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Thecal plate morphology, molecular phylogeny, and toxin analyses reveal two novel species of Alexandrium (Dinophyceae) and their potential for toxin production

Abdullah N, Teng ST, Hanifah AH, Law IK, Tan TH, Krock B, et al.

Harmful Algae, 2023 Aug;127:102475.
PMID: 37544675 DOI: 10.1016/j.hal.2023.102475

This study describes two novel species of marine dinophytes in the genus Alexandrium. Morphological characteristics and phylogenetic analyses support the placement of the new taxa, herein designated as Alexandrium limii sp. nov. and A. ogatae sp. nov. Alexandrium limii, a species closely related to A. taylorii, is distinguished by having a shorter 2'/4' suture length, narrower plates 1' and 6'', with larger length: width ratios, and by the position of the ventral pore (Vp). Alexandrium ogatae is distinguishable with its metasert plate 1' having almost parallel lateral margins, and by lacking a Vp. Production of paralytic shellfish toxins (PSTs), cycloimines, and goniodomins (GDs) in clonal cultures of A. ogatae, A. limii, and A. taylorii were examined analytically and the results showed that all strains contained GDs, with GDA as major variants (6-14 pg cell-1) for all strains except the Japanese strain of A. limii, which exclusively had a desmethyl variant of GDA (1.4-7.3 pg cell-1). None of the strains contained detectable levels of PSTs and cycloimines.

Matched MeSH terms: Phylogeny
A New Species of Branchellion (Hirudinea: Piscicolidae) Parasitizing the Gills of Short-Tail Stingrays (Batoidea: Dasyatidae) from the West Pacific

Jimi N, Shinji J, Hookabe N, Okanishi M, Woo SP, Nakano T

Zoolog Sci, 2023 Aug;40(4):308-313.
PMID: 37522602 DOI: 10.2108/zs220057

A new fish leech, Branchellion brevicaudatae sp. n., is described based on specimens parasitizing the gills of the short-tail stingray, Bathytoshia brevicaudata (Hutton, 1875), collected from Japanese waters. The new species can be distinguished from other congeners by having: i) pulsating vesicles emerging from posterior base of branchiae, one pair per somite; ii) dorsal white spots, not arranged in longitudinal row; and iii) blackish body. A phylogenetic tree based on partial sequences of the mitochondrial cytochrome c oxidase subunit I gene from the new species and other piscicolid worms showed that the new species is sister to Branchellion torpedinis Savigny, 1822. This is the first record of Branchellion Savigny, 1822 from Japanese waters.

Matched MeSH terms: Phylogeny
Emergence of equine-like G3 and porcine-like G9 rotavirus strains in Sarawak, Malaysia: 2019-2021

Tahar AS, Ong EJ, Rahardja A, Mamora D, Lim KT, Ahmed K, et al.

J Med Virol, 2023 Aug;95(8):e28987.
PMID: 37501648 DOI: 10.1002/jmv.28987

Rotavirus is the leading causative viral agent of pediatric acute gastroenteritis globally, infecting mostly children 5 years old and below. Data on rotavirus prevalence in Malaysia is scarce, despite the WHO's recommendation for continuous rotavirus surveillance, and has underestimated the need for national rotavirus vaccination. Characteristics of the current rotavirus strains in Malaysia have to be determined to understand the rotavirus epidemiology and vaccine compatibility. This study sought to determine the genetic relatedness of Sarawak rotavirus strains with global strains and to determine the antigenic coverage and epitope compatibility of Rotarix and RotaTeq vaccines with the Sarawak rotavirus strains via in silico analysis. A total of 89 stool samples were collected from pediatric patients (<5 years old) with acute gastroenteritis at private hospitals in Kuching, Sarawak. Rotavirus was detected using reverse transcription-polymerase chain reaction. Positive amplicons were analyzed using nucleotide sequencing before phylogenetic analyses and assessment of epitope compatibility. Genotyping revealed G1P[8] (1/13; 7.7%), G3P[8] (3/13; 23%), G9P[4] (1/13; 7.7%), and G9P[8] (3/13; 23%), G9P[X] (1/13; 7.7%), GXP[4] (1/13; 7.7%), and GXP[8] (3/13; 23%) in samples. All wild-type Sarawak rotavirus strains, with the exception of G1, showed variations in their phylogenetic and antigenic epitope characteristics.

Matched MeSH terms: Phylogeny
Fulltext Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Gardner EM, Bruun-Lund S, Niissalo M, Chantarasuwan B, Clement WL, Geri C, et al.

Proc Natl Acad Sci U S A, 2023 Jul 11;120(28):e2222035120.
PMID: 37399402 DOI: 10.1073/pnas.2222035120

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

Matched MeSH terms: Phylogeny
Molecular epidemiology of Bartonella species from sympatric mammals collected in urban and rural areas of Punjab, Pakistan

Rizwan M, Ali S, Javid A, von Fricken ME, Rashid MI

Acta Trop, 2023 Jul;243:106940.
PMID: 37160189 DOI: 10.1016/j.actatropica.2023.106940

Bartonella can infect a variety of mammals including humans and has been detected in the Americas, Europe, Africa, and Asia. Roughly two-thirds of identified Bartonella species are found and maintained in rodent reservoirs, with some of these species linked to human infections. Rodents (N=236) were caught from the Sahiwal division of Punjab, Pakistan and tested for Bartonella using PCR targeting gltA and rpoB genes, followed by sequencing of rpoB-positive samples. Genetic relatedness to other published Bartonella spp. rpoB gene sequences were examined using BLAST and phylogenetic analysis. Overall, 7.62% (18/236) of rodents were positive for both gltA and rpoB fragments. Rattus rattus and R. norvegicus had 7.94% (12/151) and 7.05% (6/85) positivity rates for Bartonella DNA, respectively. Phylogenetic analysis revealed a close relatedness between Bartonella spp. from Pakistan to Bartonella spp. from China, Nepal, and Malaysia. This study is the first reported detection of Bartonella spp. in R. rattus and R. norvegicus from the Sahiwal area of Punjab, Pakistan.

Matched MeSH terms: Phylogeny
Fulltext Identification of the Tembusu Virus in Mosquitoes in Northern Thailand

Hamel R, Vargas REM, Rajonhson DM, Yamanaka A, Jaroenpool J, Wichit S, et al.

Viruses, 2023 Jun 27;15(7).
PMID: 37515135 DOI: 10.3390/v15071447

Among emerging zoonotic pathogens, mosquito-borne viruses (MBVs) circulate between vertebrate animals and mosquitoes and represent a serious threat to humans via spillover from enzootic cycles to the human community. Active surveillance of MBVs in their vectors is therefore essential to better understand and prevent spillover and emergence, especially at the human-animal interface. In this study, we assessed the presence of MBVs using molecular and phylogenetic methods in mosquitoes collected along an ecological gradient ranging from rural urbanized areas to highland forest areas in northern Thailand. We have detected the presence of insect specific flaviviruses in our samples, and the presence of the emerging zoonotic Tembusu virus (TMUV). Reported for the first time in 1955 in Malaysia, TMUV remained for a long time in the shadow of other flaviviruses such as dengue virus or the Japanese encephalitis virus. In this study, we identified two new TMUV strains belonging to cluster 3, which seems to be endemic in rural areas of Thailand and highlighted the genetic specificities of this Thai cluster. Our results show the active circulation of this emerging flavivirus in Thailand and the need for continuous investigation on this poorly known but threatening virus in Asia.

Matched MeSH terms: Phylogeny
Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

Kho CJY, Lau MML, Chung HH, Chew IYY, Gan HM

Curr Microbiol, 2023 Jun 25;80(8):255.
PMID: 37356021 DOI: 10.1007/s00284-023-03354-5

Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain.

Matched MeSH terms: Phylogeny
Fulltext Marine-montane transitions coupled with gill and genetic convergence in extant crustacean

Liu H, Zheng Y, Zhu B, Tong Y, Xin W, Yang H, et al.

Sci Adv, 2023 Jun 23;9(25):eadg4011.
PMID: 37352347 DOI: 10.1126/sciadv.adg4011

Marine-terrestrial transition represents an important aspect of organismal evolution that requires numerous morphological and genetic innovations and has been hypothesized to be caused by geological changes. We used talitrid crustaceans with marine-coastal-montane extant species at a global scale to investigate the marine origination and terrestrial adaptation. Using genomic data, we demonstrated that marine ancestors repeatedly colonized montane terrestrial habitats during the Oligocene to Miocene. Biological transitions were well correlated with plate collisions or volcanic island formation, and top-down cladogenesis was observed on the basis of a positive relationship between ancestral habitat elevation and divergence time for montane lineages. We detected convergent variations of convoluted gills and convergent evolution of SMC3 associated with montane transitions. Moreover, using CRISPR-Cas9 mutagenesis, we proposed that SMC3 potentially regulates the development of exites, such as talitrid gills. Our results provide a living model for understanding biological innovations and related genetic regulatory mechanisms associated with marine-terrestrial transitions.

Matched MeSH terms: Phylogeny
Reassortment and genomic analysis of a G9P[8]-E2 rotavirus isolated in China

Peng R, Li D, Wang J, Xiong G, Wang M, Liu D, et al.

Virol J, 2023 Jun 22;20(1):135.
PMID: 37349792 DOI: 10.1186/s12985-023-02064-5

OBJECTIVE: To isolate a prevalent G9P[8] group A rotavirus (RVA) (N4006) in China and investigate its genomic and evolutionary characteristics, with the goal of facilitating the development of a new rotavirus vaccine.
METHODS: The RVA G9P[8] genotype from a diarrhea sample was passaged in MA104 cells. The virus was evaluated by TEM, polyacrylamide gel electrophoresis, and indirect immunofluorescence assay. The complete genome of virus was obtained by RT-PCR and sequencing. The genomic and evolutionary characteristics of the virus were evaluated by nucleic acid sequence analysis with MEGA ver. 5.0.5 and DNASTAR software. The neutralizing epitopes of VP7 and VP4 (VP5* and VP8*) were analyzed using BioEdit ver. 7.0.9.0 and PyMOL ver. 2.5.2.
RESULTS: The RVA N4006 (G9P[8] genotype) was adapted in MA104 cells with a high titer (105.5 PFU/mL). Whole-genome sequence analysis showed N4006 to be a reassortant rotavirus of Wa-like G9P[8] RVA and the NSP4 gene of DS-1-like G2P[4] RVA, with the genotype constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2). Phylogenetic analysis indicated that N4006 had a common ancestor with Japanese G9P[8]-E2 rotavirus. Neutralizing epitope analysis showed that VP7, VP5*, and VP8* of N4006 had low homology with vaccine viruses of the same genotype and marked differences with vaccine viruses of other genotypes.
CONCLUSION: The RVA G9P[8] genotype with the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2) constellation predominates in China and may originate from reassortment between Japanese G9P[8] with Japanese DS-1-like G2P[4] rotaviruses. The antigenic variation of N4006 with the vaccine virus necessitates an evaluation of the effect of the rotavirus vaccine on G9P[8]-E2 genotype rotavirus.

Matched MeSH terms: Phylogeny
Increase in rotavirus prevalence with the emergence of genotype G9P[8] in replacement of genotype G12P[6] in Sabah, Malaysia

Amit LN, John JL, Mori D, Chin AZ, Mosiun AK, Ahmed K

Arch Virol, 2023 Jun 03;168(6):173.
PMID: 37269384 DOI: 10.1007/s00705-023-05803-9

Rotaviruses are major causative agents of acute diarrhea in children under 5 years of age in Malaysia. However, a rotavirus vaccine has not been included in the national vaccination program. To date, only two studies have been carried out in the state of Sabah, Malaysia, although children in this state are at risk of diarrheal diseases. Previous studies showed that 16%-17% of cases of diarrhea were caused by rotaviruses and that equine-like G3 rotavirus strains are predominant. Because the prevalence of rotaviruses and their genotype distribution vary over time, this study was conducted at four government healthcare facilities from September 2019 through February 2020. Our study revealed that the proportion of rotavirus diarrhea increased significantly to 37.2% (51/137) after the emergence of the G9P[8] genotype in replacement of the G12P[8] genotype. Although equine-like G3P[8] strains remain the predominant rotaviruses circulating among children, the Sabahan G9P[8] strain belonged to lineage VI and was phylogenetically related to strains from other countries. A comparison of the Sabahan G9 strains with the G9 vaccine strains used in the RotaSiil and Rotavac vaccines revealed several mismatches in neutralizing epitopes, indicating that these vaccines might not be effective in Sabahan children. However, a vaccine trial may be necessary to understand the precise effects of vaccination.

Matched MeSH terms: Phylogeny
Occurrence of five distinct clades of mermithid nematodes (Nematoda: Mermithidae) infecting black fly larvae (Diptera: Simuliidae) in tropical streams in Malaysia

Lourdes EY, Low VL, Izwan-Anas N, Dawood MM, Sofian-Azirun M, Takaoka H, et al.

Parasitol Int, 2023 Jun;94:102733.
PMID: 36693472 DOI: 10.1016/j.parint.2023.102733

Mermithids are the most common parasites of black flies and are associated with host feminization and sterilization in infected hosts. However, information on the species / lineage of black fly mermithids in Southeast Asia, including Malaysia requires further elucidation. In this study, mermithids were obtained from black fly larvae collected from 138 freshwater stream sites across East and West Malaysia. A molecular approach based on nuclear-encoded 18S ribosomal RNA (18S rRNA) gene was used to identify the species identity / lineage of 77 nematodes successfully extracted and sequenced from the specimens collected. Maximum likelihood and neighbor-joining phylogenetic analyses demonstrated five distinct mermithid lineages. Four species delimitation analyses: automated simultaneous analysis phylogenetics (ASAP), maximum likelihood Poisson tree processes with Bayesian inferences (bPTP_ML), generalized mixed yule coalescent (GMYC) and single rate Poisson tree processes (PTP) were applied to delimit the species boundaries of mermithid lineages in this data set along with genetic distance analysis. Data analysis supports five distinct lineages or operational taxonomic units for mermithids in the present study, with two requiring further investigation as they may represent intraspecific variation or closely related taxa. One mermithid lineage was similar to that previously observed in Simulium nigrogilvum from Thailand. Co-infection with two mermithids of different lineages was observed in one larva of Simulium trangense. This study represents an important first step towards exploring other aspects of host - parasite interactions in black fly mermithids.

Matched MeSH terms: Phylogeny
Molecular cloning and in silico analysis of chalcone isomerase from Polygonum minus

Shah FLA, Baharum SN, Goh HH, Leow TC, Ramzi AB, Oslan SN, et al.

Mol Biol Rep, 2023 Jun;50(6):5283-5294.
PMID: 37148413 DOI: 10.1007/s11033-023-08417-1

BACKGROUND: Chalcone isomerase (CHI; EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthetic pathway that is responsible for the intramolecular cyclization of chalcones into specific 2S-flavanones.
METHODS AND RESULTS: In this study, the open reading frame (ORF) of CHI was successfully isolated from the cDNA of Polygonum minus at 711-bp long, encoding for 236 amino acid residues, with a predicted molecular weight of 25.4 kDa. Multiple sequence alignment and phylogenetic analysis revealed that the conserved residues (Thr50, Tyr108, Asn115, and Ser192) in the cleft of CHI enzyme group active site are present in PmCHI protein sequence and classified as type I. PmCHI comprises more hydrophobic residues without a signal peptide and transmembrane helices. The three-dimensional (3D) structure of PmCHI predicted through homology modeling was validated by Ramachandran plot and Verify3D, with values within the acceptable range of a good model. PmCHI was cloned into pET-28b(+) plasmid, expressed in Escherichia coli BL21(DE3) at 16 °C and partially purified.
CONCLUSION: These findings contribute to a deeper understanding of the PmCHI protein and its potential for further characterization of its functional properties in the flavonoid biosynthetic pathway.

Matched MeSH terms: Phylogeny
Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing

Fauzia KA, Aftab H, Miftahussurur M, Waskito LA, Tuan VP, Alfaray RI, et al.

BMC Microbiol, 2023 Jun 01;23(1):159.
PMID: 37264297 DOI: 10.1186/s12866-023-02889-8

BACKGROUND: Infection with Helicobacter pylori as the cause of gastric cancer is a global public health concern. In addition to protecting germs from antibiotics, biofilms reduce the efficacy of H. pylori eradication therapy. The nucleotide polymorphisms (SNPs) related with the biofilm forming phenotype of Helicobacter pylori were studied.
RESULTS: Fifty-six H. pylori isolate from Bangladeshi patients were included in this cross-sectional study. Crystal violet assay was used to quantify biofilm amount, and the strains were classified into high- and low-biofilm formers As a result, strains were classified as 19.6% high- and 81.4% low-biofilm formers. These phenotypes were not related to specific clades in the phylogenetic analysis. The accessories genes associated with biofilm from whole-genome sequences were extracted and analysed, and SNPs among the previously reported biofilm-related genes were analysed. Biofilm formation was significantly associated with SNPs of alpA, alpB, cagE, cgt, csd4, csd5, futB, gluP, homD, and murF (P

Matched MeSH terms: Phylogeny
Detection of Enterocytozoon hepatopenaei (EHP) (microsporidia) in several species of potential macrofauna-carriers from shrimp (Penaeus vannamei) ponds in Malaysia

Wan Sajiri WMH, Kua BC, Borkhanuddin MH

J Invertebr Pathol, 2023 Jun;198:107910.
PMID: 36889458 DOI: 10.1016/j.jip.2023.107910

Infection by the microsporidian parasite Enterocytozoon hepatopenaei (EHP) has become a significant problem in the shrimp cultivation industry in Asian countries like Thailand, China, India, Vietnam, Indonesia, and Malaysia. The outbreak of this microsporidian parasite is predominantly related to the existence of macrofauna-carriers of EHP. However, information about potential macrofauna-carriers of EHP in rearing ponds is still limited. In this study, the screening of EHP in potential macrofauna-carriers was conducted in farming ponds of Penaeus vannamei in three states in Malaysia, namely Penang, Kedah, and Johor. A total of 82 macrofauna specimens (phyla: Arthropoda, Mollusca, and Chordata) were amplified through a polymerase chain reaction (PCR) assay targeting genes encoding spore wall proteins (SWP) of EHP. The PCR results showed an average prevalence of EHP (82.93%) from three phyla (Arthropoda, Mollusca and Chordata). The phylogenetic tree generated from the macrofauna sequences was revealed to be identical to the EHP-infected shrimp specimens from Malaysia (MW000458, MW000459, and MW000460), as well as those from India (KY674537), Thailand (MG015710), Vietnam (KY593132), and Indonesia (KY593133). These findings suggest that certain macrofauna species in shrimp ponds of P. vannamei are carriers of EHP spores and could be potential transmission vectors. This study provides preliminary information for the prevention of EHP infections that can be initiated at the pond stage by eradicating macrofauna species identified as potential vectors.

Matched MeSH terms: Phylogeny
Theama japonica sp. nov., an Interstitial Polyclad Flatworm Showing a Wide Distribution along Japanese Coasts

Tsuyuki A, Oya Y, Jimi N, Hookabe N, Fujimoto S, Kajihara H

Zoolog Sci, 2023 Jun;40(3):262-272.
PMID: 37256573 DOI: 10.2108/zs220105

We establish a new interstitial polyclad species, Theama japonica sp. nov., based on specimens collected from coarse-sandy habitats in three Japanese main islands (Hokkaido, Honshu, and Shikoku) along the coasts of the Pacific Ocean and the Sea of Japan. Theama japonica is characterized by i) two pairs of cerebral eyespots and four to six precerebral eyespots; ii) eosinophilic secretion glands distributed in the distal half of the inner ventral part of the prostatic vesicle; iii) a conical penis papilla, bent up dorsally, with a sclerotized inner wall; iv) the prostatic sheath with an inner angular fold on the dorso-distal side; and v) the external cilia longer dorsally than ventrally. Partial sequences of the cytochrome c oxidase subunit I (COI) gene from 20 specimens collected at eight localities along Japanese coasts represented 19 haplotypes. The uncorrected p-distances among these COI haplotypes fell within intraspecific variations observed in other polyclads. A network analysis based on these COI haplotypes suggested a geographically non-cohesive genetic structure of the species, possibly indicating the species' high dispersibility. Molecular phylogenetic analyses based on a concatenated dataset of 18S and 28S rDNA sequences showed T. japonica formed a clade with other Theama species. The resulting tree also indicates that our new species is more closely related to Theama sp. from Colombia than species from Panama and Croatia.

Matched MeSH terms: Phylogeny
Fulltext Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing

Andrés C, Del Cuerpo M, Rabella N, Piñana M, Iglesias-Cabezas MJ, González-Sánchez A, et al.

Virus Res, 2023 Jun;330:199089.
PMID: 37011863 DOI: 10.1016/j.virusres.2023.199089

BACKGROUND: Influenza B viruses (FLUBV) have segmented genomes which enables the virus to evolve by segment reassortment. Since the divergence of both FLUBV lineages, B/Victoria/2/87 (FLUBV/VIC) and B/Yamagata/16/88 (FLUBV/YAM), PB2, PB1 and HA have kept the same ancestor, while some reassortment events in the other segments have been reported worldwide. The aim of the present study was to find out reassortment episodes in FLUBV strains detected in cases attended at Hospital Universitari Vall d'Hebron and Hospital de la Santa Creu i Sant Pau (Barcelona, Spain) from 2004 to 2015 seasons.
METHODS: From October 2004 to May 2015, respiratory specimens were received from patients with respiratory tract infection suspicion. Influenza detection was carried out by either cell culture isolation, immunofluorescence or PCR-based assays. A RT-PCR was performed to distinguish both lineages by agarose gel electrophoresis. Whole genome amplification was performed using the universal primer set by Zhou et al. in 2012, and subsequently sequenced using Roche 454 GS Junior platform. Bioinformatic analysis was performed to characterise the sequences with B/Malaysia/2506/2007 and B/Florida/4/2006 corresponding sequences as reference of (B/VIC) and (B/YAM), respectively.
RESULTS: A total of 118 FLUBV (75 FLUBV/VIC and 43 FLUBV/YAM), from 2004 to 2006, 2008-2011 and 2012-2015 seasons, were studied. The whole genome of 58 FLUBV/VIC and 42 FLUBV/YAM viruses was successfully amplified. Based on HA sequences, most FLUBV/VIC viruses (37; 64%) belonged to clade 1A (B/Brisbane/60/2008) except to 11 (19%), which fell within clade 1B (B/HongKong/514/2009) and 10 (17%) to B/Malaysia/2506/2004. Nine (20%) FLUBV/YAM viruses belonged to clade 2 (B/Massachusetts/02/2012), 18 (42%) to clade 3 (B/Phuket/3073/2013) and 15 (38%) fell within Florida/4/2006. Numerous intra-lineage reassortments in PB2, PB1, NA and NS were found in 2 2010-2011 viruses. An important inter-lineage reassortment event from 2008 to 2009 (11), 2010-2011 (26) and 2012-2013 (3) FLUBV/VIC (clade 1) strains to FLUBV/YAM (clade 3) was found, in addition to 1 reassortant NS in 2010-2011 B/VIC virus.
CONCLUSIONS: Intra- and inter-lineage reassortment episodes were revealed by WGS. While PB2-PB1-HA remained in complex, NP and NS reassortant viruses were found in both lineages. Despite reassorment events are not often, the characterisation only by HA and NA sequences might be underestimating their detection.

Matched MeSH terms: Phylogeny
An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing

Patil RV, Hadawale KN, Ramli ANM, Wadkar SS, Bhuyar P

Mol Biotechnol, 2023 Jun;65(6):833-848.
PMID: 36544065 DOI: 10.1007/s12033-022-00633-7

In plant development, flowering is the most widely studied process. Floral forms show large diversity in different species due to simple variations in basic architecture. To determine the floral gene expression during the past decade, MADS-box genes have identified as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by various molecular technologies such as ChIP and next-generation DNA sequencing, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Likewise, the big data analysis revealed combined activity of transcriptional regulators and floral organ identity factors regulate the flower developmental programs. Thus, with the help of cutting-edge technologies like RNA-Sequencing, sex determination is now better understood in few non-model plants Therefore, the recent advances in next-generation sequencing (NGS) should enable researchers to identify the full range of floral gene functions, which will significantly help to understand plant development and evolution. This review summarizes the floral homeotic genes in model and non-model species to understand the flower development genes and dioecy evolution.

Matched MeSH terms: Phylogeny
Molecular identification and in vitro assessment of zoonotic-potential of a novel Orthobunyavirus isolated from broiler chicken in Malaysia

M M, Azmi MA, Sani NI, Gilbert G, Reduan MHF

Trop Biomed, 2023 Jun 01;40(2):194-198.
PMID: 37650407 DOI: 10.47665/tb.40.2.011

We have previously isolated a novel avian Orthobunyavirus, Kedah Fatal Kidney Syndrome (KFKS) virus from a broiler farm in Kedah, Malaysia in 2020 with a severe kidney lesion in chickens. The virus was designated as KFKS2_CS virus. Sequence analysis of partial nucleocapsid (N) and nonstructural (NSs) sequence of this virus showed the highest sequence identity with previous KFKS1 from Malaysia (100%) and 97% with a zoonotic Umbre (UMB) virus, which was reported to cause encephalitis in immunocompromised humans in India. Phylogenetic analysis revealed that this virus was clustered together with previous KFKS1 virus from Malaysia, UMB and Cristoli viruses. This study aimed to assess the zoonotic potential of this KFKS2_CS virus in vitro by determining its ability to inhibit the production of interferon (IFN) in human glioblastoma multiforme (GBM) brain cells using reverse-transcriptase polymerase reaction (RT-PCR). This virus blocked the production of interferon-a in this human brain cells. In conclusion, this KFKS2_CS virus may have a zoonotic potential and become a public health concern in the future.

Matched MeSH terms: Phylogeny
Molecular detection of filarial nematode from Culicoides biting midges (Diptera: Ceratopogonidae) in northeastern Thailand

Pramual P, Khamluea S, Butlun P, Promdungdee A

Trop Biomed, 2023 Jun 01;40(2):188-193.
PMID: 37650406 DOI: 10.47665/tb.40.2.010

Culicoides Latreille biting midges are important blood feeding insects. Many species are pests and vectors of the disease causing agents including viruses, protozoa and filarial nematodes which can be transmitted to humans and other animals. However, knowledge of the role of Culicoides as vectors of filarial nematodes is limited, particular in Thailand, where at least 100 species of the genus Culicoides have been reported. In this study, a molecular approach using the 12S rRNA gene sequence was used to detecting the filarial nematode in four common biting midge species, C. actoni Smith, C. oxystoma Kieffer, C. peregrinus Kieffer and C. mahasarakhamense Pramual, Jomkumsing, Piraonapicha & Jumpato in animal shelters from northeastern Thailand. A total of 1,721 specimens were used for molecular screening. An unidentified Onchocercidae sp. was detected in a specimen of C. mahasarakhamense collected from Maha Sarakham province. This filarial species shows 93% sequence similarity with an unidentified Onchocercidae sp. isolated from Culex mosquitoes. Phylogenetic analyses revealed that Onchocercidae sp. from C. mahasarakhamense formed a clade with strong bootstrap support (100%) with filarial species detected in birds. Thus, it is very likely that the Onchocercidae sp. found in this study employes birds as vertebrate hosts which agrees with feeding behavior of C. mahasarakhamense which is known to feed on chicken. Further study is requiring to examine whether this biting midge species is a competent vector of this Onchocercidae sp.

Matched MeSH terms: Phylogeny
Theileria orientalis Buffeli pathotype in cows in a theileriosis-endemic region of India

Sahoo S, Sahoo N, Biswal S, Mohanty BN, Behera B, Pahari A

Trop Biomed, 2023 Jun 01;40(2):236-240.
PMID: 37650411 DOI: 10.47665/tb.40.2.015

Oriental theileriosis caused by Theileria orientalis is a growing health concern of lactating cows in its endemic areas. Rapid and sensitive diagnostic tests are demand areas for appropriate and effective prophylactic and therapeutic measures. Quantitative polymerase chain reaction (qPCR) is the answer for both detection and quantification of parasites. Present study deals with qPCR for detection of parasitemia level of T. orientalis in apparently healthy and clinically affected cows. Major piroplasm surface protein (MPSP) gene present in T. orientalis was cloned in pUC57 vector and transformed into E. coli Top 10 cells. Single and mixed infections of hemoprotozoa other than T. orientalis, causing anemia were differentiated through blood smear examination and PCR tests. T. orientalis was detected in 108 (63.15%) ill and 48 (26.66%) healthy cows. Piroplasms detected per 1000 red blood cells (RBCs) was 0-1 in the healthy group as compared to 3-22 in those showing clinical signs. Parasitemia in ill cows ranged between 6.9 × 102 and 4.5 × 103 parasites / µl of blood which was significantly higher (p<0.05) than healthy group (2.6 × 102 - 5.7 × 102 parasites / µl of blood). Phylogenetic study of the isolates showed similarity with Buffeli type that unfolded its pathogenic form in apparently healthy and ill cows.

Matched MeSH terms: Phylogeny

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