Genetic Distance Research Articles

The integrated genomic surveillance system of Andalusia (SIEGA) provides a One Health regional resource connected with the clinic

The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.

Quantitative evaluation and genome-wide association studies of chrysanthemum flower color

Chrysanthemum, one of the economically most important and highly favored ornamental crops, exhibits a wide range of flower colors that are pivotal in determining its aesthetic value and market demand. However, probably due to the high genetic complexity of flower color traits, the progress in the dissection of genetic architecture and identification of quantitative trait nucleotides (QTNs) or candidate genes moves rather slowly. In this study, we systematically assessed the genetic variation of flower color phenotypes by integrating multiple color systems (RHSCC, CIELAB, and RGB) and four principal floral pigments (anthocyanins, chlorophylls, carotenoids, and flavonoids) in a diverse collection of 141 chrysanthemums. The results showed that the flower color traits exhibited a wide range of variations, with coefficients of variation (CV) varying from 26.00 % to 203.52 %. Among the 66 pairs of flower color traits, 48 exhibited highly significant correlations at p < 0.01 or p < 0.05 levels. Moreover, eight exponential regression models were established for predicting anthocyanin and carotenoid contents. Based on the 370,562 high-quality SNPs, genome-wide association studies (GWAS) revealed 36 QTNs significantly associated with flower color phenotype traits and 109 QTNs for pigment content traits. By integrating the functional annotation and expression profiles, a total of 809 candidate genes surrounding the QTNs were initially filtered out. The candidate genes encompassed multiple transcription factor families related to flavonoid metabolism pathways, including MYB, bHLH, WD40, NAC, and AP2/ERF transcription factors, as well as cytochrome P450-type enzyme genes. The current findings contribute to the accurate assessment of flower colors and provide valuable resources for the molecular breeding and functional analysis of flower color in chrysanthemums.

The Genetic Identification of Numerous Apicomplexan Sarcocystis Species in Intestines of Common Buzzard (Buteo buteo).

The common Buzzard (Buteo buteo) was previously shown to transmit two Sarcocystis species (S. glareoli and S. microti) forming cysts in the brains of rodents. Due to a lack of research, the richness of Sarcocystis species spread by these birds of prey is expected to be much higher. A total of 30 samples of the small intestine of the Common Buzzard were collected in Lithuania and subjected to Sarcocystis species identification based on nested PCR of 28S rRNA and ITS1, following the sequencing of amplified DNA fragments. Six known Sarcocystis spp., S. cornixi, S. glareoli, S. halieti, S. kutkienae, S. turdusi, and S. wobeseri, along with three genetically distinct species (Sarcocystis sp. Rod3, Sarcocystis sp. Rod4, and Sarcocystis sp. Rod5), were identified. Phylogenetically, these three potentially new species clustered with Sarcocystis spp. characterised by a rodents-birds life cycle. Sarcocystis spp. employing rodents and birds as their intermediate hosts were detected in 66.7% and 50.0% of samples, respectively. These findings are consistent with the diet preferences of Common Buzzards. Notably, co-infections with two or more species were observed in a half of the samples. Altogether, the obtained results indicate that the Common Buzzard could serve as definitive host of various Sarcocystis species.

A New Species of Cyrtodactylus tibetanus Group (Reptilia: Squamata: Gekkonidae) from Xizang Autonomous Region, China.

A new Cyrtodactylus species, C. laevissp. nov., from the dry-hot valleys near the Yarlung Zangbo River in Re Village, Jindong Countryside, Lang County, Linzhi City, Xizang Autonomous Region, China, is described herein based upon the integrative taxonomic results combining molecular phylogenetic systematics and morphological characteristic comparisons. Our molecular phylogeny was inferred by combining three mitochondrial gene fragments (16S/CO1/ND2), and it indicated a distinct differentiation between the new species and C. tibetanus species complex, with obvious genetic distances (16S 9.9-11.8%/CO1 16.5-18.2%/ND2 16.6-18.5%) detected, supporting its validity. Morphologically, the new species can be easily distinguished from its congers by the following characters: (1) medium size (SVL 48.58-50.92 mm), (2) tubercles on dorsum sparse, (3) tail segments absent and tubercles on tails absent, (4) supralabials 10-12 and infralabials 8-10, (5) interorbital scales between anterior corners of the eyes 28-32, (6) scale rows at midbody 96-98, (7) ventral scales between mental and cloacal slit 145-153, (8) ventral scale rows 41-45, and (9) 4 to 5 white-yellow transverse bands with brown dots and black merges between the nape and sacrum. The description of C. laevissp. nov. increased the total species number of C. tibetanus group to three, and the total Cyrtodactylus species number in Xizang to six and in China to eleven. The new species is currently only known from the type locality with its extremely small populations and needs future surveys to reveal its distribution range, population status, natural history, and mechanisms so that the new species can coexist with Altiphylax medogense.

Bat Rabies in the Americas: Is Myotis the Main Ancestral Spreader?

The rabies virus (RABV) is the exclusive lyssavirus affecting both wild and domestic mammalian hosts in the Americas, including humans. Additionally, the Americas stand out as the sole region where bat rabies occurs. While carnivore rabies is being increasingly managed across the region, bats are emerging as significant reservoirs of RABV infection for humans and domestic animals. Knowledge of the bat species maintaining rabies and comprehending cross-species transmission (CST) and host shift processes are pivotal for directing surveillance as well as ecological research involving wildlife reservoir hosts. Prior research indicates that bat RABV CST is influenced by host genetic similarity and geographic overlap, reflecting host adaptation. In this study, we compiled and analyzed a comprehensive nucleoprotein gene dataset representing bat-borne RABV diversity in Argentina and the broader Americas using Bayesian phylogenetics. We examined the association between host genus and geography, finding both factors shaping the global phylogenetic structure. Utilizing a phylogeographic approach, we inferred CST and identified key bat hosts driving transmission. Consistent with CST determinants, we observed monophyletic/paraphyletic clustering of most bat genera in the RABV phylogeny, with stronger CST evidence between host genera of the same family. We further discuss Myotis as a potential ancestral spreader of much of RABV diversity.

A Functional 67-bp Duplication Locating at the Core Promoter Region within the Bovine ADIPOQ Gene Is Associated with Ovarian Traits and mRNA Expression.

ADIPOQ plays a crucial role in regulating the reproductive system, but there are few reports on the effects of ADIPOQ on ovarian in dairy cows. Previous studies have verified the presence of a 67-bp mutation in the promoter region of the ADIPOQ gene. Hence, we employed ovarian tissues (n = 2111) and blood samples (n = 108) from Chinese Holstein cows as experimental samples to examine the association between ADIPOQ promoter variants and ovarian traits. We extracted DNA from these samples and conducted genetic typing identification on each sample using advanced techniques like PCR and agarose gel electrophoresis. Consequently, the DD, ID, and II genotypes were discovered. and it has been observed that the mutation frequency of this locus is low in the Chinese Holstein cow. Importantly, the correlational analysis unveiled a significant relationship (p < 0.05) between the weight of ovaries in late estrus and the width of ovaries during the estrus interval with the mutation. Result of the RT-PCR revealed that the ID genotype partially diminished the expression of the ADIPOQ gene. The results of this study suggest that the identified variable duplication could serve as a potential genetic marker for enhancing the ovarian traits of Chinese Holstein cows.

Adaptability and nutritional analysis of a newly isolated Chlorella sp. NeZha in brackish and marine environments with potential bioeconomic impacts.

The microalga Chlorella sp. NeZha, recently isolated from a balcony environment, shows significant adaptability across various salinity conditions, including seawater (SeaW), freshwater (FreshW), and high salinity levels (45‰). This study investigates its potential for sustainable aquaculture and biotechnological applications. Morphological and genetic identification were conducted using optical microscopy and DNA sequencing. The microalga was cultivated in a 400 L outdoor photobioreactor, and its biochemical composition, including chlorophyll a, carbohydrate, protein, and lipid content, was analyzed. Its compatibility with zooplankton and growth in aquaculture wastewater were also evaluated. Chlorella sp. NeZha produced chlorophyll a at concentrations exceeding seaweed and Spirulina by 10- and 5-fold, respectively, with a dry weight chlorophyll a content of 34.25 mg/g and 25 pg./cell. The microalga also contained carbohydrate (~33%), protein (~20%), and lipids (~14%). It was compatible with zooplankton species, such as rotifers and brine shrimp, and showed promising growth in aquaculture wastewater. The findings suggest that Chlorella sp. NeZha is a viable candidate for sustainable aquaculture and biotechnological applications, offering high nutritional value and environmental resilience. Its adaptability to diverse salinity conditions and ability to thrive in wastewater highlight its potential for bioremediation and use as feedstock for zooplankton. Further research is recommended to optimize its cultivation and explore broader applications.

Assessment of Genetic Diversity and Identification of Superior Donors for Higher Yield, Nutritional and Processing Traits in Tomato through Hierarchical Clustering Analysis

The present investigation was carried out in the Department of Horticulture, BAC, BAU, Sabour, Bihar, with 22 diverse genotypes of tomato germplasms collected from diverse locations and sources. The 22 genotypes were assessed for their phonological, morphological, yield, nutritional and processing quality attributes. The hierarchical clustering analysis based on the Euclidean distance and Ward’s method were applied on these genotypes separately based on two segments namely the morphological and yield attributes; and the nutritional and processing quality attributes, aimed to find superior genotypes from both segments. Further, through the same analysis, the genetic diversity among the 22 genotypes for these traits were also established. Additionally, the association among the plant traits are also partly reported with a heatmap visualization. Our findings suggest that the genotypes 2019/TODVAR-4, 2019/TODVAR-5, 2019/TODVAR-2, 2019/TODVAR-7, and 2019/TOLOCVRES-4 exhibit superior processing quality attributes, compared to the check cultivar Kashi Chayan. In particular, genotypes with higher yields coupled with favorable nutritional and processing qualities significantly enhance the success of breeding programs. Notably, genotype 2019/TODVAR-4 has been identified as particularly suitable for developing cultivars with excellent processing qualities.

Association of genetic ancestry with molecular tumor profiles in colorectal cancer

BackgroundThere are known disparities in incidence and outcomes of colorectal cancer (CRC) by race and ethnicity. Some of these disparities may be mediated by molecular changes in tumors that occur at different rates across populations. Genetic ancestry is a measure complementary to race and ethnicity that can overcome missing data issues and better capture genetic similarity in admixed populations. We aimed to identify somatic mutations and tumor gene expression differences associated with both genetic ancestry and imputed race and ethnicity.MethodsSequencing was performed with the Tempus xT NGS 648-gene panel and whole exome capture RNA-Seq for 8454 primarily late-stage CRC patients. Genetic ancestry proportions for five continental groups—Africa (AFR), American indigenous (AMR), East Asia (EAS), Europe (EUR), and South Asia (SAS)—were estimated using ancestry informative markers. To address data gaps, race and ethnicity categories were imputed, resulting in assignments for 952 Hispanic/Latino, 420 non-Hispanic (NH) Asian, 1061 NH Black, and 5763 NH White individuals. We assessed association of genetic ancestry proportions and imputed race and ethnicity categories with somatic mutations in relevant CRC genes and in 2608 expression profiles, as well as 1957 consensus molecular subtypes (CMS).ResultsIncreased AFR ancestry was associated with higher odds of somatic mutations in APC, KRAS, and PIK3CA and lower odds of BRAF mutations. Additionally, increased EAS ancestry was associated with lower odds of mutations in KRAS, EUR with higher odds in BRAF, and the Hispanic/Latino category with lower odds in BRAF. Greater AFR ancestry and the NH Black category were associated with higher rates of CMS3, while a higher proportion of Hispanic/Latino patients exhibited indeterminate CMS classifications.ConclusionsMolecular differences in CRC tumor mutation frequencies and gene expression that may underlie observed differences by race and ethnicity were identified. The association of AFR ancestry with increased KRAS mutations aligns with higher CMS3 subtype rates in NH Black patients. The increase of indeterminate CMS in Hispanic/Latino patients suggests that subtype classification methods could benefit from enhanced patient diversity.

Canine Distemper Virus: Origins, Mutations, Diagnosis, and Epidemiology in Mexico.

This review provides an overview of the canine distemper virus (CDV), a highly infectious pathogen causing severe disease in domestic dogs and wildlife. It shares genetic similarities with the human measles virus (HMV) in humans and the rinderpest virus (RPV) in cattle. The origin of CDV likely involves a mutation from human measles strains, possibly in the New World, with subsequent transmission to dogs. CDV has been globally observed, with an increasing incidence in various animal populations. Genomic mutations, especially in the H protein, contribute to its ability to infect different hosts. Diagnosis by molecular techniques like RT-qPCR offers rapid and sensitive detection when compared with serological tests. Genomic sequencing is vital for understanding CDV evolution and designing effective control strategies. Overall, CDV poses a significant threat, and genomic sequencing enhances our ability to manage and prevent its spread. Here, the epidemiology of CDV principally in Mexico is reviewed.

Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada

Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remain unknown. Here, we integrate paleogenomics, genetic simulations, and stable δ13C and δ15N isotope analysis to investigate 700 y of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which is based on radiocarbon dating, span three time periods (1290 to 1440 CE; 1450 to 1650 CE; 1800 to 1870 CE), indicates shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450 to 1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in δ13C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered distinct mitochondrial diversity unique to the Mackenzie Delta belugas, but found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 y surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible.

Analysis of Amphora ostrearia var. minor Grunow, a blooming marine diatom (Bacillariophyceae) in French Atlantic coastal waters and its transfer to the genus Tetramphora

A marine amphoroid diatom, responsible for blooms in 2011 and 2019 in French Atlantic waters was studied using morphology and molecular phylogeny. The highest cell concentrations were reached in the region of Marennes Oléron on 19 August 2011 and were related to a greyish discolouration of gills of oysters and mussels. It was identified as Amphora ostrearia var. minor Grunow, based on morphological characteristics. To ensure the correct identification, type material was re-investigated, using the type slide n° 142 (Cleve & Möller 1878. Diatoms. Part II. Esatas Edquists Boktryckeri, Upsala: 49–108) that enabled us to establish the identity of the taxon. Plastid morphology corresponded to Mereschkowsky’s type 8 amphoroid chloroplast, a feature typical for the genus Tetramphora Mereschkowsky. Results of a phylogenetic analysis inferred from a concatenated alignment including the nuclear marker SSU and the chloroplast rbcL indicated that A. ostrearia var. minor was positioned inside the monophyletic clade Tetramphora (Mereschkowsky) Stepanek & Kociolek. This, together with the morphological data, necessitated a transfer of A. ostrearia var. minor Grunow to the genus Tetramphora (Mereschkowsky) Stepanek & Kociolek. In addition, the genetic distances (p-values) from SSU–rbcL sequences were estimated among the species of Tetramphora including T. ostrearia, the generitype. These revealed that the divergence between Tetramphora ostrearia (Brébisson) Mereschkowsky and its variety minor was higher than the mean value within species of the genus. As a consequence, the studied taxon is raised to the species level as Tetramphora minor (Grunow) Nézan, comb. et stat. nov. Toxin analysis of four strains of T. minor revealed the absence of domoic acid production. Pigment analysis of T. ostrearia revealed a high fucoxanthin production, similar to other amphoroid species.

Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4.

The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966-2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10-4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved.

Detection of Dengue Virus 1 and Mammalian Orthoreovirus 3, with Novel Reassortments, in a South African Family Returning from Thailand, 2017.

In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all family members suggested recent exposure to arthropod-borne viruses. Dengue virus 1 (Genus Orthoflavivirus) was isolated (isolate no. SA397) from the serum of the 45-year-old female via intracerebral injection in neonatal mice and subsequent passage in VeroE6 cells. Phylogenetic analysis of this strain indicated close genetic identity with cosmopolitan genotype 1 DENV1 strains from Southeast Asia, assigned to major lineage K, minor lineage 1 (DENV1I_K.1), such as GZ8H (99.92%) collected in November 2018 from China, and DV1I-TM19-74 isolate (99.72%) identified in Bangkok, Thailand, in 2019. Serum samples from the 46-year-old male yielded a virus isolate that could not be confirmed as DENV1, prompting unbiased metagenomic sequencing for virus identification and characterization. Illumina sequencing identified multiple segments of a mammalian orthoreovirus (MRV), designated as Human/SA395/SA/2017. Genomic and phylogenetic analyses classified Human/SA395/SA/2017 as MRV-3 and assigned a tentative genotype, MRV-3d, based on the S1 segment. Genomic analyses suggested that Human/SA395/SA/2017 may have originated from reassortments of segments among swine, bat, and human MRVs. The closest identity of the viral attachment protein σ1 (S1) was related to a human isolate identified from Tahiti, French Polynesia, in 1960. This indicates ongoing circulation and co-circulation of Southeast Asian and Polynesian strains, but detailed knowledge is hampered by the limited availability of genomic surveillance. This case represents the rare concurrent detection of two distinct viruses with different transmission routes in the same family with similar clinical presentations. It highlights the complexity of diagnosing diseases with similar sequelae in travelers returning from tropical areas.

Gottschelia (Gottscheliaceae, Marchantiophyta) in Indochina.

Gottschelia, collected for the first time in Indochina, inspired an attempt to review the genus phylogeny to identify a more precise position of Indochinese plants. The genetic distance between African and Asian populations of G. schizopleura sensu lato was confirmed. The two groups should be treated as different species. A new combination, G. microphylla comb. nov., has been proposed for Asian plants. Aside from molecular genetics, distinguishing this species from the presumable strictly African G. schizopleura is also possible by morphological characteristics, as well as by its distribution. At the same time, at least three groups are distinguished among Asian haplotypes of G. microphylla, each of which can be interpreted as a species or, at least, subspecies. A morphological description, intravital photographs of the general habitat, and details of the morphological structures are provided. The position of Gottschelia in the phylogenetic schema of Jungermanniales does not allow us to attribute it to any of the known families and forces us to describe a new family, Gottscheliaceae, which is phylogenetically somewhat related to the Chaetophyllopsidaceae re-evaluated here and very different from Gottscheliaceae morphologically.

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei’s genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei’s genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Inter and intra population genetic variability in ducks under conservation programs

This study focuses on estimation of the inter and intra population genetic variability of 6 duck populations. Microsatellite loci were used to assess the genetic variation and population structure of 6 duck populations under a conservation program in Poland. DNA polymorphism was assessed using 24 microsatellite markers and 50 individuals from each population. Polymorphism information content (PIC), heterozygosity with 2 estimators of genetic differentiation (FST and GST), and Nei's standard genetic distance were calculated. The results showed that these 6 endangered duck populations showed high genetic polymorphism. Observed heterozygosity within populations ranged from 0.14 to 0.83, with the average value of 0.58. PIC within populations ranged from 0.038 (P-8 and P-9 lines) to 0.89 (LsA line). Average number of alleles in the studied populations ranged from 4.5 (KhO-1 line) to 7.3 (LsA line). Based on the results, the pairs of lines LsA: P-33 and P-8: P-9 were found to be the most related; and the most genetically distant group was KhO-1 line, which originated as a cross between Khaki Campbell with Orpington duck.

The Approved Live-Attenuated Chikungunya Virus Vaccine (IXCHIQ®) Elicits Cross-Neutralizing Antibody Breadth Extending to Multiple Arthritogenic Alphaviruses Similar to the Antibody Breadth Following Natural Infection.

The first vaccine against chikungunya virus (CHIKV) was recently licensed in the U.S., Europe, and Canada (brand IXCHIQ®, referred to as VLA1553). Other pathogenic alphaviruses co-circulate with CHIKV and major questions remain regarding the potential of IXCHIQ to confer cross-protection for populations that are exposed to them. Here, we characterized the cross-neutralizing antibody (nAb) responses against heterotypic CHIKV and additional arthritogenic alphaviruses in individuals at one month, six months, and one year post-IXCHIQ vaccination. We characterized nAbs against CHIKV strains LR2006, 181/25, and a 2021 isolate from Tocantins, Brazil, as well as O'nyong-nyong virus (ONNV), Mayaro virus (MAYV), and Ross River virus (RRV). IXCHIQ elicited 100% seroconversion to each virus, with the exception of RRV at 83.3% seroconversion of vaccinees, and cross-neutralizing antibody potency decreased with increasing genetic distance from CHIKV. We compared vaccinee responses to cross-nAbs elicited by natural CHIKV infection in individuals living in the endemic setting of Puerto Rico at 8-9 years post-infection. These data suggest that IXCHIQ efficiently and potently elicits cross-nAb breadth that extends to related alphaviruses in a manner similar to natural CHIKV infection, which may have important implications for individuals that are susceptible to alphavirus co-circulation in regions of potential vaccine rollout.

The first mitogenome of the subfamily Stenoponiinae (Siphonaptera: Ctenophthalmidae) and implications for its phylogenetic position

Fleas are the most important insect vectors that parasitize warm-blooded animals and are known vectors of zoonotic pathogens. A recent study showed that Stenoponia polyspina parasitizing Eospalax baileyi in Zoige County have carried Bartonella spp. and Spotted fever group Rickettsia (SFGR). Accurate identification and differentiation of fleas are essential for prevention and control of zoonotic pathogens. To understand phylogenetic relationship of the subfamily Stenoponiinae, we described morphological characteristics of S. polyspina and sequenced its mitogenome with 14,933 bp in size and high A + T content (~ 79%). The S. polyspina mitogenome retained the ancestral pattern of mitochondrial gene arrangement of arthropods without rearrangement. The start codons of 13 protein-coding genes (PCGs) are traditional ATN and the stop codons are TAA or TAG. Anticodon loops of all tRNA genes were 7 bp except for trnL2 and trnD had anticodon loops with 9 bp and the abnormal anticodon loops may be associated with frameshifting mutation. Genetic distance and Ka/Ks ratios indicated that all 13 PCGs of S. polyspina were subjected to purifying selection, with cox1 at the slowest rate and atp8 at the fastest rate. The mitogenomes of 24 species representing 7 families in the order Siphonaptera were selected to reconstruct phylogenetic tree based on concatenated nucleotide sequences of two datasets (PCGRNA matrix and PCG12RNA matrix) using Bayesian inference (BI) and Maximum likelihood (ML) methods. Phylogenetic tree supported that the superfamilies Ceratophylloidea, Vermipsylloidea, Pulicoidea were monophyletic and the superfamily Hystrichopsylloidea was paraphyletic. The family Ctenophthalmidae was monophyletic in PCGRNA-ML (codon partition) and paraphyletic in the remain trees. S. polyspina belongs to the subfamily Stenoponiinae was closely more related to the subfamily Rhadinopsyllinae. This paper explored phylogenetic position of diverse clades within the order Siphonaptera based on morphological and mitogenome data of S. polyspina. Our research enriched NCBI database of the order Siphonaptera.

Vocal differences in note, sequence and great call sequence among three closely related Nomascus gibbon species

AbstractThe vocal structure of gibbons has long been believed to be under strong genetic control and consistent with phylogeny. Gibbon vocalizations show hierarchical structures and song coordination behaviors, which may have different functions and convey distinct information compared to basic notes. However, previous studies have not compared vocalizations at multiple levels across species. We compared the vocal structures of three Nomascus species in the wild in South China, namely the western black gibbon (Nomascus concolor), Cao vit gibbon (N. nasutus), and Hainan gibbon (N. hainanus) at the levels of note (six features of four types of notes), male sequence (eight features), and song coordination (four features of the overlap pattern between male and female songs). We selected 15 recordings for each species: N. concolor (six groups, 2006 to 2021), N. nasutus (seven groups, 2008 to 2021), and N. hainanus (six groups, 2020 to 2021). We used permuted random forest analysis to test for species differences in vocal structure and the contribution of acoustic features to species differences at each level. We used acoustic features to construct a hierarchical clustering tree, and compared it with phylogenetic relationships. We found significant differences at all levels except the boom note. Acoustic similarity did not match genetic similarity in boom and pre-modulated notes, suggesting that genetic differences are not the only factor leading to species differences in vocal structures. We also found different contributions of acoustic features to differentiation in vocal structure at different levels. Our study suggests that we need to compare gibbon vocalizations at different levels to understand their differentiation and evolution.