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Fulltext Detection of novel coronaviruses from dusky fruit bat (Penthetor lucasi) in Sarawak, Malaysian Borneo

Habeebur-Rahman SP, Noni V, Khan FAA, Tan CS

Vet Med Sci, 2023 Nov;9(6):2634-2641.
PMID: 37658663 DOI: 10.1002/vms3.1251

BACKGROUND: Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia.
OBJECTIVES: Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi).
METHODS: Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated hemi-nested consensus RNA-dependent RNA polymerase consensus primers.
RESULTS: The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α-CoV) and Betacoronavirus (β-CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α-CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with β-CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats.
CONCLUSIONS: This study provides the first available data on CoVs circulating in P. lucasi.

Matched MeSH terms: Phylogeny
Phylogenetic Relationships of Sun Bear (Helarctos malayanus) Based on Mitochondrial DNA from Sumatra and Other Southeast Asian Regions

Roesma DI, Tjong DH, Syaifullah, Aidil DR, Maulana MR, Salis VM

Pak J Biol Sci, 2023 Nov;26(12):615-627.
PMID: 38334154 DOI: 10.3923/pjbs.2023.615.627

Background and Objective: The Helarctos malayanus is the sole bear species-living in Indonesia (Sumatra and Borneo). The available biological data for sun bears (H. malayanus) in Sumatra is limited, especially for morphological and genetic data. A morphological approach is difficult to do. Therefore, a molecular approach is the most likely choice. Phylogenetic analysis was carried out on H. malayanus in Central Sumatra (Dharmasraya, South Solok and Riau) using the Cytochrome B gene. Materials and Methods: Blood samples from three individuals of H. malayanus were obtained at the Sumatran Tiger Rehabilitation Center, Dharmasraya. Three H. malayanus Central Sumatra sequences and 62 GenBank sequences were used in the analysis. The DNA sequences were analyzed using the DNA Star, AliView, Bioedit, DNA SP, haplotype network, IQ Tree and MEGA software. Results: Forty-one haplotypes were identified in 65 sequences, with 17 haplotypes belonging to H. malayanus. Haplotype network analysis divides H. malayanus into Haplogroup I (Sundaland) and Haplogroup II (Mainland). All individuals of H. malayanus in Central Sumatra have the same haplotype as Peninsular Malaysia sequence. The sun bear (H. malayanus) has a monophyletic relationship with other bear species. The H. malayanus has a higher genetic distance between the two lineages (1.0-2.3%) than the genetic distance within the subpopulations of each lineage. Conclusion: The study results supported sun bear (H. malayanus) divided into two different lineages: Mainland (subcluster 1) and Sundaland (subcluster 2 and 3). The geographic isolation causes the absence of gene flow, which results in high genetic distance between sun bears (H. malayanus) in Sundaland and Mainland lineages.

Matched MeSH terms: Phylogeny*
Fulltext Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus

Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, et al.

Virus Res, 2023 Oct 15;336:199226.
PMID: 37739268 DOI: 10.1016/j.virusres.2023.199226

Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.

Matched MeSH terms: Phylogeny
Fulltext Bathymetric evolution of black corals through deep time

Horowitz J, Quattrini AM, Brugler MR, Miller DJ, Pahang K, Bridge TCL, et al.

Proc Biol Sci, 2023 Oct 11;290(2008):20231107.
PMID: 37788705 DOI: 10.1098/rspb.2023.1107

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250-3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

Matched MeSH terms: Phylogeny
Genetic and morphological concordance and discordance within the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae)

Grismer LL, Anuar MSS, Muin MA, Ahmad N, Quah ESH

Zootaxa, 2023 Oct 10;5353(3):265-275.
PMID: 38220685 DOI: 10.11646/zootaxa.5353.3.4

We use data sets from the Cyrtodactylus brevipalmatus group with limited genetic and morphological sampling to demonstrate that not accounting for sampling error may adversely influence decisions regarding species delimitation and diagnosis. Lack of geographic sampling between the endpoints of a species range may recover notable interpopulational genetic differentiation consistent with species-level differentiation. Additionally, small population sample sizes may fail recover statistically different diagnostic morphological differences. Combined, these types of sampling error can produce results seemingly consistent with the recognition of cryptic speciesgenetically delimited populations lacking diagnostic morphological characters. This is the current situation within some lineages of the C. brevipalmatus group whereas in others, sampling error is less problematic and does not jeopardize their taxonomy. We note the potential negative effects for comparative biology as a whole if sampling error is not taken into consideration prior to constructing taxonomies.

Matched MeSH terms: Phylogeny
Characterization of white rot fungi from wood decayed for lignin degradation

Nurul-Aliyaa YA, Awang NA, Mohd MH

Lett Appl Microbiol, 2023 Oct 04;76(10).
PMID: 37777838 DOI: 10.1093/lambio/ovad118

The present study was conducted to isolate and identify white rot fungi (WRF) from wood decayed and to determine their ability to produce lignin-modifying enzymes (LMEs), specifically laccase (Lac), lignin peroxidase (LiP), and manganese peroxidase (MnP), on solid and liquid media supplemented with synthetic dyes namely 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), azure B, and phenol red. A total of 23 isolates of WRF were isolated from decayed wood and identified as eight different species namely Phanerochaete australis, Perenniporia tephropora, Lentinus squarrosulus, Ganoderma australe, Trametes polyzona, Lentinus sajor-caju, Gymnopilus dilepis, and Fomitopsis palustris based on morphological characteristics, DNA sequences of the internal transcribed spacer (ITS) region, and phylogenetic inference. The fungal isolates can be divided into four groups based on the type of LMEs produced, namely A (Lac-LiP-MnP) with 16 isolates, B (Lac-MnP) (three isolates), C (Lac) (three isolates), and D (MnP) (one isolate). This study highlights P. australis (BJ38) as the best producer of Lac and LiP, while L. squarrosulus (IPS72) is the best producer of MnP. The present study is the first reported P. australis as an efficient lignin degrader by demonstrating the highest activity of two important LMEs.

Matched MeSH terms: Phylogeny
A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

Grismer LL, Pawangkhanant P, Idiiatullina SS, Trofimets AV, Nazarov RA, Suwannapoom C, et al.

Zootaxa, 2023 Oct 02;5352(1):109-136.
PMID: 38221458 DOI: 10.11646/zootaxa.5352.1.4

An integrative taxonomic analysis recovers a distinctive new species of the gekkonid genus Cyrtodactylus Gray, 1827 from Satun Province in extreme southern Thailand as the sister species to the Cyrtodactylus intermedius group of southern Indochina, approximately 600 km to the northeast across the Gulf of Thailand. Based on 1449 base pairs of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNAs, the new species, C. disjunctus sp. nov., bears a pairwise sequence divergence from the mean divergences of the intermedius group species ranging from 17.923.6%. Three different principal component analyses (PCA) and a multiple factor analysis (MFA) recover C. disjunctus sp. nov. as a highly distinctive karst cave-adapted species based on morphology and color pattern. Its sister species relationship to the intermedius groupto which it is added herefurther underscores a growing body of analyses that have recovered a trans-Gulf of Thailand connection across the submerged Sunda Shelf between the southern Thai-Malay Peninsula and southern Indochina. Fragmented karstic archipelagos stretching across Indochina have served as foci for the independent evolution of nearly 25% of the species of Cyrtodactylus. The description of C. disjunctus sp. nov. continues to highlight the fact that karstic habitats support an ever-increasing number of threatened site-specific endemics that compose much of the reptile diversity of many Asian nations but, as of yet, most of these landscapes have no legal protection.

Matched MeSH terms: Phylogeny
Vishniacozyma pseudocarnescens sp. nov., a new anamorphic tremellomycetous yeast species

Zhu HY, Wei YH, Guo LC, Wei XY, Li JN, Zhang RP, et al.

Int J Syst Evol Microbiol, 2023 Oct;73(10).
PMID: 37847534 DOI: 10.1099/ijsem.0.006076

Three strains belonging to the basidiomycetous yeast genus Vishniacozyma were isolated from marine water samples collected from intertidal zones in Liaoning province, northeast China. Phylogenetic analyses based on the sequences of the small subunit (SSU) ribosomal DNA (rDNA), the D1/D2 domain of the large subunit (LSU) ribosomal DNA (rDNA), the internal transcribed spacer region (ITS), the two subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1), and the mitochondrial gene cytochrome b (CYTB) showed that these strains together with 20 strains from various geographic and ecological origins from other regions of the world represent a novel species in the genus Vishniacozyma. We propose the name Vishniacozyma pseudocarnescens sp. nov. (holotype CGMCC 2.6457) for the new species, which differs phenotypically from its close relatives V. carnescens, V. tephrensis, and V. victoriae by its ability to grow at 30 °C and on 50 % (w/v) glucose-yeast extract agar.

Matched MeSH terms: Phylogeny
Fulltext Positive effects of tree diversity on tropical forest restoration in a field-scale experiment

Veryard R, Wu J, O'Brien MJ, Anthony R, Both S, Burslem DFRP, et al.

Sci Adv, 2023 Sep 15;9(37):eadf0938.
PMID: 37713486 DOI: 10.1126/sciadv.adf0938

Experiments under controlled conditions have established that ecosystem functioning is generally positively related to levels of biodiversity, but it is unclear how widespread these effects are in real-world settings and whether they can be harnessed for ecosystem restoration. We used remote-sensing data from the first decade of a long-term, field-scale tropical restoration experiment initiated in 2002 to test how the diversity of planted trees affected recovery of a 500-ha area of selectively logged forest measured using multiple sources of satellite data. Replanting using species-rich mixtures of tree seedlings with higher phylogenetic and functional diversity accelerated restoration of remotely sensed estimates of aboveground biomass, canopy cover, and leaf area index. Our results are consistent with a positive relationship between biodiversity and ecosystem functioning in the lowland dipterocarp rainforests of SE Asia and demonstrate that using diverse mixtures of species can enhance their initial recovery after logging.

Matched MeSH terms: Phylogeny
Fulltext Native diversity buffers against severity of non-native tree invasions

Delavaux CS, Crowther TW, Zohner CM, Robmann NM, Lauber T, van den Hoogen J, et al.

Nature, 2023 Sep;621(7980):773-781.
PMID: 37612513 DOI: 10.1038/s41586-023-06440-7

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5-7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.

Matched MeSH terms: Phylogeny
Cenozoic colonisation of the Indian Ocean region by the Australian freshwater-originating glassperch family Ambassidae (Teleostei)

Ghazali SZ, Lavoué S, Sukmono T, Habib A, Tan MP, Nor SAM

Mol Phylogenet Evol, 2023 Sep;186:107832.
PMID: 37263456 DOI: 10.1016/j.ympev.2023.107832

We examined the phylogeny and biogeography of the glassperch family Ambassidae (Teleostei), which is widely distributed in the freshwater, brackish and marine coastal habitats across the Indo-West Pacific region. We first built a comprehensive time-calibrated phylogeny of Ambassidae using five genes. We then used this tree to reconstruct the evolution of the salinity preference and ancestral areas. Our results indicate that the two largest genera of Ambassidae, Ambassis and Parambassis, are each not monophyletic. The most recent common ancestor of Ambassidae was freshwater adapted and lived in Australia about 56 million years ago. Three independent freshwater-to-marine transitions are inferred, but no marine-to-freshwater ones. To explain the distribution of ambassids, we hypothesise two long-distance marine dispersal events from Australia. A first event was towards Southeast Asia during the early Cenozoic, followed by a second one towards Africa during mid-Cenozoic. The phylogenetic signal associated with the salinity adaptation of these events was not detected, possibly because of the selective extinction of intermediate marine lineages. The Ambassidae shares two characteristics with other freshwater fish groups distributed in continental regions surrounding the Indian Ocean: They are too young to support the hypothesis that their distribution is the result of the fragmentation of Gondwana, but they did not retain the phylogenetic signal of their marine dispersal.

Matched MeSH terms: Phylogeny
Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR)

Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M, Kundu BC

Mol Biol Rep, 2023 Sep;50(9):7619-7637.
PMID: 37531035 DOI: 10.1007/s11033-023-08693-x

BACKGROUND: A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers.
METHODS AND RESULTS: The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei's genetic distance was maximum between Roko and Karu (0.124). Based on Nei's genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%).
CONCLUSIONS: The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

Matched MeSH terms: Phylogeny
Fulltext Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus

Chen Y, Guo R, Liang Y, Luo L, Han Y, Wang H, et al.

Virus Res, 2023 Sep;334:199183.
PMID: 37499764 DOI: 10.1016/j.virusres.2023.199183

Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.

Matched MeSH terms: Phylogeny
Prevalence, potential risk factors and genetic diversity of Blastocystis in ruminant livestock animals from Penang, Malaysia

Rauff-Adedotun AA, Lee IL, Abd Talib N, Shaari N, Yahaya ZS, Meor Termizi FH

Parasitol Res, 2023 Sep;122(9):2193-2205.
PMID: 37462745 DOI: 10.1007/s00436-023-07920-5

Blastocystis is a unicellular, anaerobic protist inhabiting the intestinal tract of diverse animal hosts, including human. Information regarding Blastocystis in small ruminants, namely goats and sheep, is limited globally; thus, this study was carried out to investigate the distribution and determinants of Blastocystis in ruminant livestock animals from Penang, Malaysia. Fecal samples from 127 cattle, 149 goats, and 100 sheep were examined for Blastocystis by in vitro cultivation using modified Jones' medium, while DNA barcoding was used for subtyping. Overall, 23.1% (87/376) of animals screened were positive for Blastocystis sp. The prevalence of infection was significantly higher in goats than in cattle and sheep, while the female gender, semi-intensive farming system, and the Northeast Penang Island district were identified as potential risk factors for Blastocystis infection. Blastocystis sp. ST5, ST14, and ST25 were identified in cattle; ST5, ST10, ST13, and ST14 in goats; and ST4, ST5, ST14, and ST15 in sheep. ST5 and ST14 were found to be the most abundant and widespread subtypes in the study area. To the best of our knowledge, this is the first report of ST4 from sheep and ST13 from goats, thus serving as an update to the host range of Blastocystis sp. ST4 and ST13. The isolation of ST4 and ST5 in this study suggests that ruminant livestock animals could serve as reservoirs of human infection.

Matched MeSH terms: Phylogeny
Development of the muscular and nervous systems during the larval ontogeny of the stalked barnacle, Octolasmis angulata Aurivillius 1894 (Cirripedia: Thoracicalcerea: Poecilasmatidae)

Yap FC, Wong WL, Chong VC, Bong CW, Lim LS

Arthropod Struct Dev, 2023 Sep;76:101298.
PMID: 37672818 DOI: 10.1016/j.asd.2023.101298

The advancements in microscopic techniques have stimulated great interest in the muscular and neural architectures of invertebrates, specifically using muscle and neural structures to infer phylogenetic relationships. Here, we provide the data on the development of the muscular and nervous systems during the larval development of stalked barnacle, Octolasmis angulata using the phalloidin F-actin and immunohistochemical labelling (e.g. acetylated α-tubulin and serotonin) and confocal laser scanning microscopy analysis. All naupliar stages shared the same muscle and neural architectures with only the discrepancy in size. The nauplii have a complex muscle arrangement in their feeding apparatus and naupliar appendages. Most naupliar muscles undergo histolyse during the cyprid metamorphosis. The cyprid muscles form beneath the head shield at the end of nauplius VI. The naupliar and cyprid central nervous systems exhibit the typical tripartite brain comprising the protocerebrum, deutocerebrum and tritocerebrum. The serotonin-like immunoreactivity is mainly found in the naupliar brain, mandibular ganglia, cyprid brain and posterior ganglia. Our study revealed that numerous muscle and neural architectures in the naupliar and cyprids have phylogenetic significance, but future studies on the myoanatomy and neuroanatomy of other barnacle species are necessary to determine the homology of these structures.

Matched MeSH terms: Phylogeny
Fulltext Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family

Wang H, Ren L, Liang Y, Zheng K, Guo R, Liu Y, et al.

Microbiol Spectr, 2023 Aug 17;11(4):e0533522.
PMID: 37272818 DOI: 10.1128/spectrum.05335-22

Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.

Matched MeSH terms: Phylogeny
Fulltext Nelson Bay Reovirus Isolated from Bats and Blood-Sucking Arthropods Collected in Yunnan Province, China

Kuang G, Xu Z, Wang J, Gao Z, Yang W, Wu W, et al.

Microbiol Spectr, 2023 Aug 17;11(4):e0512222.
PMID: 37306586 DOI: 10.1128/spectrum.05122-22

Nelson Bay reovirus (NBV) is an emerging zoonotic virus that can cause acute respiratory disease in humans. These viruses are mainly discovered in Oceania, Africa, and Asia, and bats have been identified as their main animal reservoir. However, despite recent expansion of diversity for NBVs, the transmission dynamics and evolutionary history of NBVs are still unclear. This study successfully isolated two NBV strains (MLBC1302 and MLBC1313) from blood-sucking bat fly specimens (Eucampsipoda sundaica) and one (WDBP1716) from the spleen specimen of a fruit bat (Rousettus leschenaultii), which were collected at the China-Myanmar border area of Yunnan Province. Syncytia cytopathic effects (CPE) were observed in BHK-21 and Vero E6 cells infected with the three strains at 48 h postinfection. Electron micrographs of ultrathin sections showed numerous spherical virions with a diameter of approximately 70 nm in the cytoplasm of infected cells. The complete genome nucleotide sequence of the viruses was determined by metatranscriptomic sequencing of infected cells. Phylogenetic analysis demonstrated that the novel strains were closely related to Cangyuan orthoreovirus, Melaka orthoreovirus, and human-infecting Pteropine orthoreovirus HK23629/07. Simplot analysis revealed the strains originated from complex genomic reassortment among different NBVs, suggesting the viruses experienced a high reassortment rate. In addition, strains successfully isolated from bat flies also implied that blood-sucking arthropods might serve as potential transmission vectors. IMPORTANCE Bats are the reservoir of many viral pathogens with strong pathogenicity, including NBVs. Nevertheless, it is unclear whether arthropod vectors are involved in transmitting NBVs. In this study, we successfully isolated two NBV strains from bat flies collected from the body surface of bats, which implies that they may be vectors for virus transmission between bats. While the potential threat to humans remains to be determined, evolutionary analyses involving different segments revealed that the novel strains had complex reassortment histories, with S1, S2, and M1 segments highly similar to human pathogens. Further experiments are required to determine whether more NBVs are vectored by bat flies, their potential threat to humans, and transmission dynamics.

Matched MeSH terms: Phylogeny
From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam

Putt QY, Ya'cob Z, Adler PH, Chen CD, Hew YX, Izwan-Anas N, et al.

Parasit Vectors, 2023 Aug 07;16(1):266.
PMID: 37545007 DOI: 10.1186/s13071-023-05892-0

BACKGROUND: Prompt and precise identification of black flies (Simuliidae) is crucial, given their biting behaviour and significant impact on human and animal health. To address the challenges presented by morphology and chromosomes in black fly taxonomy, along with the limited availability of molecular data pertaining to the black fly fauna in Vietnam, this study employed DNA-based approaches. Specifically, we used mitochondrial and nuclear-encoded genes to distinguish nominal species of black flies in Vietnam.
METHODS: In this study, 135 mitochondrial cytochrome c oxidase subunit I (COI) sequences were established for 45 species in the genus Simulium in Vietnam, encompassing three subgenera (Gomphostilbia, Nevermannia, and Simulium), with 64 paratypes of 27 species and 16 topotypes of six species. Of these COI sequences, 71, representing 27 species, are reported for the first time.
RESULTS: Combined with GenBank sequences of specimens from Malaysia, Myanmar, Thailand, and Vietnam, a total of 234 DNA barcodes of 53 nominal species resulted in a 71% success rate for species identification. Species from the non-monophyletic Simulium asakoae, S. feuerborni, S. multistriatum, S. striatum, S. tuberosum, and S. variegatum species groups were associated with ambiguous or incorrect identifications. Pairwise distances, phylogenetics, and species delimitation analyses revealed a high level of cryptic diversity, with discovery of 15 cryptic taxa. The current study also revealed the limited utility of a fast-evolving nuclear gene, big zinc finger (BZF), in discriminating closely related, morphologically similar nominal species of the S. asakoae species group.
CONCLUSION: This study represents the first comprehensive molecular genetic analysis of the black fly fauna in Vietnam to our knowledge, providing a foundation for future research. DNA barcoding exhibits varying levels of differentiating efficiency across species groups but is valuable in the discovery of cryptic diversity.

Matched MeSH terms: Phylogeny
Simulium (Gomphostilbia) wijiti, a new species of black fly (Diptera: Simuliidae) from northern Thailand and its genetic position with related species in the Simulium ceylonicum species-group

Srisuka W, Takaoka H, Aupalee K, Saeung A

Acta Trop, 2023 Aug;244:106947.
PMID: 37196907 DOI: 10.1016/j.actatropica.2023.106947

A new black fly species, Simulium (Gomphostilbia) wijiti, is described based on adult females, males, pupal exuviae and mature larvae from Mae Hong Son Province, Thailand. This new species is placed in the Simulium ceylonicum species-group. It is distinguished from four Thai members of the S. ceylonicum species-group [S. (G.) curtatum Jitklang et al., S. (G.) pangsidaense Takaoka, Srisuka & Saeung, S. (G.) sheilae Takaoka & Davies, and S. (G.) trangense Jitklang et al.], in the female by the short to medium long sensory vesicle; in the male by the large number of upper-eye (large) facets in 15 vertical columns and 15 or 16 horizontal rows; in the pupa by the dorsum of abdominal segments darkened; and in the larva by the antenna as long as or slightly shorter than the stem of the labral fan (longer than the stem of the labral fan in four other species). Phylogenetic analysis based on the COI gene sequences revealed that this new species is genetically closely related to S. leparense of the S. ceylonicum species-group, but is clearly separated from the latter species, and also from the three Thai related species (S. curtatum, S. sheilae and S. trangense) of the same species-group with interspecific genetic distances ranging from 9.65% to 12.67%. This is the fifth member of the S. ceylonicum species-group recorded from Thailand.

Matched MeSH terms: Phylogeny
Fulltext Molecular characterization of Brazilian FeLV strains in São Luis, Maranhão Brazil

Martins NDS, Rodrigues APS, Bicalho JM, Albuquerque JJ, Reis LL, Alves LL, et al.

Virus Genes, 2023 Aug;59(4):562-571.
PMID: 37195404 DOI: 10.1007/s11262-023-01997-x

The feline leukemia virus (FeLV) belongs to the Retroviridae family and Gammaretrovirus genus, and causes a variety of neoplastic and non-neoplastic diseases in domestic cats (Felis catus), such as thymic and multicentric lymphomas, myelodysplastic syndromes, acute myeloid leukemia, aplastic anemia, and immunodeficiency. The aim of the present study was to carry out the molecular characterization of FeLV-positive samples and determine the circulating viral subtype in the city of São Luís, Maranhão, Brazil, as well as identify its phylogenetic relationship and genetic diversity. The FIV Ac/FeLV Ag Test Kit (Alere™) and the commercial immunoenzymatic assay kit (Alere™) were used to detect the positive samples, which were subsequently confirmed by ELISA (ELISA - SNAP® Combo FeLV/FIV). To confirm the presence of proviral DNA, a polymerase chain reaction (PCR) was performed to amplify the target fragments of 450, 235, and 166 bp of the FeLV gag gene. For the detection of FeLV subtypes, nested PCR was performed for FeLV-A, B, and C, with amplification of 2350-, 1072-, 866-, and 1755-bp fragments for the FeLV env gene. The results obtained by nested PCR showed that the four positive samples amplified the A and B subtypes. The C subtype was not amplified. There was an AB combination but no ABC combination. Phylogenetic analysis revealed similarities (78% bootstrap) between the subtype circulating in Brazil and FeLV-AB and with the subtypes of Eastern Asia (Japan) and Southeast Asia (Malaysia), demonstrating that this subtype possesses high genetic variability and a differentiated genotype.

Matched MeSH terms: Phylogeny

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