Partial Gene Sequences Research Articles (Page 1)

Bats are associated with some of the most significant and virulent emerging zoonoses globally, yet research and surveillance of bat pathogens remains limited across parts of the world. We surveyed the prevalence and genetic diversity of coronaviruses from bats in Taita Hills, southeastern Kenya, as part of ongoing surveillance efforts in this remote part of eastern Africa. We collected fecal and intestinal samples in May 2018 and March 2019 from 16 bat species. We detected one genus of coronavirus (alphacoronavirus), with an overall RNA prevalence of 6.5% (30/463). The prevalence of coronavirus RNA was 3.8% (9/235) and 11.6% (21/181) for the two most captured free-tailed bat species, Mops condylurus and M. pumilus respectively, with no detections from other bat species (0/90). Phylogenetic analyses based on the partial RNA-dependent RNA polymerase gene and whole genome sequences revealed that the sequences clustered together and were closely related to alphacoronavirus detected in free tailed bats in Eswatini, Nigeria and Rhinolophus simulator bats in South Africa. The sequences were more distantly related to alphacoronavirus isolated from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. These findings highlight coronavirus transmission among bats that share habitats with humans and livestock, posing a potential risk of exposure. Future research should investigate whether coronaviruses detected in these bats have the potential to spillover to other hosts.

Apis spp. are crucial pollinators that support biodiversity, agriculture, and global food production. Proper identification, understanding genetic diversity, and molecular characteristics of honey bee populations are vital for conservation and sustainable beekeeping practices. This study focuses on the DNA barcoding based on partial mt-COI gene sequences of different Apis species in Bangladesh. Samples were collected from various locations across Bangladesh, followed by DNA extraction, polymerase chain reaction (PCR) amplification, and sequencing. By comparing the unique nucleotide sequences of the COI gene to the reference GenBank database, four honey bee species (Apis dorsata, A. cerana, A. florea, and A. mellifera) were identified. Different castes (queen, worker, and drone) of A. mellifera were also sequenced and identified. Over 82% sequence similarity was observed among different species, with nearly 100% commonality within the A. mellifera castes. The mitochondrial A+T content (74%) exceeded G+C (26%). Genetic distance analysis (Kimura's 2-parameter) indicated minimal divergence between A. dorsata and A. cerana (0.120). Phylogenetic analysis revealed significant genetic variations among different Apis species. A. florea showed the highest mutation rate (40 steps) from its immediate common ancestor. This study enhances the genotypic and phenotypic identification of honey bee species, including A. mellifera castes, in Bangladesh. Bangladesh J. Zool. 53(2): 137-148, 2025

ABSTRACT This paper describes the investigation of the epidemiology of fowl adenoviruses (FAdVs) among fast-growing meat-type breeder parent chickens in Sweden, based on serology, PCR and partial genome sequencing of samples collected during rearing and egg production. Blood samples (n = 1910) from breeder flocks at 16 (79 flocks), 24 and 36 (52 flocks) weeks of age were analysed for FAdV antibodies. Ninety-four percent of the flocks had seroconverted at 16 weeks of age, and at 36 weeks of age all 52 flocks were seropositive. From 35 of these flocks, dead-in-shell chicks (DIS, n = 949) from eggs laid at 26–27 and 36–37 weeks of age were sampled, and pooled liver and caecal tonsils were analysed by PCR. Nucleic acid from FAdV was not detected. Negative PCR results were confirmed by testing tissues from 62 broiler breeders and 80 DIS from four additional seropositive flocks, collected at age 24–26 weeks. From six other breeder flocks, liver and caecal tonsils were sampled from one bird (when available) per day during rearing from 1–112 days of age. From 6 weeks of age, in 4/6 flocks, FAdV species A and/or D were detected by PCR and partial hexon gene sequencing. In conclusion, FAdVs were detected during rearing in breeder birds but not in DIS. This suggests that vertical transmission of FAdVs was prevented by immunity acquired early in life. However, it should be noted that high antibody titres in breeder birds does not necessarily confer protection against vertical transmission. RESEARCH HIGHLIGHTS The majority of 16-week-old parent flocks were seropositive to FAdV. FAdV was not detected by PCR in dead-in-shell chicks from seroconverted flocks. FAdV-A and D were detected in broiler breeders during rearing from 6 weeks of age. Results suggest that vertical spread was prevented by immunity in breeder birds.

Garra gotyla is a benthopelagic freshwater cyprinid fish native to Asia, valued for both food and ornamental purposes; nevertheless, its parasitic diseases are poorly understood. The present study investigated the presence and ecological indices (prevalence and intensity) of monogenean parasites infecting G. gotyla in Mizoram, northeast India. Additionally, the study aimed to assess the phylogenetic relationships among three closely related dactylogyrid genera: Dactylogyrus, Dogielius, and Dactylogyroides. Monogeneans were initially identified based on the comparative morphology of their sclerotised haptoral and reproductive structures, followed by BLASTn comparisons of their partial 28S rRNA gene sequences. Two dactylogyrid species, Dactylogyrus labro sp. n. and Dogielius salpinx sp. n., were recovered and are described herein as new to science. Dactylogyrus labro was found to infect all examined fish, whereas D. salpinx had a slightly lower prevalence, ranging from 76.5% to 83.3% across different sampling sites. The phylogenetic insights from these species presented in this study highlight the complex evolutionary relationships within these three genera. Further, this study provides the first confirmed molecular data for a Dogielius species, allowing for much-needed phylogenetic studies on the genus and filling a gap in sequencing data for Indian monogeneans. Since all monogeneans are potentially hazardous parasites, more studies are needed to map their diversity and effects on host fishes in this region.

Abstract Background Mineral-dissolving rhizobacteria are considered ecological friendly rhizonutrifying agents capable of promoting rhizospheric enzymatic activities, microbial biomass, and nutrient availability even under nutrient-deficient alkaline soil conditions. However, comprehensive studies on their effectiveness in calcareous soil are lacking. The current study hypothesized that beneficial rhizobacteria improve soil biochemical properties in calcareous soil through their impact on enzymatic activities, microbial biomass, and nutrient availability in the rhizosphere. Methods Rhizobacterial strains were isolated from wheat rhizosphere and characterized in vitro for their mineral solubilization potential, production of beneficial metabolites, and various enzymatic activities. A pot experiment was conducted to investigate the effect of sole and co-inoculation treatments on wheat growth, grain attributes, nutrient availability in soil and absorption in plants, soil enzymatic activities, and microbial biomass accumulation in wheat rhizosphere under calcareous soil conditions. Results The most effective mineral-dissolving rhizobacteria were identified as Bacillus altitudinis (strains SAM1, SAM7, SAM13, and SAM15) and Bacillus cereus (strain SAM9) through 16S rRNA partial gene sequencing. These strains demonstrated the dissolution of insoluble tricalcium phosphate, mica, zinc oxide, and manganese oxide, and promoted nutrient availability in the soil by producing organic acids. Inoculation enhanced wheat growth and grain development by promoting nutrient acquisition and stimulating rhizospheric microbial activity. Both sole and co-inoculation with rhizobacterial strains significantly increased soil enzymatic activities, microbial biomass carbon, nitrogen, and phosphorus, and nutrient availability in the wheat rhizosphere through organic matter decomposition. Among treatments, sole inoculation with B. cereus SAM9 and co-inoculation with B. cereus SAM9 + B. altitudinis SAM13 demonstrated the most dominant increase in wheat growth and grain attributes, nutrient availability in soil and absorption in plants, deposition of microbial biomass, and soil enzymatic activities. Conclusions The sole inoculation with B. cereus SAM9 and co-inoculation with B. cereus SAM9 + B. altitudinis SAM13 showed strong potential as bioinoculants for calcareous soils. These strains could be effectively integrated into commercial biofertilizer formulation as sustainable alternatives or supplements to chemical fertilizers, enhancing soil productivity and crop performance. Graphical Abstract

In May 2023, fruit rot lesions were observed in 'Honeycrisp' apple (Malus domestica), fruit in commercial storage conditions in Nova Scotia, Canada. Rot lesions were observed on 10% of the fruits from some orchards and were brown, soft, and of irregular shape. To isolate causal pathogens, symptomatic apples were surface-sterilized in 70 % ethanol for 2 min and 1% NaOCl for 3 min, and then rinsed three times with sterilized water. A sterile scalpel was used to cut 5 mm x 5mm pieces from the margin between diseased and healthy tissue which were then plated on potato dextrose agar (PDA; Difco) amended with Novobiocin (100 mg/l) and incubated at 22℃ under light for 3-4 days. Two fungal colonies that consistently grew on PDA plates were hyphal-tip transferred to fresh PDA plates. Colonies were pale yellow to golden in color, becoming lighter at the margins, and produced cottony aerial mycelium after 7 days on PDA in the dark at 22℃. Microconidia were ovoid to fusiform with 0-1 septa (mean length 12 ± 1.8 μm, mean width 3.8 ±0.6 μm, n=50). Macroconidia were slightly curved, with 3-5 transverse septa (mean length 26 ± 4.9 μm, mean width 5.1 ±0.92 μm, n=50). Based on morphological characteristics, the two isolates resemble F. avenaceum (Fr.) Sacc., as described by Booth (1971) in Descriptions of Fungi and Bacteria (C. Booth, Ed.). To identify the species of Fusarium, genomic DNA from two isolates was subjected to PCR amplification and sequencing of TEF1α region (O’Donnell et al. 1998), ITS region (de Hoog and Van den End 1998; Masclaux et al. 1995), and RPB2 region (O’Donnell et al. 2022). The sequences were deposited in GenBank (TEF1α: accession numbers, PP549540 and PP549541, ITS: accession numbers, PP496676 and PP496677 and RPB2: accession numbers, PP525085 and PP525086) for isolate 187-1A and 898-2B respectively. BLASTn analyses of TEF-1-α partial gene sequences established both isolates’ identity as F. avenaceum with 100 % identity and 97% query coverage to isolate (Accession number KM189442). RPB2 sequences were 99.8 % identical with 100% query coverage to F. avenaceum isolate (Accession number MFG80214). To further confirm the identification of the causal pathogen, 1000 bootstrap searches were performed to obtain the best-scoring Maximum Likelihood (ML) tree. The phylogenetic tree was rooted to F. lateritium. Phylogenetic analysis of concatenated sequences of ITS, RPB2, and TEF-1-α confirmed that the isolates were F. avenaceum. Koch’s postulates were tested using pathogenicity assay, five 'Honeycrisp ' apple fruit were wounded/not wounded on the skin and inoculated with a 6 mm PDA disc containing mycelium from the margin of 7 days old F. avenaceum colonies, and five fruit were inoculated with sterile PDA disc and five with non- apple pathogenic F. avenaceum isolate. Fruit were stored in trays lined with sterile paper towels moistend with sterile water, covered with domed lids to maintain high humidity, and incubated in the dark at 22℃ . Rot lesions were observed after 7 days, non-pathogenic isolate did not produce any symptoms up to three weeks post-inoculation. Lesions with a mean diameter of 14.7±2.86 mm were observed on F. avenaceum inoculated fruit, while no lesions were observed on fruit inoculated with sterile PDA or with non- apple pathogenic F. avenaceum isolate. This experiment was repeated twice with similar results. F. avenaceum was successfully reisolated from the lesion of an inoculated apple both times and confirmed by sequencing of the RPB2 and TEF1α regions. In another assay unwounded apples fruits were placed in contact with inoculated apples. Symptoms appeared on the unwounded fruits approximately four weeks later, confirming that lesion development is delayed without wounding. F. avenaceum has been identified as a rot pathogen affecting apple fruit during postharvest storage in the United States, Croatia, and Morocco (Khadiri et al. 2024; Sever et al. 2012). This could become a serious problem for Canada’s apple industry during storage, therefore further studies are required to understand the epidemiology of the disease and recommend a phytosanitary program for its control. This report will help to better understand F. avenaceum causing apple fruit rot during post harvest storage in Canada.

Mycoplasma aquilae sp. nov., Mycoplasma paraquilae sp. nov., Mycoplasma haliaeeti sp. nov., Mycoplasma milvi sp. nov., and Mycoplasma razini sp. nov., isolated from predatory birds of the Accipitridae family.

IntroductionFeline coronavirus (FCoV) is a widespread viral infection affecting domestic and wild cats globally, with higher prevalence in young cats and multi-cat environments.MethodsIn this study, a total of 208 clinical samples (blood, fecal, ascitic fluid, pleural fluid, tissue) were collected between January 2018 and January 2020 from diseased cats. Clinical and demographic data were recorded, and hematobiochemical and molecular detection analyses were performed.ResultsA total of 189 blood samples (90.9%) were found seropositive for FCoV, while 79 fecal samples (38%) were found positive for FCoV RNA by real-time RT-qPCR. No significant association was found between FCoV-RNA positivity and age or gender, while a significant association was found with crossbreed cats (p < 0.05). Notable clinical signs included weight loss (47%), dullness (44%), respiratory distress (16%), vomiting (13%), ascites (13%), epileptic fits (13%), diarrhea (6%), and fever (5%). Fever, depression, diarrhea, and ascites were significantly more common in PCR-positive cats than in PCR-negative cats (p < 0.05). The relationship between FCoV-RNA positivity and hematobiochemical indices was variable. Elevated monocyte and neutrophil levels were observed in 51 and 29% of cases, respectively. Additionally, elevated ALT activity and bilirubinemia were detected in 19 and 28% of cats, respectively. Partial S gene nucleotide analysis showed a deletion of multiple nucleotides in all sequences obtained in the present study. Interestingly, these deletions were absent in all reference strains belonging to FCoV type 2. Among 68 FCoV strains, 42 formed a separate cluster with the reference strain (AY307020) during phylogenetic analysis. This cluster was further divided into several small sub-clusters. Several unique recombinant events and recombination signals were observed among partial S1 gene sequences. Notable histopathological findings included fibrinous serositis and pyogranulomatous inflammation in vital organs.DiscussionThis study provides comprehensive information on FCoV infections among cats in Turkey. The findings could significantly contribute to understanding the hematobiochemical manifestations, epidemiology, and risk factors associated with FCoV, ultimately aiding in the development of better prevention and treatment strategies. A continuous molecular surveillance program is required to understand the evolution and emergence of virulent strains of FCoV to design new antiviral therapies and vaccines.

The microparasite species Hoferellus matosi sp. nov. was found parasitizing the urinary bladder of the fish species Ageneiosus ucayalensis collected from the Coaracy Nunes hydroelectric reservoir in Ferreira Gomes, Amap, Brazil. Plasmodia and myxospores were identified in fragments of the urinary bladder and characterized through microscopic and molecular analyses. Myxospores were subspherical in sutural view, with fine striations or projections on the posterior portion of the valves, measuring an average length and width of 8.5 (8.28.8) m and 7.9 (7.68.2) m, respectively. Each spore contained two ovoid polar capsules of equal size, with an average length and a width of 3.4 (3.23.6) m and 3.1 (2.93.3) m, respectively. Comparing a partial sequence (1,153base pairs) of the small subunit ribosomal DNA gene revealed that H. matosi sp. nov. is clearly distinct from other Hoferellus species deposited in the GenBank, as confirmed through a phylogenetic analysis using Bayesian inference. A morphometric analysis also supported this distinction. Therefore, H. matosi sp. nov. is a newly identified myxosporean species that clusters with H. azevedoi, H. tartarugualis, and H. jutubensis in the phylogenetic tree, forming a distinct lineage of Amazonian Hoferellus.

Molecular and morphological characterization of Rhabdias luzonensis n. sp. (Nematoda: Rhabdiasidae) from Sanguirana luzonensis (Boulenger, 1896) (Amphibia: Ranidae) from Luzon Island, Philippines.

Detection of alphacoronaviruses in Rhinolophus ferrumequinum in Ehime, Japan.

Hemibagrus punctatus (Jerdon, 1849) is endemic to the Western Ghats and native to the Cauvery River system. The species faces distributional uncertainty due to misidentifications and the lack of voucher specimens. This study confirms the range extension of H. punctatus from the Cauvery River tributary, Bhavani River to the Bharathappuzha River in Kerala. Samples were collected from both rivers, with larger number of samples collected from the Bhavani River (n=230). The analysis revealed subtle morphometric variations between the two populations in head length (21.2-27.3% vs 24.7-26.4% in SL), dorsal to adipose distance (16.5-21.2% vs 13.7-16.5% in SL) and eye diameter (12.6-17.8% vs 10.3-16.9% in HL). Species confirmation was done using the mitochondrial DNA (mtDNA) Cytochrome Oxidase I (COI) gene sequencing, and taxonomic position was compared with known Hemibagrus species. Genetic analysis revealed that Hemibagrus punctatus differs from its sister taxon H. menoda with a divergence of 4.4% and other Hemibagrus species with 12.5-19.8% in partial mitochondrial COI gene sequences. Keywords: Bharathappuzha, Critically Endangered, Hemibagrus punctatus, Molecular confirmation, New range

Meta-analysis of genetic diversity of VP1 gene of foot and mouth disease virus serotypes prevalent in Bangladesh from 2010 to 2024.

Porcine reproductive and respiratory syndrome virus (PRRSV) infection causes significant economic losses in swine production. In May 2021 and March 2023, we detected PRRSV genes in serum samples from two weaned pigs with respiratory disorders on a farm in Japan. Partial gene sequences of these strains closely resembled those of a PRRS vaccine strain. We subsequently isolated two PRRSV field strains, KU-IG21-1 and KU-IG23-1, from the 2021 and 2023 samples, respectively. The KU-IG21-1 strain exhibited more pronounced cytopathic effects and significantly higher replication efficiency in cultured cells compared to both the vaccine and KU-IG23-1 strains. Despite these phenotypic differences, complete genome sequencing revealed high genetic similarity between the field isolates and the vaccine strain, with only 16 and 24 amino acid differences in the KU-IG21-1 and KU-IG23-1 strains, respectively. These findings suggest that the field strains likely emerged through the accumulation of point mutations in the vaccine strain rather than through homologous recombination. Furthermore, we identified three amino acid substitutions that may contribute to the enhanced replication of the KU-IG21-1 strain. This study underscores the potential impact of point mutations on PRRSV phenotypes and provides new insights into the complex evolutionary dynamics of PRRSV.

A new species of leucothoid amphipod, Leucothoe limidicola sp. nov. was collected from the mantle cavity and tentacles of the file clam, Limaria hirasei (Limidae). Commensalism associated with bivalves has been relatively rare in the genus Leucothoe and the present new species represents the sixth species of bivalve-associated commensal in the genus. According to the molecular phylogenetic analyses based on the partial sequence of the 18S gene, this new species was recovered as sister to Leucothoe akaisen. There were ~1.5% and ~9.4% differences between these two species in the 18S and COI sequences, respectively, and seven species-specific indels in the former. Morphologically, the new species can be distinguished from Le. akaisen by the distally dentate lateral surface of male gnathopod 2 carpus and straight or weakly concave, oblique posterodistal margin of pereopods 6, 7 bases.

Platnickina mneon (Bsenberg & Strand, 1906) is a theridiid species originally described based on a female specimen collected in Saga Prefecture, Kyushu, Japan. Although P. mneon was recently considered a junior synonym of Yunohamella lyrica (Walckenaer, 1841), the two species can be clearly distinguished by body coloration and markings, genital morphology, and molecular data. Based on these findings, we reestablish P. mneon as a valid species under the genus Yunohamella, Yunohamella mneon stat. rev. Based on a partial mitochondrial COI gene sequence analysis, our study also revealed that the female of Y. mneon stat. rev. is conspecific to the male currently associated with Yunohamella varietas Lee & Kim, 2021 and we propose Y. mneon stat. rev. = Y. varietas syn. nov. The species is compared with Y. lyrica and Platnickina adamsoni Berland, 1934 and molecular data of Yunohamella species in East Asia are presented, with a summary of the taxonomic history of relevant species in Japan and Korea.

Screening of yeasts in the oral microbiota of bats (Chiroptera) in Piauí, Brazil

The emergence of beta-lactamase producing multidrug-resistant (MDR) gram-negative bacteria presents a significant challenge to effective treatment of infections. This study focuses on the isolation, amplification, and molecular characterization of β-lactamase genes from clinical strains of Escherichia coli and Klebsiella pneumoniae. Seven new partial gene sequences, including novel variants of blaOXA and blaNDM, were identified after screening 108 clinical samples and submitted to NCBI GenBank. In silico analysis revealed considerable diversity and distribution of these resistance genes among different strains of bacteria. Gene structure predictions using GENSCAN showed that blaOXA genes typically contain single exons with moderate GC content, whereas blaNDM genes feature longer exons with higher GC content. Multiple sequence alignment showed that NDM and OXA β-lactamases were highly similar, with only slight differences in a few amino acids. The study also analyzed the physico-chemical properties, functional domains, and phosphorylation patterns of the β-lactamase proteins. Secondary structure prediction indicated a dominance of beta sheets, contributing to protein stability, while tertiary modeling provided insights into their 3D structure. Overall, these findings provide critical insights into the genetic diversity and potential mechanisms of β-lactamase-mediated resistance, offering valuable information for the development of novel therapeutic strategies and surveillance programs.

First description of Hepatozoon canis in raccoon dog (Nyctereutes procyonoides)

Marphysa fujianensis sp. nov., a new species collected from coastal waters of Fujian Province, China, was described based on both morphological and molecular analyses. The new species belongs to Group B of the Marphysa sanguinea complex, and it is characterized by having a deeply bilobed prostomium, bearing three types of pectinate chaetae (i.e., IS1, AN1, and AN2), 12 neuroaciculae, and only unidentate subacicular hooks. The partial COI gene sequences of the new species exhibit 4.00%28.14% divergence from those of other sequenced Marphysa species in public databases. An updated key to Group B Marphysa species from East Asian waters is provided.