High Level Of Genetic Similarity Research Articles

Phylogenetic analysis of the trypanosomatid parasite Lotmaria passim in honey bees (Apis mellifera) in Poland.

Lotmaria passim (L. passim) is a single-celled flagellate which colonises the bee gastrointestinal tract and is highly prevalent in honey bees. This parasite is associated with colony losses. Honey bee (Apis mellifera) colonies were sampled from five apiaries in the north-eastern part of Poland for the phylogenetic analysis of L. passim. Each apiary consisted of approximately 60 bee colonies, of which 20 were randomly selected. Samples of 60 differently aged worker bees were collected from each colony and pooled. A total of 100 bee colonies from five apiaries were examined. Protozoa of the Trypanosomatidae family were identified by PCR. L. passim was detected in 47 (47%) of the samples. The 18S ribosomal (r) RNA amplicons of L. passim were sequenced by a commercial service. Their sequences were analysed with BLASTN and noted to be compatible with the GenBank sequences of this region of the organism's genome. A sequence analysis was performed using the BioEdit Sequence Alignment Editor and Clustal W software. The amplicon sequences of L. passim were 100% homologous with the sequences deposited in GenBank under accession numbers KM066243.1., KJ684964.1 and KM980181.1. This is the first study to perform a phylogenetic analysis of L. passim in Polish honey bees. The analysis demonstrated high levels of genetic similarity between isolates of L. passim colonising apiaries in the north-eastern region of Poland.

Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections

BackgroundThe emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections.ResultsAntimicrobial susceptibility testing showed that both blaNDM-5 carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-5 resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene.ConclusionsThe data presented in this study showed that the conjugative blaNDM-5 plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the blaNDM-5 gene from one single patient with multiple infections.

Whole-genome sequence analysis of a novel orthobunyavirus isolated in Japan in the 1980s.

Two viruses isolated from Culicoides biting midges in Japan and preserved in a frozen state for over three decades were genetically characterized by next-generation sequencing. The viruses have a tripartite RNA genome with the typical coding strategy of orthobunyaviruses. They also share a high level of genetic similarity and are thus regarded as isolates of the same virus. Pairwise sequence comparisons and phylogenetic analysis including viruses of the Simbu serogroup demonstrated that the new viruses are members of clade A of this serogroup. In addition, a discrepancy in the phylogenetic trees indicated that a genetic reassortment had occurred in the evolution of the studied viruses. The L protein of the virus reported here showed no more than 94.6% amino acid sequence identity to that of any other Simbu serogroup virus, indicating that it should be regarded as a novel virus according to a criterion for species definition in the genus Orthobunyavirus. Therefore, this novel virus is tentatively named 'Taniyama virus' based on the location where the infected midges were collected.

Genomic analysis of an outbreak of toxin gene bearing Corynebacterium diphtheriae in Northern Queensland, Australia reveals high level of genetic similarity.

Toxigenic diphtheria is rare in Australia with generally fewer than 10 cases reported annually; however, since 2020, there has been an increase in toxin gene-bearing isolates of Corynebacterium diphtheriae cases in North Queensland, with an approximately 300% escalation in cases in 2022. Genomic analysis on both toxin gene-bearing and non-toxin gene-bearing C. diphtheriae isolated from this region between 2017 and 2022 demonstrated that the surge in cases was largely due to one sequence type (ST), ST381, all of which carried the toxin gene. ST381 isolates collected between 2020 and 2022 were highly genetically related to each other, and less closely related to ST381 isolates collected prior to 2020. The most common ST in non-toxin gene-bearing isolates from North Queensland was ST39, an ST that has also been increasing in numbers since 2018. Phylogenetic analysis demonstrated that ST381 isolates were not closely related to any of the non-toxin gene-bearing isolates collected from this region, suggesting that the increase in toxigenic C. diphtheriae is likely due to the expansion of a toxin gene-bearing clone that has moved into the region rather than an already endemic non-toxigenic strain acquiring the toxin gene.

Genetic diversity of the Chinese medicinal plant Astragali Radix based on transcriptome-derived SSR markers

BackgroundAstragali Radix is regarded as an important traditional medicinal plant and has been widely used as a Qi-Invigoratin medicine for more than 2000 years. However, the mechanism of its medicinal and nutritional components in different accessions is unexplored. Moreover, the lack of SSR markers for Astragali Radix has stalled genetic breeding and variety identification. To develop EST-SSRs, transcriptome sequencing was performed based on the Illumina platform. ResultsApproximately 99.6 million raw data points were collected, and 296,618 unigenes with an average length of 1,459 bp were obtained. A total of 71,207 SSR loci within 56,097 SSR-containing unigenes were identified. Of these SSR-containing unigenes, 26,188 (46.7%), 16,736 (29.8%), and 8,858 (15.8%) were related to items in the GO database, KEGG database, and COG database, respectively. The motifs A/T, AG/CT, AT/AT, and AAT/ATT were the most common types, accounting for 39.78%, 19.14%, 10.12%, and 4.60%, respectively, and the average length of the EST-SSRs was 17.16 bp. We acquired 8 functional markers linked to key genes correlated with the biosynthesis of flavonoids. The genetic similarity among the 60 AR varietal resources ranged from 0.2692 to 0.8077, with an average of 0.5742. The dendrogram results indicated that the 60 AR samples tested had high levels of genetic similarity. ConclusionsThe 71,207 EST-SSR loci identified here offer valuable source of DNA markers for the genetic diversity identification of 60 Astragali Radix varieties. These results will facilitate genetic map construction, functional gene identification, variety identification, molecular marker-assisted breeding, and genetic diversity analysis in Astragali Radix.How to cite: Jiang M, Yan S, Ren W, et al. Genetic diversity of the Chinese medicinal plant Astragali Radix based on transcriptome-derived SSR markers. Electron J Biotechnol 2023;62. https://doi.org/10.1016/j.ejbt.2022.12.001.

Genetic Diversity Assessment of Sweetpotato Germplasm in China Using InDel Markers

Sweetpotato (Ipomoea batatas (L.) Lam.), whose roots are rich in starch, is widely grown around the world and plays a prominent role in ensuring food security. At present, there are no reports on the genetic diversity of sweetpotato germplasm revealed by InDel markers. In this study, we developed a set of 30 InDel markers to evaluate the genetic diversity and relationships of 240 accessions, comprising 77 landraces, 80 introduced accessions, 82 improved varieties released in China, and a diploid wild relative Ipomoea trifida. A total of 94 reliable loci were obtained, with a mean of 3.13 loci per primer, and the PIC value ranged from 0.143 to 0.821. The whole population could be divided into three sub-populations according to a structure analysis based on the Bayesian model, which was consistent with the results of principal component analysis (PCA). A neighbor-joining tree was constructed based on Nei’s genetic distance ranging from 0 to 0.556 and discriminated the panel of the population into three main groups (Ⅰ, Ⅱ, Ⅲ). Group Ⅲ was further split into seven subgroups (ⅢA–ⅢG). The clustering pattern of the 240 accessions was unrelated to their geographic origins. Most of the accessions, whether landraces, improved varieties released in China or introduced germplasm, were mixed, which revealed the high level of genetic similarity among accessions from different regions. There was little difference in the level of genetic diversity between landraces and improved varieties, which was probably due to the exchange and utilization of accessions from different regions. More efforts should be made to collect and utilize sweetpotato germplasm resources and further broaden the genetic basis of sweetpotato cultivars.

Organotypic Retinal Explant Cultures from Macaque Monkey

Hereditary retinal degeneration (RD) is characterized by progressive photoreceptor cell death. Overactivation of the cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) pathway in photoreceptor cells causes photoreceptor cell death, especially in models harboring phosphodiesterase 6b (PDE6b) mutations. Previous studies on RD have used mainly murine models such as rd1 or rd10 mice. Given the genetic and physiological differences between mice and humans, it is important to understand to which extent the retinas of primates and rodents are comparable. Macaques share a high level of genetic similarity with humans. Therefore, wild-type macaques (aged 1-3 years) were selected for the in vitro culture of retinal explants that included the retina-retinal pigment epithelium (RPE)-choroid complex. These explants were treated with different concentrations of the PDE6 inhibitor zaprinast to induce the cGMP-PKG signaling pathway and simulate RD pathogenesis. cGMP accumulation and cell death in primate retinal explants were subsequently verified using immunofluorescence and the TUNEL assay. The primate retinal model established in this study may serve for relevant and effective studies into the mechanisms of cGMP-PKG-dependent RD, as well as for the development of future treatment approaches.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Infection in a Bat Gastrointestinal Organoid Model

Abstract The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, is thought to have originated in bats, since multiple viruses with a high level of genetic similarity have been identified in bats. In addition to respiratory symptoms, COVID-19 frequently involves gastrointestinal symptoms such as diarrhea and vomiting, indicating the SARS-CoV-2 can target the gastrointestinal (GI) tract. However, there is no robust in vitro model for assessing the SARS-CoV-2 infection in the bat GI tract. Here, we established gastrointestinal organoid cultures from Jamaican fruit bats (JFB),( Artibeus jamaicensis), which replicated the characteristic morphology of the gastrointestinal epithelium and showed tissue specific gene expression patterns and cell differentiation. To analyze whether JFB intestinal epithelial cells are susceptible to SARS-CoV-2, we performed in vitro infection experiments. While increased SARS-CoV-2 RNA was detected in both cell lysates and supernatants from the infected organoids after 48 h, there was no evidence of active viral replication, and no infectious virus was produced. However, the JFB distal organoids significantly upregulated anti-viral and pro-inflammatory genes in response to SARS-CoV-2. Unexpectedly, SARS-CoV-2 infected JFB organoids had a decreased incidence of apoptotic cell death. Collectively, our data suggest that primary intestinal epithelial cells from JFBs are resistant to SARS-CoV-2 infection and cell damage, likely because they are able to mount a strong antiviral interferon response.

DNA barcodes in identification of some species of hawkmoths (Lepidoptera: Sphingidae)

The use of DNA barcodes is a molecular method commonly used for the identification of specimens that are difficult to pinpoint accurately by traditional morphological methods. DNA barcoding uses standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to identify species in the genus. The hawkmoth genus Cechetra (Zolotuhin & Ryabov, 2012) was proposed for a group of morphologically similar, stripe-patterned species. Based on the seven specimens of the three species of Cechetra genus collected from the Central of Vietnam, we used morphological analysis to initially identified their scientific name of Cechetra lineosa (Walker, 1856) for 04 specimens (LB_F01, LB_G01, LB_H01 and LK_G05); 02 specimens (MK_H04 and MK_B07) were identified with the scientific name of Cechetra minor (Butler, 1875) and 01 specimen (SG_D7) with scientific name Cechetra subangustata (Rothschild, 1920). Then, the COI (Cytochrome C oxidase I) sequence was used for molecular analysis. Total DNA was extracted from the legs of specimens, COI with over 600 bp in length from each specimen was amplified by PCR reactions. The PCR products are hence purified and sequenced. COI gene cloning results showed a very high level of genetic similarity (over 99%) and 7 specimens are of the genus Cechetra, Sphingidae family. For three homomorphic species belonging to the genus Cechetra Zolotuhin & Ryabov, 2012 including Cechetra lineosa (Walker, 1856); Cechetra minor (Butler, 1875) and Cechetra subangustata (Rothschild, 1920). The studied sequences have been added to the current database at GenBank (NCBI) with accession numbers MT994230, MT994231, MT994232, MT994233, MT994234, MT994235, and MT994236.

Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars.

Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop’s region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean’s regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments.

Characterization of Influenza D Virus in Danish Calves.

Influenza D virus (IDV) was first described in 2011 and has been found to mainly circulate among cattle and swine populations worldwide. Nasal swab samples were collected from 100 Danish calf herds (83 dairy and 17 veal herds) from 2018–2020. Influenza D virus was detected in 12 of the herds. Samples with the lowest cycle quantification value were selected for full genome sequencing. A hemagglutinin-esterase fusion (HEF) gene sequence from a Danish IDV collected in 2015 was also included in this study. Phylogenetic analysis showed that viruses from seven of the IDV-positive herds belonged to the D/OK lineage and clustered together in the HEF tree with the IDV collected in 2015. Viruses from the four other herds belonged to the D/660 lineage, where three of the viruses clustered closely together, while the fourth virus was more phylogenetically distant in all gene segments. The high level of genetic similarity between viruses from two different herds involved in calf trading suggests that transmission occurred through the movement of calves. This study is, to our knowledge, the first to describe the characterization of IDV in calves in Denmark.

Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control.

SummaryIntensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage‐based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 phages against F. columnare from Finland and Sweden in 2017. Bacterial isolates were virulent on rainbow trout (Oncorhynchus mykiss) and fell into four previously described genetic groups A, C, E and G, with genetic groups C and E being the most virulent. Phage host range studied against a collection of 227 bacterial isolates (from 2013 to 2017) demonstrated modular infection patterns based on host genetic group. Phages infected contemporary and previously isolated bacterial hosts, but bacteria isolated most recently were generally resistant to previously isolated phages. Despite large differences in geographical origin, isolation year or host range of the phages, whole‐genome sequencing of 56 phages showed high level of genetic similarity to previously isolated F. columnare phages (Ficleduovirus, Myoviridae). Altogether, this phage collection demonstrates a potential for use in phage therapy.

Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

BackgroundThe genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers.Methods and resultsA total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean.ConclusionIn the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar’s pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

The burial ground on Tankovoye Lake (Iturup Island): brief history and results of researches

The burial ground located on a bank of Tankovoye Lake (Kuibyshevskoye) is one of the key sites in the archaeology of the Kuril Islands. This is due not only to the fact that huge archaeological collections reflecting all stages of peopling of the region have been collected here over many years of excavations but also to the fact that this burial ground still remains the only object of this kind throughout the entire islands chain. Moreover, apart of the burials themselves, the stone burial structures, which have not yet been recorded on other sites of the Kuril Islands, but have analogies in the Jōmon culture, were also revealed at the site. Interest in this site is also enhanced by recent genetic studies, which unexpectedly demonstrated a high level of genetic similarity of a person buried here with modern Koryaks and Itelmens. At the same time, despite the site’s uniqueness, it is heavily underrepresented in available scientific publications. Information about it can be found only in the field reports and in few the hard-to-reach regional publications. Therefore, this article provides a brief overview of all data gathered at this site. It is based on the field reports, data from the private archive of Y. Knorozov, museum collections of the Sakhalin Regional Museum, and on the results of the author’s own research as well. Summing up the outcomes of long-term researches, we have to state that the site’s unique objects remain almost unexplored. For many years, studies here were limited to visual examination, cleaning up of the dune opening, and surface artifact gathering. Therefore, the nature of the burial objects found at the site might be recognized only in the most general terms. Their cultural affiliation also remains questionable. Radiocarbon dates suggest that the early Epi-Jōmon epoch is most powerfully represented near the lake, while the bulk of the ceramics collected here belongs to the later stage of this epoch (in accordance with archaeological data from Hokkaido). In addition, artifacts of Middle and Final Jōmon, Okhotsk culture, Satsumon-Tobinitai culture, and Ainu are presented here as well. Presumably, people could bury their dead here during the epochs of Final Jōmon, Epi-Jōmon and, possibly, the Okhotsk culture.

Study on the genetic diversity of wax trees (Rhus succedanea L.) in Northern mountainous region of Vietnam by SSR and SCoT markers

Wax tree has been cultivated to get lacquer, a valuable source of material that is necessary for many industries and handicrafts. Evaluating not only phenotype but also genotype is essential in order to increase the efficiency of new breeding program. In this study, the genetic relationship at the molecular level of 90 wax trees collected in three regions, i.e., Tam Nong, Thanh Son (Phu Tho) and Chiem Hoa (Tuyen Quang), was analyzed by SSR and ScoT markers. The results revealed a significant diversity among the individuals, with similarity coefficient from 0.41 to 0.98. The sample group collected in Chiem Hoa was significantly different from that in Tam Nong. Most of samples which had a high level of genetic similarity, from 0.95 to 0.98, were pairs of samples at the same geographical origin. The high similarity degree of these samples is likely due to the practice of selecting seeds from high-yield wax tree to be kept for seeds. These results provide the necessary information for new wax tree breeding program.

Analysis of the Morphological Diversity of Inflorescence of Six Tunisian Date Palm (Phoenix dactylifera L.) Pollinators

Six Tunisian date palm pollinators were morphologically characterized at the inflorescence level. The aim was to assess the level of similarity between the spathe of the three flowering stages. Nineteen qualitative and quantitative characteristics were explored and subjected to multivariate analyzes. The results showed that inflorescences morphological similarity oscillated between 97.9 and 62.2% with an average of 80.1%, which testifies strong genetic relations among the six genotypes and among flowering stages/cycles within each genotype. Principal Component Analysis (PCA) analysis shows that weight of the spathe (SW), number of spathe (NS), shape of spathe (SS), total length of the spathe (TLS), shape of spikelets (SPS), number of spikelets per spathe (NS), These characteristics are defined by axis 1 and 2 which absorbing a total of 56.3% of total variability. Phylogenetic relationship analysis showed that two groups were distinguished by a high level of genetic similarity of inflorescences at each flowering stage. According to the analysis, the second flowering stage is the most distinguished morphologically with the highest sizes of the quantitative characteristics studied.

Mutational Landscape and Evolutionary Pattern of Liver and Brain Metastasis in Lung Adenocarcinoma.

A comprehensive genomic analysis of paired primary tumors and their metastatic lesions may provide new insights into the biology of metastatic processes and therefore guide the development of novel strategies for intervention. To date, our knowledge of the genetic divergence and phylogenetic relationships among diverse metastatic lesions from cancer remains limited. We performed whole-exome sequencing in 84 tissue and blood samples from 26 patients with lung adenocarcinoma having liver metastases (LiM) or brain metastases (BrM) before any systemic therapy, with the goal to molecularly characterize the metastatic process. Mutational landscape and evolutionary patterns were compared between paired primary lesions (primary lesion of LiM or BrM) and metastases (metastatic site of LiM or BrM). We found that common driver mutations, including TP53 and EGFR, were highly consistent between paired primary and metastatic tumors. Although tumor mutational burden was comparable among groups, the LiM group had significantly higher mutational and copy number variational similarity than the BrM group between paired primary lesions and metastases (p= 0.019 and p= 0.035, respectively). Phylogenetic analysis further revealed that LiM-competent disseminations had a higher level of genetic similarity to their paired primary lesions and were genetically diverged from their primary tumors at a relatively later stage than those of BrM. These results suggest that LiM favorably followed the linear progression model, whereas BrM was more consistent with the parallel progression model. This study suggests that the mutational landscape and evolutionary pattern was distinctly different between the LiM and BrM of lung adenocarcinoma.

Genetic analysis reveals unique characteristics of Plasmodium falciparum parasite populations in Haiti

BackgroundWith increasing interest in eliminating malaria from the Caribbean region, Haiti is one of the two countries on the island of Hispaniola with continued malaria transmission. While the Haitian population remains at risk for malaria, there are a limited number of cases annually, making conventional epidemiological measures such as case incidence and prevalence of potentially limited value for fine-scale resolution of transmission patterns and trends. In this context, genetic signatures may be useful for the identification and characterization of the Plasmodium falciparum parasite population in order to identify foci of transmission, detect outbreaks, and track parasite movement to potentially inform malaria control and elimination strategies.MethodsThis study evaluated the genetic signals based on analysis of 21 single-nucleotide polymorphisms (SNPs) from 462 monogenomic (single-genome) P. falciparum DNA samples extracted from dried blood spots collected from malaria-positive patients reporting to health facilities in three southwestern Haitian departments (Nippes, Grand’Anse, and Sud) in 2016.ResultsAssessment of the parasite genetic relatedness revealed evidence of clonal expansion within Nippes and the exchange of parasite lineages between Nippes, Sud, and Grand'Anse. Furthermore, 437 of the 462 samples shared high levels of genetic similarity–at least 20 of 21 SNPS–with at least one other sample in the dataset.ConclusionsThese results revealed patterns of relatedness suggestive of the repeated recombination of a limited number of founding parasite types without significant outcrossing. These genetic signals offer clues to the underlying relatedness of parasite populations and may be useful for the identification of the foci of transmission and tracking of parasite movement in Haiti for malaria elimination.

ANALYSIS OF GENETIC CHARACTERISTICS OF INFLUENZA VIRUS A/CHICKEN/CHELYABINSK/30/2019 H9N2 ISOLATED IN CHELYABINSK OBLAST

The paper presents data on the study of genetic characteristics of the infl uenza virus A/chicken/ Chelyabinsk/30/2019 H9N2 isolated from pathological material (chicken internal organs) in February 2019 and received from the poultry farm in the Chelyabinsk Oblast. The H9N2 subtype of the isolated virus was identifi ed based on virological analysis. Sequencing of the hemagglutinin gene segment revealed that the amino acid sequence at the cleavage site was RSSR/GLF, which is characteristic of a low virulent avian infl uenza virus. Phylogenetic analysis of the obtained nucleotide sequences of the hemagglutinin gene fragment (1–1539 bp open reading frame) showed that the A/chicken/Chelyabinsk/30/2019 H9N2 isolate belongs to the G1 genetic group of the low virulent infl uenza virus A/H9, the representatives of which are widely spread in the Middle Eastern and Central Asian countries. The complete nucleotide genome sequence of the studied pathogen was determined. The comparative analysis of all genomic segments using the GenBank database revealed a close relationship (over 99%) between the A/chicken/Chelyabinsk/30/2019 H9N2 virus and the A/H9 infl uenza virus isolates circulating in Israel in 2006–2012. According to the analysis of the predicted amino acid sequence of the studied isolate, the positions of some molecular markers that determine the biological properties of the virus have been identifi ed. Most amino acid positions of hemagglutinin (according to H3 subtype sequence numbering) suggest affi nity for the ACA2-3Gal-receptors of avian epithelial cells. Amino acid substitutions were detected at the site within the receptor-binding domain as compared to the A/H9N2 infl uenza virus isolates obtained in Russia in 2018. The primary structure of the A/chicken/Chelyabinsk/30/2019 H9N2 isolate demonstrates a very high level of genetic similarity to the infl uenza virus isolate A/chicken/ Israel/215/2007 H9N2 used as a vaccine strain.

PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations

Abstract Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which leads to a loss of the genetic diversity necessary for survival in the changing habitat conditions. To infer the population structure and genome-wide diversity of wild reindeer, the Taymyr (TAI, n = 33) and Yakut populations including Tundra Leno-Olenek (LNO, n = 20), the Island (ISL, n = 6), the Sundrun (SUN, n = 6) and the Taiga (TGA, n = 5) were genotyped with the Illumina Bovine HD BeadChip. Data set consisting of 8801 polymorphic SNP markers was used to calculate population genetic parameters in PLINK 1.9, SplitsTree 4.14.6. software, R packages “diveRsity” and “StAMMP.” We detected the similar level of observed heterozygosity across the TAI, ISL, SUN and LNO: 0.187, 0.188, 0.184, and 0.189 respectively. Meanwhile, allelic richness was slightly higher in Taimyr population compared to the Yakut groups. The lowest level of genetic diversity was recorded in the Taiga reindeer (Ho=0.168; Ar = 1.476). All populations showed heterozygotes deficiency (uFIS 95%, CI > 0) with higher uFIS values in TGA (0.079). MDS analysis revealed the high level of genetic similarity of TAI, ISL and LNO and placed SUN in close proximity to them. The first and the second MDS components (2.36% and 2.15% of the genetic variability) clearly divided the Taiga reindeer, the genetic apartness of which was also confirmed by the results of the Neighbour-Net tree analysis. Information obtained here, might be helpful for further effective use and maintenance of the reindeer populations as well as for overcoming the negative effects of decreasing their number. The study was supported by Russian Science Foundation within Pr. no. 16-16-10068.