Capsalid monogeneans of fishes from the Seto Inland Sea, Japan: Description of Benedenia kobudai n. sp. parasitic on Semicossyphus reticulatus (Perciformes: Labridae).

The Seto Inland Sea, the largest inland sea in Japan, is a rich fishery with high biodiversity and productivity. Monogeneans have been studied for more than 120 years, and 58 nominal species have been recorded in the Seto inland Sea. This study provided DNA information on five species of Benedenia sensu lato (Capsalidae) from marine fishes from the sea, and one of them, Benedenia kobudai n. sp., is described from Semicossyphus reticulatus (Perciformes: Labridae). This new species differs from the other congeners by the hooded appearance between the anterior attachment organs, the morphology of the penis, the absence of the lobe near the vaginal pore and the common genital pore, the position of the vaginal pore, the germarium lying near the slightly hexagonal testes, the morphology of the haptor, and the shape and position of the hamuli. Phylogenetic analysis showed B. kobudai n. sp. in a separate clade from the other Benedenia species, B. epinepheli, B. hoshinai, B. sekii, and B. seriolae collected from the sea. Each of the newly provided DNA sequences (28S rDNA, ITS1-5.8S-ITS2, cox1) of the above four species are based on specimens obtained from the type hosts and/or type localities and are considered important for future taxonomic re-examination and confirmation of the reliability of the registered sequences. Furthermore, these four species are important causes of fish diseases in aquaculture, and it is expected that information on the distribution, host range, and occurrence of fish diseases for each capsalid secured by molecular identification will be accumulated. The Life Science Identifier (LSID): urn:lsid:zoobank.org:pub:26C15D17-CFD1-450D-9FCE-EFFF692D2133.

Evolutionary dynamics of topotype ME-SA/Ind-2001 of foot and mouth disease virus serotype-O in Pakistan: 2017-2022.

Background: During past few years, the Ind-2001 lineage of the Middle East-South Asia topotype (ME-SA) of the foot-and-mouth disease (FMD) virus has been implicated in FMD outbreaks in Pakistan. Aims: This work conducts a comprehensive evolutionary analysis of the Ind-2001 and Pan Asia II lineages, with a specific emphasis on their geographical distribution, lineage classification, and sub-lineage distribution within the region. Furthermore, it aims to expand our understanding of the conserved region of the VP1 protein. Methods: Total samples (n=50) were subjected to antigen detection ELISA and RT-PCR for serotype determination. Confirmed serotype-O isolates (n=17) underwent sequencing for lineage comparison, mutation impact assessment on the VP1 protein GH loop, 3D structure prediction, and further comparative analysis. Results: Isolates collected from 2017 to 2020 were identified as serotypes O/ME-SA/Pan Asia II ANT10 and O/ME-SA/Pak14. Notably, isolates collected from 2020 to 2022 belonged to a novel FMDV serotype O/ME-SA/Ind-2001e lineage. Phylogenetic analyses indicated that these strains were distinct from dominant contemporaneous strains which may challenge Pakistan's FMD control measures. These isolates exhibited variance in the VP1 epitope, specifically in amino acid residues 135-155, known to influence neutralizing antibody generation. Conclusion: Observed mutations suggest potential challenges to current vaccination efficacy against FMD. This emphasizes enhanced FMD surveillance and demonstrates that tracking the emergence of the O/ME-SA/Ind-2001e lineage is important for determining FMD control strategies in Asia.

Identification of diffusion routes of O/EA-3 topotype of foot-and-mouth disease virus in Africa and Western Asia between 1974 and 2019 - a phylogeographic analysis.

Foot-and-mouth disease (FMD) affects the livestock industry and socioeconomic sustainability of many African countries. The success of FMD control programs in Africa depends largely on understanding the dynamics of FMD virus (FMDV) spread. In light of the recent outbreaks of FMD that affected the North-Western African countries in 2018 and 2019, we investigated the evolutionary phylodynamics of the causative serotype O viral strains all belonging to the East-Africa 3 topotype (O/EA-3). We analyzed a total of 489 sequences encoding the FMDV VP1 genome region generated from samples collected from 25 African and Western Asian countries between 1974 and 2019. Using Bayesian evolutionary models on genomic and epidemiological data, we inferred the routes of introduction and migration of the FMDV O/EA-3 topotype at the inter-regional scale. We inferred a mean substitution rate of 6.64 × 10-3  nt/site/year and we predicted that the most recent common ancestor for our panel of samples circulated between February 1967 and November 1973 in Yemen, likely reflecting the epidemiological situation in under sampled cattle-exporting East African countries. Our study also reinforces the role previously described of Sudan and South Sudan as a frequent source of FMDVs spread. In particular, we identified two transboundary routes of O/EA-3 diffusion: the first from Sudan to North-East Africa, and from the latter into Israel and Palestine AT; a second from Sudan to Nigeria, Cameroon, and from there to further into West and North-West Africa. This study highlights the necessity to reinforce surveillance at an inter-regional scale in Africa and Western Asia, in particular along the identified migration routes for the implementation of efficient control measures in the fight against FMD.

Molecular Characterization of Newly Emerging Foot-and-Mouth Disease Virus Serotype SAT 2 of Lib-12 Lineage Isolated from Egypt.

An outbreak of foot-and-mouth disease virus (FMDV) serotype SAT 2 occurred in Egypt in 2018, which affected cattle and water buffalo. Previous phylogenetic studies on FMDV circulating in Egypt have mainly focused on genomic regions encoding structural proteins which determine FMDV serotype. So far, none of these studies have analyzed the open reading frame (ORF) sequence of Egyptian SAT 2/Lib-12 lineage. The present study aimed to analyze and identify the ORF genome sequence of Lib-12 lineage which belongs to FMDV serotype SAT 2 topotype VII in Egypt. The protocol workflow was optimized and tested using a representative field isolate of FMDV/SAT 2/Lib-12 from a bovine tongue sample collected in 2018 from Ismailia governorate (SAT2/EGY/Ismailia/2018). The protocol was based on reverse transcription polymerase chain reaction with multiple overlapping primers, amplicons sequencing, and assembly to complete the ORF consensus sequence. Alignments of the sequence fragments formed consensus genome sequence of 7219 nucleotides in length. The complete nucleotide sequence of the Egyptian isolate was related to Ethiopian, Nigerian, and Ghanaian strains, with identity not exceeding 95%. The divergence in the genetic identity of the Egyptian SAT 2/Lib-12 lineage from other Egyptian strains and Libyan isolates was 7%, and this may be attributed to the absence of the Lib-12 lineage ORF sequence from Egypt and Libya in the database. The present study significantly advances knowledge of the molecular analysis of FMDV SAT 2 and the design of vaccine selection for FMDV SAT 2 in Egypt. The study protocol could be applied to other FMDV serotypes.

Characterization of the complete mitochondrial genome and phylogenetic status of a recently described species of Mountain Dragon, Diploderma vela (Reptilia: Squamata: Agamidae), from the upper Lantsang valley in west China.

The mountain dragon, Diploderma vela, is an endemic and protected valley lizard that inhabits the upper Lantsang Valley in West China. In this study, we sequenced the complete mitochondrial genome of a male individuals of D. vela using next-generation sequencing methodologies. The complete mitogenome is 16,432 bp in length and contains one noncoding control regions, 13 protein-coding, 22 transfer RNA and two ribosomal RNA genes. The mitogenome content and structure of D. vela was consistent with the previously published representatives of the family. A Bayesian phylogenetic analysis using the complete mitochondrial genomes of Agamidae fully resolved D. vela in the Draconinae, a result consistent with previous investigations. This study provides bioinformatic data for better understanding the evolution and the phylogenetic history of the mountain dragon.

Bluetongue virus serotype 12 enters Australia - a further incursion of novel western lineage genome segments.

Bluetongue virus (BTV) is an arbovirus (genus: Orbivirus) that occurs worldwide. It infects domestic and wild ruminant species and can cause disease in livestock, producing high economic impact. Recently, it gained extra prominence throughout Europe, with disease occurring in regions traditionally free of BTV. BTV enters Australia from Southeast Asia via wind-borne infected Culicoides spp. The first Australian isolation was 1975 (BTV-20) and further serotypes were isolated between 1979-86 (BTV-1, -3, -9, -15, -16, -21, -23). Despite increased, more sensitive, monitoring, no more were detected in over two decades, implying a stable BTV episystem of eastern ancestry. Isolations of BTV-2, -7 and -5 then occurred between 2007-15, with the latter two possessing genome segments with high sequence identity to western isolates. We report on the first isolation and genomic characterization of BTV-12, which revealed that three more novel western topotype gene segments have entered northern Australia.

Rediscovery of a poorly known Chinese stonefly, Flavoperla ovalolobata (Wu, 1948) (Plecoptera: Perlidae).

A poorly known perlid species, Flavoperla ovalolobata (Wu, 1948) is redescribed based on an adult male and four females newly collected at the type locality, Wuyishan located in Fujian Province of southeastern coastal China. Illustrations and color photographs are provided for this species. The taxonomic relationship of this taxon is discussed with related taxa.

Designation of a neotype for Mazama americana (Artiodactyla, Cervidae) reveals a cryptic new complex of brocket deer species.

Mazama americana (red brocket deer) is the genus-type species (first species described for this genus) and the basis for the identity of other Mazama species. Mazama americana is one of the most abundant and widely distributed deer species in the neotropical forest. However, recent studies suggest that this taxon belongs to a species complex. Our goal was to collect an animal at the type locality (topotype) in French Guiana with the aim of characterizing the morphological (biometric, craniometric), cytogenetic (Giemsa, C-banding, G-banding and NOR) and molecular (mitochondrial DNA) features. The comparisons showed that the collected specimen was very similar morphologically to specimens from other South American populations, but it was cytogenetically and molecularly very different from any of the cytotypes already described for this species, corroborating the existence of a complex of cryptic species. The data suggest that the M. americana topotype is a different species from all the cytotypes already described in the literature and which occupy the southern region of the Amazon River. The characterization and designation of the M. americana neotype is the first step toward a taxonomic reorganization of the genus Mazama, with the potential identification of new species.

First description of the female of Clubiona milingae Barrion-Dupo, Barrion & Heong, 2013 (Araneae, Clubionidae).

BACKGROUND: Clubiona milingae Barrion-Dupo, Barrion & Heong, 2013 was described from a single male and no additional specimens have been recorded. The original description was brief and the illustrations were inadequate. NEW INFORMATION: Clubiona milingae is redescribed and illustrated based on new material from the type locality and the new distribution region (Jianfeng Mountains and Limu Mountains of Hainan Island, China). The female is reported for the first time.

The complete mitochondrial genome of the Asian pitviper Gloydius changdaoensis (Squamata, Viperidae).

Asian pitviper Gloydius changdaoensis is a coastal species, distributed in Shandong province, China. In this study, we successfully sequenced the mitochondrial genome of one individual of G. changdaoensis. The complete mitochondrial genome is circular molecular with 17,224 bp, containing an origin of light-strand replication (OL), two non-coding control regions (CRs), and 37 classical genes of vertebrate, which contain 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A Bayesian phylogenetic tree using the complete mitochondrial genomes of all viper species available showed a consistent result with previous studies.

Supplementary descriptions of Pergalumna amamiensis Aoki, 1984 (Acariformes, Galumnoidea) from Ryukyu Islands.

A species of oribatid mites, Pergalumna amamiensis was collected from Amami-Ohshima Island, Ishigaki Island, and Okinawa Island, Southwestern Japan. The specimens were studied in detail, and supplementary descriptions are provided; these include features of the rostrum, the subcapitulum and the surface pattern of pteromorphs. The main morphological traits for this species are summarized as follows; body length 519-570 µm, body width 363-410 µm, rostral tip pointed, sensillus with a long stalk covered by minute barbs, porose areas Aa bulbous, porose areas A1, A2, and A3 circular, surface of pteromorphs ornamented by fine granular structure and dense wrinkles, fine granular structure on prodorsum, subcapitulum, genital plates and anal plates, median pore on the notogaster represented as single pore.

Low topotype diversity of recent foot-and-mouth disease virus serotypes O and A from districts located along the Uganda and Tanzania border.

Foot-and-mouth disease (FMD) is one of the most important livestock diseases in East Africa with outbreaks reported annually that cause severe economic losses. It is possible to control disease using vaccination, but antigenic matching of the vaccine to circulating strains is critical. To determine the relationship between foot-and-mouth disease viruses circulating in districts along the Uganda and Tanzanian border between 2016 and 2017 and currently used vaccines, phylogenetic analysis of the full VP1 virus sequences was carried out on samples collected from both sides of the border. A total of 43 clinical samples were collected from animals exhibiting signs of FMD and VP1 sequences generated from 11 of them. Eight out of the 11 sequences obtained belonged to serotype O and three belonged to serotype A. The serotype O sequences obtained showed limited nucleotide divergence (average of 4.9%) and belonged to topotype East Africa-2, whereas the most common O-type vaccine strain used in the region (O/KEN/77/78) belonged to East Africa-1. The serotype A viruses belonged to topotype Africa-G1 (average nucleotide divergence 7.4%), as did vaccine strain K5/1980. However, vaccine strain K35/1980 belonged to Africa G VII with an average sequence divergence of 20.5% from the study sequences. The genetic distances between current vaccine strains and circulating field strains underscores the crucial need for regular vaccine matching and the importance of collaborative efforts for better control of FMD along this border area.

Identification and genomic characterization of the first isolate of bluetongue virus serotype 5 detected in Australia.

Bluetongue virus (BTV), transmitted by midges (Culicoides sp), is distributed worldwide and causes disease in ruminants. In particular, BT can be a debilitating disease in sheep causing serious trade and socio-economic consequences at both local and global levels. Across Australia, a sentinel cattle herd surveillance program monitors the BTV activity. Prior to 2014, BTV-1, -2, -3, -7, -9, -15, -16, -20, -21 and -23 had been isolated in Australia, but no bluetongue disease has occurred in a commercial Australian flock. We routinely use a combination of serology, virus isolation, RT-PCR and next generation and conventional nucleotide sequencing technologies to detect and phylogenetically characterize incursions of novel BTV strains into Australia. Screening of Northern Territory virus isolates in 2015 revealed BTV-5, a serotype new to Australia. We derived the complete genome of this isolate and determined its phylogenetic relationship with exotic BTV-5 isolates. Gene segments 2, 6, 7 and 10 exhibited a close relationship with the South African prototype isolate RSArrrr/5. This was the first Australian isolation of a Western topotype of segment 10. Serological surveillance data highlighted the antigenic cross-reactivity between BTV-5 and BTV-9. Phylogenetic investigation of segments 2 and 6 of these serotypes confirmed their unconventional relationships within the BTV serogroup. Our results further highlighted a need for a revision of the current serologically based system for BTV strain differentiation and importantly, implied a potential for genome segments of pathogenic Western BTV strains to rapidly enter Southeast Asia. This emphasized a need for continued high-level surveillance of vectors and viruses at strategic locations in the north of Australia The expansion of routine characterization and classification of BTV to a whole genome approach is recommended, to better monitor the presence and level of establishment of novel Western topotype segments within the Australian episystem.

Low topotype diversity of recent foot-and-mouth disease virus serotypes O and A from districts located along the Uganda and Tanzania border

Foot-and-mouth disease (FMD) is one of the most important livestock diseases in East Africa with outbreaks reported annually that cause severe economic losses. It is possible to control disease using vaccination, but antigenic matching of the vaccine to circulating strains is critical. To determine the relationship between foot-and-mouth disease viruses circulating in districts along the Uganda and Tanzanian border between 2016 and 2017 and currently used vaccines, phylogenetic analysis of the full VP1 virus sequences was carried out on samples collected from both sides of the border. A total of 43 clinical samples were collected from animals exhibiting signs of FMD and VP1 sequences generated from 11 of them. Eight out of the 11 sequences obtained belonged to serotype O and three belonged to serotype A. The serotype O sequences obtained showed limited nucleotide divergence (average of 4.9%) and belonged to topotype East Africa-2, whereas the most common O-type vaccine strain used in the region (O/KEN/77/78) belonged to East Africa-1. The serotype A viruses belonged to topotype Africa-G1 (average nucleotide divergence 7.4%), as did vaccine strain K5/1980. However, vaccine strain K35/1980 belonged to Africa G VII with an average sequence divergence of 20.5% from the study sequences. The genetic distances between current vaccine strains and circulating field strains underscores the crucial need for regular vaccine matching and the importance of collaborative efforts for better control of FMD along this border area.

Molecular characterization of circulating Foot and mouth disease virus (FMDV) serotype O topotype EA-3 and serotype A (African topotype) genotype IV in Egypt, 2016.

In January-April 2016, cattle and buffalo farm owners and veterinarians reported clinical signs suggestive of foot and mouth disease virus (FMDV) outbreaks among non-vaccinated cattle and buffalo herds in Egypt. The clinical disease observed was either mild (small oral lesions and speedy recovery) or severe (extensive oral lesions and/or mortalities), and the form of the disease (either mild or severe) segregated by farm. This study aimed to confirm the presence of FMDV and to characterize the circulating strains associated with the outbreaks. Vesicular epithelia were collected from 41 animals representing 15 affected cattle and buffalo farms in five governorates (Behira, Cairo, Daqahlia, Giza and Ismailia), and tested by real time (rt) RT-PCR. Consequently, 92% (38/41) of examined samples were positive. Furthermore, the VP1 coding region of 60% (23/38) of positive specimens were amplified by RT-PCR and sequenced. The phylogenetic analysis identified two distinct strains characterized as serotype O topotype EA-3 and serotype A (African topotype) of genotype IV in the severe and mild disease forms, respectively. The newly identified strains clustered in distinct clades in the phylogenetic trees, indicating the likelihood of new incursions into Egypt. Those strains were most closely related to previously described Sudanese strains.

Foot-and-mouth disease virus serotype SAT1 in cattle, Nigeria.

The knowledge of foot-and-mouth disease virus (FMDV) dynamics and epidemiology in Nigeria and the West Africa subregion is important to support local and regional control plans and international risk assessment. Foot-and-mouth disease virus serotype South African territories (SAT)1 was isolated, identified and characterized from an FMD outbreak in cattle in Nigeria in 2015, 35 years after the last report of FMDV SAT1 in West Africa. The VP1 coding sequence of the Nigerian 2015 SAT1 isolates diverges from reported SAT1 topotypes resulting in a separate topotype. The reporting of a novel FMDV SAT1 strain in the virus pool 5 (West and Central Africa) highlights the dynamic and complex nature of FMDV in this region of Africa. Sustained surveillance is needed to understand the origin, the extent and distribution of this novel SAT1 topotype in the region as well as to detect and monitor the occurrence of (re-)emerging FMDV strains.

Dual Infection with Bluetongue Virus Serotypes and First-Time Isolation of Serotype 5 in India.

Bluetongue is endemic in India and has been reported from most Indian states. Of late, the clinical disease is most frequently seen in the states of Andhra Pradesh, Telangana (erstwhile Andhra Pradesh state), Tamil Nadu and Karnataka. Our analysis of diagnostic samples from bluetongue outbreaks during 2010-2011 from the state of Karnataka identified bluetongue virus (BTV) serotype 5 (BTV-5) for the first time in India. One of the diagnostic samples (CH1) and subsequent virus isolate (IND2010/02) contained both BTV-2 and BTV-5. Segment 2 (seg-2) sequence data (400 bp: nucleotides 2538-2921) for IND2010/02-BTV5, showed 94.3% nucleotide identity to BTV-5 from South Africa (Accession no. AJ585126), confirming the virus serotype and also indicating that Seg-2 was derived from a Western topotype, which is in contrast to serotype 2, that belongs to an Eastern topotype. BTV-5 has been recently reported from Africa, China, French islands and the Americas. Although the exact source of the Indian BTV-5 isolate is still to be confirmed, recent identification of additional exotic serotypes in India is of real concern and might add to the severity of the disease seen in these outbreaks.

Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China.

BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species. RESULTS: Our phylogeny was finely resolved, especially for the N. confucianus-like species. Our data provided the first support for N. brahma and N. eha as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of N. confucianus and one of N. fulvescens were supported as genetically distinct in our species delimitation analyses, while three recognized species (N. coninga, N. huang, and N. lotipes) were not strongly supported as distinct. CONCLUSIONS: Our results suggested that several genetically distinct species may be contained within the species currently known as N. confucianus and N. fulvescens. In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for N. coninga, N. huang, and N. lotipes indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results.

Full genome sequencing of the bluetongue virus-1 isolate MKD20/08/Ind from goat in India

ABSTRACT This communication reports full genome sequencing of the bluetongue virus-1 (BTV-1) isolate MKD20/08/Ind from goat in northern India. The total BTV-1 genome size was found to be 19,190 bp. A comparison study between the Indian isolate and other global isolates revealed that it belongs to the 'Eastern' BTV topotype. The full genome sequence of BTV-1 will provide vital information on its geographical origin and it will also be proved useful for comparing the Indian isolate with global isolates from other host species.

Full genome sequencing of the bluetongue virus-1 isolate MKD20/08/Ind from goat in India.

This communication reports full genome sequencing of the bluetongue virus-1 (BTV-1) isolate MKD20/08/Ind from goat in northern India. The total BTV-1 genome size was found to be 19,190bp. A comparison study between the Indian isolate and other global isolates revealed that it belongs to the 'Eastern' BTV topotype. The full genome sequence of BTV-1 will provide vital information on its geographical origin and it will also be proved useful for comparing the Indian isolate with global isolates from other host species.