 21 (16.15%) samples and 9 (23.68%) farms were positive for the viral genome. The positive rate was 59.26% for ducks at ages 2-4weeks, which was significantly higher than for ducks at ages >4weeks and<2weeks. Genetic analysis of the partial envelope gene (891bp) sequences indicated that the five Vietnamese TMUVs shared 99.55-100% nucleotide identity, while the rates were in the range 99.59-100% based on the pre-membrane gene sequences (498bp). The five Vietnamese TMUV strains obtained formed a novel single subcluster. These strains were closely related to Chinese strains and differed from the vaccine strain, suggesting that Vietnamese TMUV strains were field viruses. It needs to be further studied on vaccine development to prevent effects of TMUV infection on poultry production across Vietnam. [ABSTRACT FROM AUTHOR]

Background: Hepatozoon canis is a protozoan parasite transmitted to dogs through ingesting the arthropod vector (hard ticks), which contains mature protozoal oocysts harboring infectious sporozoites. Aims: This study aims to evaluate the blood parameters, biochemical assays and histopathological appraisal of infected police dogs with Hepatozoon canis, from kennels in the police academy of Egypt during 2020–2021. Methods: Red blood cells count, hemoglobin, hematocrit, blood platelets and white blood cells count from collected blood samples were analyzed, and serum albumin, creatinine, urea, aspartate aminotransferase and alanine aminotransferase were analyzed from serum samples. Polymerase chain reaction amplified the 18S ribosomal RNAgene of the Hepatozoon species for genetic analysis, and the deoxyribonucleic acid products were sequenced and added to GenBank. Results: The present study resulted in 5% of the police dog population being infested with Rhipicephalus sanguineus. This study registered the sequences of the Hepatozoon canis 18S ribosomal RNAgene in Egypt for the first time in Genbank (MW362244.1–MW362245.1). The biochemical assay revealed that the parasite severely affected the protein, significantly increasing serum albumin in positive polymerase chain reaction testing dogs. Conclusion: A thorough inspection discovered that 100 police dogs had clinical symptoms like fever, emaciation and anemia, while the other 200 were healthy and had no evident clinical indicators. [ABSTRACT FROM AUTHOR]

The high genetic heterogeneity of small ruminant lentiviruses (SRLV) renders the genetic characterization of the circulating strains crucial for the epidemiological investigation and the designation of effective diagnostic tools. In Greece, research data regarding the genetic diversity of the circulating SRLV strains is scarce, hindering the implementation of efficient surveillance and control programs. The objective of the study was to genetically characterize SRLV strains isolated from intensive dairy sheep farms in Greece and evaluate the variability of the immunodominant regions of the capsid protein. For this reason, a total of 12 SRLV-infected animals from four intensive dairy sheep farms with purebred Chios and Lacaune ewes were used for the amplification and sequencing of an 800 bp gag-pol fragment. The phylogenetic analyses revealed a breed-related circulation of strains; Chios ewes were infected with strains belonging exclusively to a separate group of genotype A, whereas strains belonging to subtype B2 were isolated from Lacaune ewes. Immunodominant epitopes of capsid protein were quite conserved among the strains of the same genotype, except for the Major Homology Region which showed some unique mutations with potential effects on viral evolution. The present study contributes to the extension of the current knowledge regarding the genetic diversity of SRLV strains circulating in sheep in Greece. However, broader genetic characterization studies are warranted for the exploration of possible recombinant events and the more comprehensive classification of the circulating strains. [ABSTRACT FROM AUTHOR]

Simple Summary: Small ruminant lentiviruses are a group of viruses characterized by a high genetic and antigenic variability. In the absence of control measures, they are characterized by high prevalence in goat and sheep farms. In Greece, a country characterized by one of the highest small ruminant populations in Europe, SRLVs are well-known pathogens, but so far, few studies have investigated the circulating viral strains and their prevalence in the islands and mainland. The results of this research highlighted the presence of both A and B subtypes as well as the predominance of a novel A viral cluster. In many cases, the combined serological–molecular approach allowed us to identify more than one viral subtype in a single farm. Small ruminant lentiviruses are a group of viruses infecting goat and sheep worldwide. These viruses exhibit an extraordinary degree of genetic and antigenic variability that severely influence in vivo and in vitro features, as well as diagnostic test results. Small ruminant farming is the most important animal farming business in Greece, with a high impact on the Greek primary economy. Although SRLV infection and its impact on animal production are well established in the country, little is known about the circulating SRLV strains and their prevalence. The aim of this study was to characterize SRLVs circulating in Greece with a combined serological and molecular approach, using the bulk milk matrix collected from 60 farms in different municipalities. This study allowed us to estimate a seroprevalence of around 52% at the herd level. The B1, B2 and A3 subtypes and a novel A viral cluster were identified. Moreover, the amplicon sequencing method allowed us to identify more than one viral subtype in a sample. These results again confirm the high variability of these viruses and highlight the importance of the constant monitoring of viral evolution, in particular in antigens of diagnostic interest. [ABSTRACT FROM AUTHOR]

The growing interest in maize landraces over the past two decades has led to the need to characterize the Italian maize germplasm. In Italy, hundreds of maize landraces have been developed, but only a few of them have been genetically characterized, and even fewer are currently employed in agriculture or for breeding purposes. In the present study, 13 maize landraces of the west Emilia-Romagna region were morphologically and genetically characterized. These accessions were sampled in 1954 from three provinces, Modena, Parma, and Piacenza, during the characterization project of Italian maize landraces. The morphological characterization of these 13 accessions was performed according to the UPOV protocol CPVO/TP2/3, examining 34 phenotypic traits. A total of 820 individuals were genotyped with 10 SSR markers. The genetic characterization revealed 74 different alleles, a FST mean value of 0.13, and a Nm mean of 1.73 over all loci. Moreover, AMOVA analysis disclosed a low degree of differentiation among accessions, with only 13% of genetic variability found between populations, supporting PCoA analysis results, where the first two coordinates explained only 16% of variability. Structure analysis, supported by PCoA, showed that only four accessions were clearly distinguished for both K = 4 and 6. Italian landraces can be useful resources to be employed in maize breeding programs for the development of new varieties, adapted to different environmental conditions, in order to increase crop resilience and expand the maize cultivation area. [ABSTRACT FROM AUTHOR]

Leaf samples of 226 cultivated olive trees were collected from traditionally managed olive orchards and genotyped with eleven consensual SSR markers. The proportion of shared allele distance was used for the estimation of distances between olive genotypes. Cluster analyses were performed using a Fitch–Margoliash least-squares algorithm. The number of different genetic subgroups of olive genotypes (K) was investigated using STRUCTURE analysis. The standardization of allele lengths was performed to enable the comparison SSR profiles of Croatian olive genotypes with olive profiles obtained with the same SSR primers in OleaDB and WOGB databases. Overall, 73 SSR profiles of known Croatian varieties and 53 profiles of unknown olive genotypes were differentiated. Synonyms were detected in 18 varieties, and we found intra-varietal differences in 15 varieties. Three genetic subgroups of olive genotypes were determined. Following allele length standardization achieved using nine referral samples, the genetic profiles of 126 cultivated olive genotypes were compared to OleaDB and WOGB databases, out of which 92 genotypes were found to be unique to Croatian olive germplasm. The results revealed the wide genetic diversity of olive germplasm beyond the known, registered varieties. The FAZ_oliveDB database containing the profiles of 126 Croatian olive genotypes was created and made available for public use. [ABSTRACT FROM AUTHOR]

Pigeon Newcastle disease (ND) is a serious infectious illness caused by the pigeon Newcastle disease virus (NDV) or Paramyxovirus type 1 (PPMV-1). Genotype VI NDV is a primary factor in ND among Columbiformes (such as pigeons and doves). In a recent study, eight pigeon NDV strains were discovered in various provinces in China. These viruses exhibited mesogenic characteristics based on their MDT and ICPI values. The complete genome sequences of these eight strains showed a 90.40% to 99.19% identity match with reference strains of genotype VI, and a 77.86% to 80.45% identity match with the genotype II vaccine strain. Additionally, analysis of the F gene sequence revealed that these NDV strains were closely associated with sub-genotypes VI.2.2.2, VI.2.1.1.2.1, and VI.2.1.1.2.2. The amino acid sequence at the cleavage site of the F protein indicated virulent characteristics, with the sequences 112KRQKRF117 and 112RRQKRF117 observed. Pigeons infected with these sub-genotype strains had a low survival rate of only 20% to 30%, along with lesions in multiple tissues, highlighting the strong spread and high pathogenicity of these pigeon NDV strains. Molecular epidemiology data from the GenBank database revealed that sub-genotype VI.2.1.1.2.2 strains have been prevalent since 2011. In summary, the findings demonstrate that the prevalence of genotype VI NDV is due to strains from diverse sub-genotypes, with the sub-genotype VI.2.1.1.2.2 strain emerging as the current epidemic strain, highlighting the significance of monitoring pigeon NDV in China. [ABSTRACT FROM AUTHOR]

ABSTRACT: Toxoplasma gondii (T. gondii) is an intracellular protozoan that can cause toxoplasmosis in all warm-blooded hosts. This study focused on the prevalence and genetic characterize of T. gondii in ducks from Fujian province, China. Genomic DNA was extracted from duck tissue samples (heart, liver, lung, and muscle). To assess the genetic diversity of the T. gondii isolates, it was determined by using multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. A total of 586 ducks from 5 cities in Fujian province were tested, and 35 (6.0%) of which were found to be positive for the T. gondii B1 gene. Further genotyping of these positive samples at 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) using PCR-RFLP revealed that one tissue samples (heart samples from Fuzhou ducks) were identified as Type I (ToxoDB#10). This study is the first report on the prevalence and genetic characterization of T. gondii in ducks in Fujian province, and Type I (ToxoDB#10) is found in ducks in China for the first time. The findings document the genetic characterization of T. gondii in free-range ducks from Fujian Province, thereby enriching the understanding of T. gondii genetic diversity in China. Moreover, these results provide essential data support for further prospective studies and underscores the “One Health” concept, emphasizing the integral link among human, animal, and environmental health.

Influenza A viruses (IAV) impose significant respiratory disease burdens in both swine and humans worldwide, with frequent human-to-swine transmission driving viral evolution in pigs and highlighting the risk at the animal-human interface. Therefore, a comprehensive One Health approach (interconnection among human, animal, and environmental health) is needed for IAV prevention, control, and response. Animal influenza genomic surveillance remains limited in many Latin American countries, including Colombia. To address this gap, we genetically characterized 170 swine specimens from Colombia (2011–2017). Whole genome sequencing revealed a predominance of pandemic-like H1N1 lineage, with a minority belonging to H3N2 and H1N2 human seasonal-like lineage and H1N1 early classical swine lineages. Significantly, we have identified reassortant and recombinant viruses (H3N2, H1N1) not previously reported in Colombia. This suggests a broad genotypic viral diversity, likely resulting from reassortment between classical endemic viruses and new introductions established in Colombia's swine population (e.g. the 2009 H1N1 pandemic). Our study highlights the importance of a One Health approach in disease control, particularly in an ecosystem where humans are a main source of IAV to swine populations, and emphasizes the need for continued surveillance and enhanced biosecurity measures. The co-circulation of multiple subtypes in regions with high swine density facilitates viral exchange, underscoring the importance of monitoring viral evolution to inform vaccine selection and public health policies locally and globally.

ABSTRACTImmune checkpoint inhibitors (ICIs) have emerged as a promising therapeutic option for large cell neuroendocrine carcinoma (LCNEC). However, various studies have suggested a potential risk of hyperprogressive disease (HPD) in patients receiving ICI, which might be associated with gene alterations. Here, this is the first report on an unknown primary LCNEC patient who had achieved a long-term response from ICI treatment (atezolizumab), but developed HPD after tumor progression due to receiving another ICI agent (serplulimab). The mutation region of FAT4, SMARCA4, CYLD, CTNNB1, and KIT was altered prior to serplulimab treatment compared to before atezolizumab treatment. This case suggested a potential association between these mutated genes and HPD. Patients with the aforementioned genes should caution when selecting ICI treatment. These findings required further confirmation in a larger study cohort.

Introduction: Equine theileriosis, an economically important disease that affects horses and other equids worldwide, is caused by a tick-borne intracellular apicomplexan protozoa Theileria equi. Genotyping of T. equi based on the 18S rRNA gene revealed the presence of two, three, four or five genotypes. In previous published reports, these genotypes have been labelled either alphabetically or numerically, and there is no uniformity in naming of these genotypes. The present study was aimed to revisit the phylogeny, genetic diversity and geographical distribution of T. equi based on the nucleotide sequences of the V4 hypervariable region of the 18S rRNA gene available in the nucleotide databases. Methods: Out of 14792 nucleotide sequences of T. equi available in the GenBank™, only 736 sequences of T. equi containing the complete V4 hypervariable region of the 18S rRNA gene (>207 bp) were used in multiple sequence alignment. Subsequently, a maximum likelihood phylogenetic tree was constructed based on the Kimura 2-parameter model (K2+I). Results: The phylogenetic tree placed all the sequences into four distinct clades with high bootstrap values which were designated as T. equi clades/genotypes A, B, C and D. Our results indicated that the genotype B of Nagore et al. and genotype E of Qablan et al. together formed the clade B with a high bootstrap value (95%). Furthermore, all the genotypes probably originated from clade B, which was the most dominant genotype (52.85%) followed by clades A (27.58%), and C (9.78%) and D (9.78%). Genotype C manifested a comparatively higher genetic diversity (91.0-100% identity) followed by genotypes A (93.2-99.5%), and B and D (95.7-100%). The alignment report of the consensus nucleotide sequences of the V4 hypervariable region of the 18S rRNA gene of four T. equi genotypes (A-D) revealed significant variations in one region, between nucleotide positions 113-183, and 41 molecular signatures were recognized. As far as geographical distribution is concerned, genotypes A and C exhibited far-extending geographical distribution involving 31 and 13 countries of the Asian, African, European, North American and South American continents, respectively. On the contrary, the genotypes B and D exemplified limited distribution with confinement to 21 and 12 countries of Asian, African and European continents, respectively. Interestingly, genotypes A and C have been reported from only two continents, viz., North and South America. It was observed that genotypes A and C, and B and D exhibit similar geographical distribution. Discussion: The present study indicated the presence of only four previously described T. equi genotypes (A, B, C and D) after performing the molecular analyses of all available sequences of the complete V4 hypervariable region of the 18S rRNA gene of T. equi isolates in the GenBank™. [ABSTRACT FROM AUTHOR]

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness. [ABSTRACT FROM AUTHOR]

Mozambique does not have a tradition of farming Coffea arabica or Coffea canephora, the two species that dominate the worldwide coffee market. However, native coffee plants have been growing spontaneously and in some cases cultivated in the Ibo and Quirimba islands in the north of the country and Inhambane province in the south. Historically there has been confusion over the precise taxonomic classification of these indigenous coffee plants, with different botanists identifying the species as C. racemosa, C. zanguebariae or various synonyms of both. The present research aims to clarify the subject and provide new information on these little-described coffee species which may prove valuable as new breeding material for future cultivars, something that is sorely needed to face the present and future challenges of coffee production. Leaf samples were collected from 40 accessions from Ibo Island, Quirimba Island and Inhambane province. The samples were sequenced by whole-genome technology and WGS reads were filtered to identify relevant SNP variants. Diversity among the samples was assessed by PCA, and a phylogenetic tree including several Coffea species was built using additional data available in public databases. Experimental data confirm the presence of C. zanguebariae as the only coffee species present in both Ibo and Quirimba Islands, while it appears that C. racemosa is exclusive to the southern Inhambane province. The present research provides the most detailed analysis so far on the genetic identity of the traditional Mozambican coffee crops. This is the prerequisite for undertaking further scientific studies on these almost unknown coffee species and for starting agronomic development programs for the economic revival of Ibo and Quirimba islands based on coffee cultivation. Furthermore, these species could provide much-needed genetic material for the breeding of new hybrids with the two main commercial coffee species. [ABSTRACT FROM AUTHOR]

In Spain, several local studies have highlighted the likely presence of unknown olive cultivars distinct from the approximately 260 ones previously described in the literature. Furthermore, recent advancements in identification techniques have significantly enhanced in terms of efficacy and precision. This scenario motivated a new nationwide prospecting effort aimed at recovering and characterizing new cultivated germplasm using high-throughput molecular markers. In the present study, the use of 96 ESTSNP markers allowed the identification of a considerable amount of new material (173 new genotypes) coming from areas with low intensification of production in different regions of Spain. As a result, the number of distinct national genotypes documented in the World Olive Germplasm Bank of IFAPA, Cñrdoba (WOGBC-ESP046) increased to 427. Likewise, 65 and 24 new synonymy and homonymy cases were identified, respectively. This rise in the number of different national cultivars allowed to deepen the knowledge about the underlying genetic structure. The great genetic variability of Spanish germplasm was confirmed, and a new hot spot of diversity was identified in the northern regions of La Rioja and Aragon. Analysis of the genetic structure showed a clear separation between the germplasm of southern and northern-northeastern Spain and indicated a significantly higher level of admixture in the latter. Given the expansion of modern olive cultivation with only a few cultivars, this cryptic germplasm is in great danger of disappearing. This underlines the fact that maintaining as many cultivars as possible will increase the genetic variability of the olive gene pool to meet the future challenges of olive cultivation. [ABSTRACT FROM AUTHOR]

Indian cattle breeds are diverse and well adapted to 15 different agro-climatic regions. Assessment of genetic diversity and population structure is highly essential for conservation and utilization of indigenous cattle genetic resources. Genome-wide Single Nucleotide Polymorphism (SNP) information is widely used for genetic characterization among the cattle population. Average heterozygosity was estimated as 0.35 among 11 diverse dairy, dual and draft type Indian cattle breeds, which provided scope for their genetic improvement through selection. Indian indigenous breeds are genetically distinct from exotic dairy cattle breeds, whereas a substantially shorter genetic distance was observed among Indian breeds. This supports the evolutionary theory of Indicine zebu cattle and their divergence from Taurine cattle. Principal component analysis revealed that the draft/dual breeds i.e. Vechur, Kangayam and Ongole are clustered separately from dairy type breeds. Population structure analysis identified the presence of highest level of admixture in Vechur cattle, due to which its population is sizably declining. Genetic characterization is essential to preserve the genomic variability which can further be used for genetic improvement of performance traits in a population. Therefore, this review suggests the genetic characterization of indigenous cattle population for formulating conservation policies in order to prevent our native population from extinction. [ABSTRACT FROM AUTHOR]

Genetic characterization in native livestock is essential to conserve the genetics standard of livestock for pure-breeding programs. This research aimed to characterize four Indonesian cattle breeds using 156 sites of Parentage SNP Markers, includingARS-USMARC-Parent (119 sites) and ARS-USMARC (37 sites). Total of 113 mixed-sex animals were used for the evaluation, including 16 Bali (Bos javanicus), 16 Madura (Bos indicus), 33 Ongole grade (Bos indicus), and 48 Sumba Ongole (Bos indicus) cattle breeds. Results showed Bali, Madura, and Ongole lineage (Ongole grade and Sumba Ongole) cattle can be discriminated against with the Parentage SNP Markers. The pairwise genetic distance analysis revealed that Bali cattle had a closer genetic relationship with Madura cattle (0.043 - 0.151) than Ongole lineage cattle (0.073 - 0.325). However, the phylogenetic tree explained that the Ongole lineage cattle are grouped into two different clades. At the same time, Bali, Madura and Ongole lineage cattle are grouped into their original cluster. The study suggests that the Parentage SNP Markers can be used to characterize Bali, Madura, and Ongole lineage cattle accurately. [ABSTRACT FROM AUTHOR]

The aim of the study was to track the spread of antimicrobial resistance among the different sectors of One Health through the detection of Multidrug-Efflux-System in multidrug-resistant Staphylococcus aureus isolates. Multidrug-resistant (MDR) and methicillin-resistant (MRSA) S. aureus isolates were selected: 25 of human, one of animal and eight of food origin. The efflux system genes norA, norB, norC, LmrS, tet38 and msrA were screened by PCR. The activity of the efflux systems was determined by the minimum inhibitory concentration (MIC) of tetracycline and ciprofloxacin in the presence and absence of CCCP and in the quantification of ethidium bromide efflux. Furthermore, biofilm formation was determined in the presence and absence of the CCCP. The molecular epidemiology of the isolates was traced with the aid of PFGE. The gene norC was the most prevalent, detected in all isolates and msrA was the least prevalent, detected in only two isolates from humans. There was no difference in the MICs of tetracycline and ciprofloxacin in the presence of CCCP, but 55.9% of isolates showed ethidium bromide efflux. The presence of CCCP decreased the biofilm formation. Regarding the molecular epidemiology, in three clusters was a mixture of the isolates from different origins. Therefore, S. aureus MDR with active multidrug efflux systems are circulating between One Health domains and it is necessary to consider strategies to decrease this circulation in order to prevent the dissemination of resistance mediated by MES. [ABSTRACT FROM AUTHOR]

Leptographium wageneri is a native fungal pathogen in western North America that causes black stain root disease (BSRD) of conifers. Three host-specialized varieties of this pathogen were previously described: L. wageneri var. wageneri on pinyon pines (Pinus monophylla and P. edulis); L. wageneri var. ponderosum, primarily on hard pines (e.g., P. ponderosa, P. jeffreyi); and L. wageneri var. pseudotsugae on Douglas-fir (Pseudotsuga menziesii). Morphological, physiological, and ecological differences among the three pathogen varieties have been previously determined; however, DNA-based characterization and analyses are needed to determine the genetic relationships among these varieties. The objective of this study was to use DNA sequences of 10 gene regions to assess phylogenetic relationships among L. wageneri isolates collected from different hosts. The multigene phylogenetic analyses, based on maximum likelihood and Bayesian inference, strongly supported species-level separation of the three L. wageneri varieties. These results, in conjunction with previously established phenotypic differences, support the elevation of L. wageneri var. ponderosum and L. wageneri var. pseudotsugae to the species level as L. ponderosum comb. nov. and L. pseudotsugae comb. nov., respectively, while maintaining L. wageneri var. wageneri as Leptographium wageneri. Characterization of the three Leptographium species, each with distinct host ranges, provides a baseline to further understand the ecological interactions and evolutionary relationships of these forest pathogens, which informs management of black stain root disease. [ABSTRACT FROM AUTHOR]

A variety of illnesses, including arthritis, tenosynovitis, stunted growth, and malabsorption syndrome, are caused by Avian Reoviruses (ARVs), which have become more prevalent in Egypt during recent years and resulted in significant economic losses. This study investigated 27 suspected samples collected from 14 broiler breeders and 13 broilers suffering from immunosuppression, decreased body weight, and diarrhea. Fourteen samples tested positive based on RT-PCR, and the virus could be isolated from ten samples in Specific Pathogen Free (SPF) embryonated chicken eggs. Ten isolates were subjected to molecular and genetic analysis of the S1 gene (sigma C) and S2 gene (sigma A). The amino acid identity of the S1 gene revealed that these viruses are closely related to the viruses that were identified in Israel during 2020 (91.8%-97.2% identity) and belonged to the genetic cluster 5 (genotype 5), which also includes some viruses that are circulating in the United States and Canada. They also showed weak similarity (48.9%-50.2%) with the available vaccine strains in the Egyptian field that belong to cluster 1, genotype 1. The S2 gene showed amino acid homology of 91.7%-98.2% with the current vaccine used in Egypt. However, the Egy-Reo-7-2021 virus had the lowest similarity (84.2%-87.6%) to the available vaccine. It is hypothesized that the difference between field and vaccine strains may have contributed to the failure of current vaccinations to produce protective immunity against current ARV strains circulated in Egypt, which made the disease a problem to the poultry industry. Developing homologous vaccines and evaluating their potency and efficacy are required in Egypt. [ABSTRACT FROM AUTHOR]

Introduction: Since its identification in April 2009, influenza A(H1N1)pdm09 virus has continued to cause significant outbreaks of respiratory tract infections, including pandemics in humans. In the course of its evolution, the virus has acquired many mutations that cause increased disease severity. Regular molecular surveillance of the virus is essential to mark the evolutionary changes that may cause a shift in viral behavior. Methods: Twenty-five (H1N1)pdm09 isolates from Huzhou, China, in 2023 were randomly selected for whole-genome sequencing along with analysis of nucleotide and amino acid sequence identity, average genetic distance, antigen variation sites, receptor binding sites, pathogenicity, potential glycosylation sites, and drug resistance gene sites. Results: The 25 (H1N1)pdm09 strains and representative 2023–2024 northern hemisphere vaccine strain A/Wisconsin/67/2022 showed nucleotide and amino acid similarity of 98.41 %–99.22 % and 98.41 %–99.36 %, respectively. This virus belongs to the 6B1A.5a.2a evolutionary lineage. There were 19 amino acid variations in hemagglutinin (HA) protein. Substitutions S137P and R142K occurred in the epitope Ca2 cluster. A total of 13 amino acids were mutated in neuraminidase (NA) protein, and 9 key protease active sites and amino acid sites related to NA inhibitor (NAI) resistance were not mutated. Five amino acid sites of matrix-2 (M2) protein associated with drug resistance were not replaced, but amino acid 31 of M2 protein was shown to be N in the 2023 pandemic strain (H1N1)pdm09 and vaccine strain A/Wisconsin/67/2022. There were seven and eight potential glycosylation sites for HA protein and NA protein, respectively. Compared with the vaccine strains, there were no new or missing potential glycosylation sites in the 25 (H1N1)pdm09 influenza virus isolates. No multiple continuous alkaline amino acids were found in the HA cleavage site of the 25 isolates. Conclusions: The recommended vaccine strain A/Wisconsin/67/2022 has good prevention potential against the current circulating influenza (H1N1)pdm09. At present, NAIs have good therapeutic and preventive effects against (H1N1)pdm09 circulating in Huzhou, China, but the virus is naturally resistant to amantadines. At present, the (H1N1)pdm09 strain circulating in Huzhou, China, is characterized by low pathogenicity. However, regular molecular surveillance of (H1N1)pdm09 is important to monitor the behavior of the virus in terms of increases in virulence, drug resistance, and emergence of novel strains.

A morphological and genetic characterization of autochthonous ‘Saragolla’ wheats, currently cultivated in Abruzzo Region (Italy), was carried out. Using 15 simple sequence repeat (SSR) markers and 24 UPOV morphological traits we compared: (a) 13 ‘Saragolla’ genotypes with traits of the italicum/apulicum botanical varieties (Saragolla (Sar.) italicum), (b) 26 ‘Saragolla’ genotypes with traits of leucurum/affine botanical varieties (Sar. leucurum), (c) 8 breeding varieties (pure lines), and (d) 5 Italian autochthonous wheats and 1 turanicum line (old wheats). One hundred twenty-six (126) alleles were identified. The number of alleles per locus spanned from 4 to 15 and the number of alleles per genotype varied between 12 and 21. Values of gene diversity (Nei) across the 53 genotypes was 0.17. The groups of Sar. leucurum and Sar. italicum genotypes were morphologically distinguishable from the groups of old wheats and pure lines. Likewise, the analysis of molecular data using the discriminant analysis revealed that genotypes with the Sar. italicum phenotype displayed distinct genetic differences from Sar. leucurum, pure lines and old wheats. These results make Sar. italicum genotypes distinguishable and eligible as a conservation variety. Ward's clustering analysis of the 53-genotype pool showed that the ‘Saragolla’ landrace is a valuable repository of genetic diversity.

The investigation of genetic differentiation of subspecies and breeds is nowadays fundamental for understanding their adaptation to specific environments and for facilitating selection processes for production purposes. These aspects allow us both to safeguard their biodiversity and to protect the products with a high nutritional value that derive from them and to which consumers today pay particular importance.In this study, a genomic approach by RAPD-PCR and DNA-barcoding was used to identify possible genetic markers to discriminate Italian Mediterranean Buffalo (IMB) and Romanian Buffalo (RB). The two molecular tools have been widely used in this study not only to clarify genetic differences between breeds but also to avoid food frauds, given the great importance of Italian buffalo mozzarella recognized all over the world and protected by Denomination of Protected Origin (DPO).The research did not reveal any difference between the two breeds, despite belonging to two geographically different areas.

Background and Aim: Newcastle disease (ND) is a major viral disease of poultry worldwide. However, data on the molecular characterization of Newcastle disease virus (NDV) in Vietnam are limited. This study aimed to identify the molecular characteristics of NDV strains from the vaccinated chickens farmed in Northern Vietnam. Materials and Methods: We used reverse-transcription polymerase chain reaction (PCR), sequencing and phylogenetic analysis to characterize NDV strains from vaccinated chicken farms in Northern Vietnam. Results: Seven out of 72 (9.7%) chicken tissue samples collected from seven chicken farms in the four cities/provinces in northern Vietnam were positive for the NDV genome by PCR method. The complete sequences of the fusion (F) and hemagglutinin-neuraminidase (HN) genes of NDVs isolated in the North of Vietnam from 2021 to 2022 were further evaluated. The results indicated that all seven Vietnamese isolates obtained were reported as virulent NDV strains with the amino acid (AA) sequence of the F0 protein proteolytic cleavage site motif (112RRRKRF117). Phylogenetic analysis revealed that they were grouped with other NDV class II from subgenotype VII.2, including the two previous Vietnamese NDV (2015), the Chinese (2017), and Southern African (2013) NDV strains. In addition, some AA substitutions were observed in the neutralizing epitopes of the F and HN proteins of the current Vietnamese NDV strains. Conclusion: The present findings provide useful information for future studies of the evolution of NDVs and improve strategies for ND-controlling programs in Vietnam.

Newcastle disease (ND) is caused by virulent strains of avian paramyxovirus type 1, also known as Newcastle disease virus (NDV). Despite vaccination, the frequency of reported outbreaks in Ethiopia has increased. From January to June 2022, an active outbreak investigation was conducted in six commercial chicken farms across areas of central Ethiopia to identify the circulating NDV strains. Thirty pooled tissue specimens were collected from chickens suspected of being infected with NDV. A questionnaire survey of farm owners and veterinarians was also carried out to collect information on the farms and the outbreak status. NDV was isolated using specific-pathogen-free (SPF)-embryonated chicken eggs and detected using haemagglutination and the reverse transcriptase–polymerase chain reaction (RT–PCR). The genotype and virulence of field NDV isolates were determined using phylogenetic analysis of fusion (F) protein gene sequences and the mean death time (MDT) test in SPF-embryonated chicken eggs. The questionnaire results revealed that ND caused morbidity (23.1%), mortality (16.3%), case fatality (70.8%), and significant economic losses. Eleven of thirty tissue specimens tested positive for NDV using haemagglutination and RT–PCR. The MDT testing and sequence analysis revealed the presence of virulent NDV classified as genotype VII of class II velogenic pathotype and distinct from locally used vaccine strains (genotype II). The amino acid sequences of the current virulent NDV fusion protein cleavage site motif revealed 112RRQKR↓F117, unlike the locally used avirulent vaccine strains (112GRQGR↓L117). The epidemiological data, MDT results, cleavage site sequence, and phylogenetic analysis all indicated that the present NDV isolates were virulent. The four NDV sequences were deposited in GenBank with accession numbers F gene (PP726912-15) and M gene (PP726916-19). The genetic difference between avirulent vaccine strains and circulating virulent NDV could explain the low level of protection provided by locally used vaccines. Further studies are needed to better understand the circulating NDV genotypes in different production systems.

Porcine parvovirus 7 (PPV7) was first discovered in swine in 2016, and PPV7 infection has been detected in aborted pig fetuses and in sows that experienced reproductive failure. The objective of this study was to report the prevalence and genetic characterization of PPV7 in Hunan, China. Seventy of the four hundred and twenty-two (16.6%) serum, semen, and tissue samples collected from pigs were positive for PPV7. One complete PPV7 strain and eighteen complete cap gene sequences were obtained; nucleotide and amino acid identity among the nineteen Cap sequences were 88.1–99.4% and 88.1–100%, respectively. They shared identity with previously discovered sequences ranging from 86.6 to 98.9% and 83.7 to 99.8% at the nucleotide- and amino acid-level, respectively. The phylogenetic tree analysis exhibited that PPV7 strains had two major groups based on the presence or absence of five amino acid (181–185) insertions on the Cap protein. Analysis of the Cap protein demonstrated that PPV7 Cap had significant variability, implying that PPV7 evolved at high substitution rates. Substantial variations of that PPV7 Cap may enable the emergence of newly mutated capsid profiles due to its viral adaptation to host responses. Furthermore, antigenic alteration owing to PPV7 Cap protein amino acid mutations at immune epitopes may enable viruses to escape from the host’s immune system. This study determined the prevalence and genetic characteristics of PPV7 circulating in swine in Hunan, China, and provided the impetus and basis to further investigate the pathogenicity and epidemiology of PPV7.

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes.

Molecular biological methods have emerged as inevitable tools to accompany the process of cell line development for the generation of stable and highly productive manufacturing cell lines in the biopharmaceutical industry. PCR-based methods are especially useful for screening and characterization of cell lines due to their low cost, scalability, precision and propensity for multidimensional read-outs. In this study, the diverse applications of droplet digital PCR (ddPCR) as a molecular biological tool for cell line development are demonstrated. Specifically, it is shown that ddPCR can be used to enable precise, sensitive and reproducible absolute quantification of genomically integrated transgene copies during cell line development and cell bank characterization. Additionally, an amplitude multiplexing approach is applied to simultaneously run multiple assays on different genetic targets in a single reaction and advance clonal screening by measuring gene expression profiles to predict the assembly and homogeneity of difficult-to-express (DTE) proteins. The implementation of ddPCR-based assays during cell line development allows for early screening at a transcriptional level, particularly for complex, multidomain proteins, where balanced polypeptide chain ratios are of primary importance. Moreover, it is demonstrated that ddPCR-based genomic characterization improves the robustness, efficiency and comparability of absolute transgene copy number quantification, an essential genetic parameter that must be demonstrated to regulatory authorities during clinical trial and market authorization application submissions to support genetic stability and consistency of the selected cell substrate. • Gene expression analysis by ddPCR can predict the assembly of bispecific antibodies. • Amplitude-multiplexing allows for a simultaneous quantification of several genes. • Precise and sensitive absolute quantification of transgene copy numbers. • High correlation between RNA sequencing, ddPCR and capillary gel electrophoresis. [ABSTRACT FROM AUTHOR]

Zavot cattle is one of Türkiye's native cattle breeds raised in the provinces of Kars and Ardahan in the Northeast Anatolian region. The Zavot cattle breed has emerged as a crossbreed of Simmental, Brown Swiss, and Eastern Anatolian Red cattle breeds. However, there is not enough information about which of the breeds that contribute to the genetic formation of today's Zavot cattle is closer genetically. In this study, Zavot, East Anatolian Red, Simmental and Brown Swiss cattle were genotyped in term of STAT5A-AvaI, GH-AluI, PRL-RsaI, TLR1-Bs1I and TLR4-BstUI polymorphisms. In the study, 70 cattle of each breed were genotyped. At the end of the genotyping process, it was determined that the Zavot breed was genetically closer to the Eastern Anatolian Red cattle breed. On the other hand, it has been concluded that SNP markers, which are known to be polymorphic, can be used in studies investigating the genetic relationships between breeds. [ABSTRACT FROM AUTHOR]

The investigation of genetic differentiation of subspecies and breeds is nowadays fundamental for understanding their adaptation to specific environments and for facilitating selection processes for production purposes. These aspects allow us both to safeguard their biodiversity and to protect the products with a high nutritional value that derive from them and to which consumers today pay particular importance. In this study, a genomic approach by RAPD-PCR and DNA-barcoding was used to identify possible genetic markers to discriminate Italian Mediterranean Buffalo (IMB) and Romanian Buffalo (RB). The two molecular tools have been widely used in this study not only to clarify genetic differences between breeds but also to avoid food frauds, given the great importance of Italian buffalo mozzarella recognized all over the world and protected by Denomination of Protected Origin (DPO). The research did not reveal any difference between the two breeds, despite belonging to two geographically different areas. [ABSTRACT FROM AUTHOR]

The Gobra zebu genetic breeding program has resulted in the genetic improvement of a new population. This population gained genetic characteristics that set them apart from the other cattle populations reared in Senegal. The cause of these differences might be the reproductive isolation and selection to which this population of the “Centre de Recherches Zootechniques” of Dahra has been subjected since the 1950s. This study aimed to assess the genetic differentiation and structuration of this population compared to the main cattle breeds used in Senegal. A total of 180 individuals, selected from the Gobra selection nucleus and bovine populations from four main breeds in Senegal, were included in this study. We used a panel of 21 microsatellite markers among those recommended by the Food Agriculture Organization, to conduct the molecular genotyping of our sampled populations. The basic genetic parameters of differentiation and structuration were calculated using various bioinformatics software. The results of this study, particularly the degrees of genetic differentiation (Fst), the coefficient of genetic homogeneity (Gst), and the gene flow (Nm), show a significant genetic differentiation of the Gobra from the station compared to the other populations studied. Structuring and phylogeny analyses reveal a micro-structuring within the Gobra population as a novelty. This micro-structuring clearly identifies the Gobra individuals from Dahra’s station among the other Gobra populations studied. The main causes of these observations would be reproductive isolation and the selection pressure exerted on this population for several decades. [ABSTRACT FROM AUTHOR]

Background: Chicken infectious anemia (CIA) caused by the CIA virus (CIAV) is considered one of the most important immunosuppressive diseases affecting chickens and recently poses a great economic burden to the poultry industry worldwide. Aim: This study aims to identify the presence of CIAV in the Mekong Delta (MD), Vietnam, and to determine genotypes of CIAVs that are currently circulating in this area. Methods: Organ samples (spleen, liver, and thymus) of 144 chickens suspected with CIA from 47 poultry farms were collected. A total of 47 pooled samples, each containing 2-4 chickens from each farm, were tested for the presence of CIAV. Results: Twenty out of 47 pooled organ samples (pool of 2-4 chickens per farm) were positive for CIAV using polymerase chain reaction targeting the viral VP1 gene. The VP1 amplicons of eight representative CIAVs were subjected to sequencing and genetic characterization. Phylogenetic analysis based on partial VP1 gene sequence revealed that the CIAVs detected in the MD grouped into different genotypes of II, IIIa, and IIIc together with CIAVs previously detected in the northern Vietnam and other Asian countries. The phylogenetic analysis also confirmed that detected CIAVs genetically differed from vaccine strains. In addition, deduced amino acids of the VP1 identified several critical amino acid substitutions in the VP1 protein that are likely associated with the virulence of CIAV. Conclusion: This is the first report to detect and determine the genetic characterization of the circulating CIAVs in the MD. Therefore, this study provides an important understanding of the evolution of CIAVs and highlights the importance of implementing prompt control measures against CIAVs in the MD and Vietnam. [ABSTRACT FROM AUTHOR]