Nucleotide Sequence Analysis Research Articles

DESIGNED ORF PROTEIN FOR SUSTAINABLE THIRD GENERATION BIOFUEL PRODUCTION

The increasing global energy demands and depletion of fossil fuels urge us to develop alternative energy resources. In recent years, algae has gained much attention as a third-generation biofuel feedstock. Among Algae, microalgae are considered a good source of biofuels because of their relatively more oil concentration and rapid production of biomass. Microalgae have the ability to produce a wide variety of biofuels including bio-oil, bio-diesel, bio-syngas, and bio-hydrogen. Commercial production of biofuels from microalgae is presently not in use because of the high expense of production. This research was designed to produce a hybrid ORF that might enhance the oil yielding ability of the microalgae by its translation into a working protein. Ban y using an intensive literature survey, 6 genes from 3 microalgae species were selected. Further, ORFs of selected genes were identified and Hybrid ORF was constructed by combining those ORFs. After that restriction enzyme analysis and thermodynamic analysis of the hybrid nucleotide sequence was carried out, and this showed that the hybrid sequence was stable. The Hybrid ORF nucleotide sequence was translated into the protein sequence. This protein sequence was used for the homology modeling of Hybrid ORF proteins. The protein conformation predicted by homology modeling was further verified by Ramachandran plot. The metabolic pathways were analyzed by KEGG, which showed that all selected genes were functioning in the biosynthesis of lipids. This showed that the Hybrid ORF constructed could be used in a way to enhance the oil content of microalgae for producing biofuel, particularly biodiesel. These results can be validated by further in vitro analysis and can be used for the construction of genetically engineered microalgae.

Two new species of green treefrogs (Pelodryadidae: Litoria) from the northern slopes of Papua New Guinea's Central Cordillera.

We describe two new species of moderate-sized (male body length 26.5-29.8 mm and 41.0 mm), predominantly green treefrogs in the genus Litoria from hill forest on the northern slopes of Papua New Guinea's Central Cordillera. Phylogenetic analysis of mitochondrial ND4 nucleotide sequences shows that the first species is related to Litoria iris (Tyler) and its allies. It is morphologically most similar to Litoria mystax, a small green treefrog known only from the holotype that was described more than 100 years ago from the north coast of western New Guinea but differs from that species in having longer legs and a broader head. The second species is closest to Litoria gasconi, a species known only from the foothills of the Foja Mountains in Papua Province, Indonesian New Guinea, and the Prince Alexander Mountains in northern Papua New Guinea. It has a net average sequence divergence of 10% from L. gasconi and can be distinguished morphologically from it and from other pelodryadids by the presence of a striking pattern of spots and blotches on the ventral surfaces and on the hidden surfaces of the limbs. These descriptions add to the rapidly increasing known diversity of frogs in hill and lower montane forest, habitats that support the most diverse frog communities on mainland New Guinea.

Occurrence of canine parvovirus type 2c in diarrhoeic faeces of dogs in Kolkata, India.

Canine parvovirus-2(CPV-2) causes a highly contagious disease of dogs characterised by acute hemorrhagic gastroenteritis, lethargy, vomiting, fever and usually bloody or mucoid diarrhoea. In the present study, 41 faecal samples collected from dogs exhibiting the signs of fever, vomition, bloody or mucoid diarrhoea in Kolkata, India were screened by haemagglutination test and PCR for detection of capsid protein coding VP2 gene. The viral genotype was detected by multiplex PCR and analysis of partial VP2 gene nucleotide sequences of selected PCR products with bioinformatics tool. Thirteen (31.71%) samples were found positive with HA titre ≥ 32 whereas 28 (68.29%) samples were positive by PCR of VP2 gene indicating higher sensitivity of PCR. Highest occurrence of CPV-2 was observed in the age group of 1-6 months (80.65%) and non-descript breeds with no history of vaccination (85%). Three samples were antigenic type CPV-2a, rest were CPV-2b/CPV 2c. Six CPV sequences were found to be highly similar to published CPV 2c sequences in BLAST analysis revealing a maximum identity of 99-100% with other CPV-2c strains and clustered together with CPV-2c strains of India and other countries in phylogenetic analysis. The present study highlights the need for continuous monitoring of samples to detect gradual changes in circulating CPV-2 genotypes in India.

Detection of G3 human-like rotavirus in institutionalized dogs from Brazil.

Viral gastroenteritis is a common clinical problem in dogs and group A rotavirus (RVA) is one of the agents involved in this etiology. It mainly affects dogs in the first 6months of life, and these animals are considered an important reservoir and potential transmitters of the virus to other susceptible hosts, such as humans. Among the different types of RVA, G3 is the most detected in dogs, and this genotype is also involved in infections in other animals, including humans. Thus, the present study aims to investigate the presence of RVA in samples of dogs from a public kennel. A total of 64 fecal samples from dogs with diarrhea were analyzed, collected from April 2019 to March 2020, from the kennel of the Zoonosis Control Center, located in Belém, a city in the North of Brazil. The extracted genetic material was subjected to reverse transcription followed by real-time PCR (RT-qPCR); the positives were tested by RT-PCR with a specific primer for the RVA VP7 gene, after nucleotide sequencing and phylogenetic analysis. One sample was subjected to high-performance sequencing. A positivity of 7.8% (5/64) was observed for RVA, all characterized as G3, grouping in the G3-III lineage, with greater similarity to human samples. Different regions of the RVA genome fragments were found. These results emphasize the need for animal health surveillance to better understand the global strain dispersion of RVA and elucidate possible interspecies transmission events, monitoring the genetic diversity of this pathogen.

In Silico Structural and Functional Analysis of the Mitochondrial Malate Transporters in Oleaginous Fungus Mucor circinelloides WJ11

Malate transporter proteins (MTPs) play a pivotal role in regulating flux in the citrate/malate/pyruvate shuttle to deliver acetyl-CoA from the mitochondria to the cytosol and thus regulate lipid biosynthesis in oleaginous fungi. Despite the recent successful exploration of the mitochondrial malate transporters in Mucor circinelloides, research with in silico analyses that include molecular docking and their dynamics, in addition to homology modelling of malate transporters, have not been reported. In this study, the physico-chemical properties and nucleotide sequence analysis of two mitochondrial MTPs (MT and SoDIT-a with Gene/protein ID scafold00018.48 and scafold00239.15, respectively), in M. circinelloides WJ11 were performed. The three-dimensional (3D) model of the mitochondrial MTPs was determined and the best-docked complex stabilities were demonstrated with molecular dynamic (MD) simulations. The activity domain was revealed to form hydrogen bonds and piling interactions with citrate and malate upon docking. Our study showed better binding affinities for the MTPs—reaching up to −3.44 and −7.27 kcal/mol with the MT and SoDIT-a proteins, respectively (compared to the target of −2.85 and −6.00 kcal/mol for citric acid-binding). MD simulations illustrated that the protein complexes demonstrated conformational stability throughout the simulation. This study was the first to elucidate the structural characteristics of mitochondrial MTPs in M. circinelloides WJ11, providing direct evidence regarding the transport mechanism of specific substrates. Furthermore, the current results support ongoing efforts to combine functional and structural data to better understand the MTPs (at the molecular and atomic levels) of an oleaginous fungus such as M. circinelloides.

Isolation and Identification of Endophytic Bacteria from Okra Plant and Evaluation of Its Efficiency Against Spiny Bollworm Erias insulana (Boisd)

Twenty-eight endophytic bacteria were isolated from Okra plant grown in several regions in Salah El-Din-governorate fields including Balad, Ishaqi, Tikrit and Baiji. Bacterial cell treatment of isolate SB1 gave the highest rates of mortality on the third instar larvae of the spiny bollworm E. insulana reached to 66.66%, followed by isolate SB 3, which reached to 53.33%, while the isolates ST2, ST5, ST6, SB4, SJ2, SJ3, SJ5, SS2, SS3, as well as the control did not achieve any mortality rate. The results of the treatment of bacterial filtrates in the third instar larvae of the spiny bollworm showed the highest mortality rate was 93.33% by the isolate SB1, followed by 80.00% by the isolate SB3, while the filtrates of bacterial isolates SS5, SS1, SJ7, SJ3, SB5, ST4, and ST3 did not achieve any mortality rate. The results of the molecular diagnosis according to the nucleotide sequence analysis of the 16S rRNA gene and the conformity with the strains recorded in the World Genetic Bank (NCBI) showed the highest bacterial isolates in killing the insect, which included the isolates SB1, SB3, SB6, SJ6, and ST7 return to the species Brevibacillus laterosporus, Bacillus amyloliquefaciens, Bacillus thuringiensis, Bacillus subtilis and Lysinibacillus sphaericus and recorded in the World Genetic Bank under the accession numbers ON844995.1, ON844985.1, ON844996.1, ON844994.1. ON845438.1, respectively.

Isolation, Phenotypic and Molecular Characterization of the Oyster Mushroom Pleurotus spp. and Evaluation of Its Efficacy in Producing the Antibiotic Pleurotin

Fruit bodies of the oyster mushroom, Pleurotus, were collected for 5 isolates symbolized by Has.AA-10, Has.AA-11, Has.AA-12, Has.AA-13 and Has. AA-14, which was initially diagnosed according to phenotypic characteristics. Fungal isolates were identified to the species level using the nucleotide sequence analysis method for 5.8S rRNA as P.ostreatus .strain Has.AA-10, P. floridanus strain Has.AA-12, P. cornucopiae strain Has.AA-13, P. cystidiosus strain Has.AA-11 and P. eryngii var. ferulae strain Has.AA-14 and registered in the world Gene Bank at the NCBI website with accession numbers KX688447.1, MK281340.1, KX787088.1, AB115054.1 and KU612924.1, respectively. The purity of pleurotin was tested by high performance liquid chromatography (HPLC) which showed a concentration of 7.68 μg/ml for the purified pleurutin from Pleurotus spp. The results showed that the highest pluorotin was recorded in presence of crushed sunflower seeds and wheat bran compared with the absence of those supplements in all tested media, while the results showed that no pluorutin was recorded as a result of the non-growth of all Pleurotus spp. in all media supplemented with crushed soybeans. The highest plurotin reached 24.67, 24, 21.35 and 20.99 mg/L in the treatment of P. cornucopiae grown in the (wheat straw + rice husks mixture), (barley straw + rice husk mixture), wheat straw and corn cobs supplemented with crushed sunflower seeds, respectively, while the lowest plurotin concentrations were 0.26, 1.13, 2.11 and 2.66 mg/L in Pleurotus eryngii var. ferulae grown in the unsupplemented corn cobs, wheat straw, (wheat straw + rice husks mixture) and (barley straw + rice husks mixture), respectively.

Survey of Viruses Infecting Basella alba in Hawaii.

Malabar spinach plants (Basella alba, Basellaceae) with leaves exhibiting symptoms of mosaic, rugosity, and malformation were found in a community garden on Oahu, HI in 2018. Preliminary studies using enzyme-linked immunosorbent assay and reverse-transcription (RT)-PCR identified Basella rugose mosaic virus (BaRMV) in symptomatic plants. However, nucleotide sequence analysis of RT-PCR amplicons indicated that additional potyviruses were also present in the symptomatic Malabar spinach. High-throughput sequencing (HTS) analysis was conducted on ribosomal RNA-depleted composite RNA samples of potyvirus-positive plants from three locations. Assembled contigs shared sequences similar to BaRMV, chilli veinal mottle virus (ChiVMV), Alternanthera mosaic virus (AltMV), Basella alba endornavirus (BaEV), broad bean wilt virus 2 (BBWV2), and Iresine viroid 1. Virus- and viroid-specific primers were designed based on HTS sequencing results and used in RT-PCR and Sanger sequencing to confirm the presence of these viruses and the viroid. We tested 63 additional samples from six community gardens for a survey of viruses in Malabar spinach and found that 21 of them were positive for BaRMV, 57 for ChiVMV, 21 for AltMV, 19 for BaEV, and 14 for BBWV2. This is the first characterization of the virome from B. alba.

Molecular detection and genetic characterization of Ehrlichia canis and Ehrlichia sp. in neotropical primates from Brazil

The Anaplasmataceae family includes obligate, arthropod-transmitted intracellular bacteria that can be zoonotic and potentially fatal. Studies focusing on the interaction between neotropical primates and the agents of this family are scarce. The present study aimed to identify agents of the Anaplasmataceae family in the whole blood of free-living and captive neotropical primates in the State of Mato Grosso, Central-West Brazil. Thirty-eight samples of six nonhuman primate (NHP) species were collected in seven municipalities and analysed through polymerase chain reaction (PCR), nucleotide sequencing, and phylogenetic analysis of the dsb, groEL, 16S rRNA, and gltA genes. DNA fragments similar to those of Ehrlichia canis were detected in Sapajus apella and Ehrlichia chaffeensis from Mico melanurus. The sequences generated in this study and homologous sequences retrieved from GenBank® were used for phylogenetic analyses to characterize the Ehrlichial agents detected in NHPs. The agents were then grouped into clades corresponding to different isolates from the NHP species. In addition, an Anaplasma sp. closely related to Anaplasma marginale was identified in two S. apella individuals. These findings shed light on the susceptibility of neotropical NHPs to Anaplasmataceae agents. These bacteria are known to be transmitted by ticks, which can also serve as possible sources of infection for other animals, including humans.

Pathological and molecular findings of visceral gout caused by Israel variant 2 (IS/1494/06) genotype of infectious bronchitis virus in chickens

The aim of this study was to investigate pathological lesions and the presence of of Israel variant 2 (IS /1494/06) genotype of infectious bronchitis virus (IBV) in chickens with visceral gout. Sudden deaths were observed in broiler breeders and layer hens belonging to two different flocks located in eastern Türkiye. Broiler chickens were previously vaccinated with a vaccine containing strains of IBV Massachusetts serotype, but no information was available about the vaccination history of laying hens. At necropsy, there was accumulation of white chalk-like material on the serosal surface of the heart, liver, spleen and air sacs. The kidneys were unilaterally or bilaterally enlarged and pale in color and, ureters were also enlarged. Pooled organ samples from diseased chickens and kidneys alone were examined by virus isolation, real-time reverse transcription polymerase chain reaction (rRT-PCR), nucleotide sequencing analysis and histological methods. Israel variant 2 genotype of IBV was detected in the samples of both flocks as a result of virus isolation, rRT-PCR and DNA sequencing analysis. Histological examination revealed multifocal and randomly distributed crystal deposits in the renal tubulus and adjacent interstitium. Mild to moderate crystalline deposits surrounded by heterophils and macrophages were detected in the serosal layers of the heart, spleen, liver, and air sacs. The findings of this study indicated that IBV should be taken into consideration in visceral gout cases of chickens, and detection of IBV genotypes in the field will enable us to use vaccines compatible with these genotypes in order to control the disease more efficiently.

First report of Enterobacter cloacae causing soft rot disease on potato in Iraq

Potato is an economically important crop, considered the fourth major crop worldwide. However, it has been exposed to many pathogens that cause significant yield loss. Bacterial soft rot diseases caused by Enterobacter cloacae is one of the most devastating on potatoes. The pathogenicity test conducted on several bacterial isolates isolated from potato tubers showing soft rot showed that 4 of these isolates could cause disease in potatoes. The size of damaged segments of potato slices ranged between 5.50 and 7.93 cm. The isolate H.B1 caused the most significant damage of 7.93 cm of tuber slices.
 Furthermore, the inoculation was carried out on 5-week-old potato plants. The bacteria were added through irrigation water at a concentration of 1x106 CPU. After 20 days of infection, symptoms of wilting and yellowing were observed on the inoculated plants. The biochemical tests displayed that the bacteria are negative for Gram stain and positive for the catalase test, gelatin liquefaction, starch hydrolysis and facultative aerobic.
 The nucleotide sequence analysis of 16 S marker results exhibited a similarity rate of 94%. Thus, isolate H.B1 was recorded in NCBI under registration number OP936020.

Molecular Epidemiology and Phylogenetic Analysis of Peste des Petits Ruminants Virus Circulating in Sheep in Bangladesh

Peste des petits ruminants (PPR) is a viral disease of small ruminants that is highly contagious, severe, reportable, and economically important. The present study was conducted to detect the PPR virus (PPRV) circulating in sheep in Bangladesh to determine its association with epidemiological risk factors and the degree of relationship between the F and H genes of the PPRV of sheep with those of other sheep and goat isolates. A cross-sectional study was conducted in five selected districts of Bangladesh to collect data on locations, ecological zones, breeds, age, sex, sources, time period, and farming systems using a structured questionnaire accompanied by face-to-face interviews. During sampling, 250 nasal swab samples were collected from live sheep with the typical clinical signs of PPR. Thereafter, a reverse-transcriptase polymerase chain reaction (RT-PCR) assay was employed to detect PPRV using the F and H genes. Risk factors were determined using bivariable and multivariable logistic regression analyses. Phylogenetic analysis of the detected PPRV was performed using MEGA software after sequencing both F and H genes. Using RT-PCR, 35.6% (89/250, 95% CI: 29.6%–41.6%) of the samples were found to be positive for PPRV. Locations, breeds, sources, and feeding systems were identified as potential molecular epidemiological risk factors for PPRV infection in a multivariate logistic regression model. Nucleotide sequencing and phylogenetic analysis showed that the PPRV strain was genetically related to the lineage IV virus isolates. For the F gene, the sequence divergence of our gene and other selected genes ranged from 0.01% to 0.018% within lineage IV, and the similarity ranged from 98.2% to 99.0%. In the case of the H gene, similar results were also observed in divergence, ranging from 0.017% to 0.083% among lineage IV and others, and similarity varied from 91.7% to 98.3%. To the best of our knowledge, this is the first study in Bangladesh conducted to determine the RT-PCR-based molecular epidemiology of PPRV in sheep. This study highlights the importance of establishing successful interventions for managing PPRV infections in small ruminants in Bangladesh.

Shrew-borne hantaviruses (Hantaviridae: <i>Orthohantavirus</i>) in the Far East of Russia

Insectivores are newly recognized hantaviral reservoir worldwide. Four distinct shrew-borne hantaviruses (family Hantaviridae) have been identified in two regions located in southern and northern part of the Russian Far East, two genetic variants of Seewis virus (SWSV), Lena River virus (LENV), Kenkeme virus (KKMV) and Yakeshi virus (YKSV). Here, we describe geographic distribution of shrew-borne hantaviruses in southern part of the Russian Far East: Jewish Autonomous region, Khabarovsk Krai, Primorsky Krai and Sakhalin region. Lung samples from shrews of genus Sorex, captured in the four regions of Far Eastern Russia, were examined for hantavirus RNA using reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis of the partial nucleotide sequences of viral genome was conducted using MEGA X software. New genetic variant of YKSV was identified in new reservoir host, long-clawed shrew (S. ungiuculatus) from Sakhalin Island. Genetic variant of SWSV, ARTV-Sc, has been found to circulate among S. caecutiens on the seacoast of Khabarovsk and Primorsky Krai. KKMV virus and second genetic variant of SWSV, ARTV-St, were found in S. roboratus and S. tundrensis, respectively from Jewish Autonomous region. Sorex-borne hantaviruses were found in all studied regions of Far Eastern Russia. Our results demonstrated co-evolution of SWSV, KKMV, and YKSV viruses throughout the geographic distribution of its hosts.

A Rare B-Myeloid Conversion of Follicular Lymphoma into Clonally Related Acute Myeloid Leukemia: A Case Report

Follicular lymphoma (FL) is a highly prevalent indolent lymphoma, and the risk of histological transformation is approximately 2-3% per year. Transformation of FL generally occurs in the same lineage (B cell lineage). Another rare form of disease progression is the transformation of neoplastic B-cells to another cell lineage such as acute myeloid leukemia (AML). The low incidence of B-myeloid transformation associated with poor prognosis hinders the establishment of model systems to identify molecular mechanisms. A 64-year-old woman was diagnosed with FL and achieved a satisfactory response after six cycles of R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone). Approximately one month after treatment terminated, the disease progressed to AML with an increased white blood cell count and abnormal coagulation. Interestingly, nucleotide sequence analysis of the genomic region encoding the immunoglobulin heavy-chain variable domain showed the possibility of homologous transformation from lymphoma to leukemia cells. Although the patient experienced transient improvement after undergoing treatment with one cycle of idarubicin and cytarabine combined with etoposide, she relapsed and died 8 days after venetoclax salvage therapy. Patient with B-myeloid transformation was associated with an aggressive clinical course and poor prognosis. Conventional strategies for treating histologically transformed AML were ineffective. However, treatment with a Bcl-2 inhibitor could serve as an option. Here we review the literature relevant to this rare histological transformation of FL.

Association of Dengue Virus Serotypes 1&2 with Severe Dengue Having Deletions in Their 3'Untranslated Regions (3'UTRs).

Dengue virus infections are recorded as hyper-endemic in many countries, including India. Research pertaining to the reasons for frequent outbreaks and severe dengue is ongoing. Hyderabad city, India, has been recorded as a 'hotspot' for dengue virus infections. Dengue virus strains circulating over the past few years in Hyderabad city have been characterized at the molecular level to analyze the serotype/genotypes; 3'UTRs were further amplified and sequenced. The disease severity in patients infected with dengue virus strains with complete and 3'UTR deletion mutants was analyzed. Genotype I of the serotype 1 replaced genotype III, which has been circulating over the past few years in this region. Coincidentally, the number of dengue virus infections significantly increased in this region during the study period. Nucleotide sequence analysis suggested twenty-two and eight nucleotide deletions in the 3'UTR of DENV-1. The eight nucleotide deletions observed in the case of DENV-1 3'UTR were the first reported in this instance. A 50 nucleotide deletion was identified in the case of the serotype DENV-2. Importantly, these deletion mutants were found to cause severe dengue, even though they were found to be replication incompetent. This study emphasized the role of dengue virus 3'UTRs on severe dengue and emerging outbreaks.

Seasonal Variability in Transcript Expression of Type I and Type II Keratins in Wool Follicles of Lustrous Fleece-Producing Magra Sheep

ABSTRACT Magra sheep reared around the Bikaner area of Rajasthan, India is famous for producing lustrous fleece as compared to other wool-producing native sheep breeds. Three clips of Magra wool, namely, February, July, and October months of the year are showing variations in luster and gross appearance. Present work has been conducted to unravel seasonal variations, in transcript expression patterns in major type I and type II keratin genes, that occur in wool follicles of lustrous wool-producing Magra sheep. Wool samples randomly collected were graded in high and low luster by Gloss 60° values. Wool follicles of the sheep with low (gloss 60° values; < 2.5) and high (gloss 60° values; > 2.5) luster were used for the analysis of type I and type II keratin transcripts. The results of Quantitative PCR had shown up-regulated expression of keratin genes in high-lustrous sheep as compared to low-lustrous sheep. K32, K40, and K82 transcript expression differed significantly (P ≤ .05) between high- and low-lustrous sheep. Nucleotide sequence analysis of the K40 and K82 genes revealed five and four non-synonymous mutations, respectively. From the present study, it can be speculated that the higher amount of keratin protein may play a crucial role in determining the luster property of the wool.

Variation of length and sequence of the nuclear ribosomal DNA internal transcribed spacer 1 supports “hermit-to-king” crab hypothesis

Lithodoid and paguroid crabs are morphologically assigned to the superfamilies Lithodoidea and Paguroidea, respectively. Molecular analyses, however, have revealed closer genetic proximity of the lithodoid crabs to the family Paguridae than to other families of Paguroidea, provoking a long debate. We investigated the length and nucleotide sequence variation of the nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in lithodoid and paguroid species. Uniquely short ITS1s (215–253 bp) were observed in seven lithodoid species. In contrast, ITS1 length varied considerably in 13 paguroid species belonging to the families Coenobitidae, Diogenidae, and Paguridae. Short-to-long ITS1s (238–1090 bp) were observed in five species of the family Paguridae, and medium to long ITS1s (573–1166 bp) were observed in eight species of the families Coenobitidae and Diogenidae. Considerably different size ITS1s coexisted in individual paguroid species. Nucleotide sequence analysis indicated that the short ITS1s observed in the family Paguridae were descendants of longer ITS1s and were homologous to the short ITS1 of lithodoid species. ITS1 sequences of the families Coenobitidae and Diogenidae shared no nucleotide elements with lithodoid and pagurid species. These molecular signals indicate that the short ITS1 in pagurid lineage was passed on to lithodoid lineage, strongly supporting the “hermit-to-king” crab hypothesis.

Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping.

Results of computational analysis and visualization of differences in gene structures using polarization coding are presented. A two-dimensional phase screen, where each element of which corresponds to a specific basic nucleotide (adenine, cytosine, guanine, or thymine), displays the analyzed nucleotide sequence. Readout of the screen with a coherent beam characterized by a given polarization state forms a diffracted light field with a local polarization structure that is unique for the analyzed nucleotide sequence. This unique structure is described by spatial distributions of local values of the Stokes vector components. Analysis of these distributions allows the comparison of nucleotide sequences for different strains of pathogenic microorganisms and frequency analysis of the sequences. The possibilities of this polarization-based technique are illustrated by the model data obtained from a comparative analysis of the spike protein gene sequences for three different model variants (Wuhan, Delta, and Omicron) of the SARS-CoV-2 virus. Various modifications of polarization encoding and analysis of gene structures and a possibility for instrumental implementation of the proposed method are discussed.

Genetic diversity of Siberian bovine coronavirus isolates (Coronaviridae: Coronavirinae: Betacoronavirus-1: Bovine-Like coronaviruses)

Bovine coronaviruses (BCoVs) are causative agents of diarrhea, respiratory diseases in calves and winter cow dysentery. The study of genetic diversity of these viruses is topical issue. The purpose of the research is studying the genetic diversity of BCoV isolates circulating among dairy cattle in Siberia. Specimens used in this study were collected from animals that died or was forcedly slaughtered before the start of the study. The target for amplification were nucleotide sequences of S and N gene regions. Based on the results of RT-PCR testing, virus genome was present in 16.3% of samples from calves with diarrheal syndrome and in 9.9% with respiratory syndrome. The nucleotide sequences of S gene region were determined for 18 isolates, and N gene sequences - for 12 isolates. Based on S gene, isolates were divided into two clades each containing two subclades. First subclade of first clade (European line) included 11 isolates. Second one included classic strains Quebec and Mebus, strains from Europe, USA and Korea, but none of sequences from this study belonged to this subclade. 6 isolates belonged to first subclade of second clade (American-Asian line). Second subclade (mixed line) included one isolate. N gene sequences formed two clades, one of them included two subclades. First subclade included 3 isolates (American-Asian line), and second subclade (mixed) included one isolate. Second clade (mixed) included 8 sequences. No differences in phylogenetic grouping between intestinal and respiratory isolates, as well as according to their geographic origin were identified. The studied population of BCoV isolates is heterogeneous. Nucleotide sequence analysis is a useful tool for studying molecular epidemiology of BCoV. It can be beneficial for choice of vaccines to be used in a particular geographic region.

Molecular and genetic characteristics of the multicomponent flavi-like Kindia tick virus (Flaviviridae) found in ixodes ticks on the territory of the Republic of Guinea

Ixodes ticks are vectors for pathogens of many infectious diseases. Recently, during the study of Rhipicephalus geigyi ticks collected from livestock in the Republic of Guinea, a new multicomponent flavi-like RNA virus, called Kindia tick virus (KITV), was discovered with an unusual mechanism for the implementation of genetic information. The aim of the work is to detect and study the genetic diversity of KITV in ixodes ticks collected in the territory of the Kindia province of the Republic of Guinea. In 2021, 324 specimens of ticks of the species Amblyomma variegatum, Rh. geigyi, Rh. annulatus, Rh. decoloratus, Rh. senegalensis were collected from cattle. The detection of viral RNA was carried out in individual samples of ticks by RT-PCR, followed by the determination of the nucleotide sequence and phylogenetic analysis. KITV detection rates in ticks of the species Rh. geigyi was 12.2%, Rh. annulatus 4.4%, Rh. decoloratus 3.3%. However, the KITV genetic material has not been identified in Am. variegatum ticks, which are one of the dominant species in West Africa. For all virus isolates, a partial nucleotide sequences of each of the four viral segments (GenBank, OK345271OK345306) were determined. The phylogenetic analysis showed a high level of identity (98.599.8%) for each of the four segments of the viral genome with those previously found in the Republic of Guinea. The obtained KITV isolates are most genetically close to Mogiana tick virus, which was previously detected in South America in Rh. microplus ticks and significantly differed from other multicomponent viruses circulating in Europe and Asia, including the Russian Federation. KITV genetic material was found in three species of ixodid ticks collected from livestock in a number of prefectures of the Republic of Guinea. The infection rate in ticks was 3.312.2%. The continuation of research in this direction remains relevant.