Nucleotide Sequence Similarity Research Articles

Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

Single-cell Hi-C analysis of diploid human cells is difficult because of the lack of dense chromosome contact information and the presence of homologous chromosomes with very similar nucleotide sequences. Thus here, we propose a new algorithm to reconstruct the three-dimensional (3D) chromosomal architectures from the Hi-C dataset of single diploid human cells using allele-specific single-nucleotide variations (SNVs). We modified our recurrence plot-based algorithm, which is suitable for the estimation of the 3D chromosome structure from sparse Hi-C datasets, by newly incorporating a function of discriminating SNVs specific to each homologous chromosome. Here, we eventually regard a contact map as a recurrence plot. Importantly, the proposed method does not require any imputation for ambiguous segment information, but could efficiently reconstruct 3D chromosomal structures in single human diploid cells at a 1-Mb resolution. Datasets of segments without allele-specific SNVs, which were considered to be of little value, can also be used to validate the estimated chromosome structure. Introducing an additional mathematical measure called a refinement further improved the resolution to 40-kb or 100-kb. The reconstruction data supported the notion that human chromosomes form chromosomal territories and take fractal structures where the dimension for the underlying chromosome structure is a non-integer value.

Heat-shock Protein 70: Sequence and Expression Analysis in African Catfish Clarias gariepinus after Bacterial Infection and Stress Exposures

Heat-shock protein 70 (HSP70) is a member of the Heat-shock protein family that plays an important role in cellular homeostasis against various stressors in fish. This research aimed to identify the full length of cDNA sequence HSP70 in African catfish C. gariepinus and assessed its mRNA expression under various tissues and stress conditions. The cDNA was cloned and amplified using the polymerase chain reaction (PCR) followed by bi-directional sequencing. The mRNA expression was quantified using the real-time PCR (qPCR) method. A full-length ORF of C. gariepinus HSP70 cDNA was 1932 bp long, encoded 643 amino acids. Three signature sequences of the HSP70 family were detected in the predicted amino acid sequence. The C. gariepinus HSP70 showed the highest similarity in nucleotide and amino acid sequence (>90%) to HSP70 from other Siluriformes catfish species. The HSP70 mRNA was expressed in all tested tissues, with the highest expression found in the liver and spleen, followed by the intestine, heart, head-kidney, and gill. The C. gariepinus HSP70 expression was significantly induced generally after 6 hours of bacterial infection, transportation, heat shock, and high nitrite exposure. The results indicated that the HSP70 gene could serve as an early stress biomarker in C. gariepinus

Clonal relationship of tet(X4)-positive Escherichia coli ST761 isolates between animals and humans.

To characterize the relationship of tet(X4)-positive isolates from different hosts and environments. PCR and MALDI-TOF MS were used to identify the tet(X4)-positive isolates. The MICs of 13 antimicrobial agents were determined by broth microdilution. Illumina technology was used to sequence all of the isolates. One isolate was randomly selected from Escherichia coli ST761 clones for long-read sequencing to obtain plasmid sequences. Bioinformatics analysis was used to determine the phylogeny of 46 tet(X4)-positive E. coli ST761 strains. A total of 12 tet(X4)-positive isolates, 8 E. coli and 4 Aeromonas simiae, were obtained from six lairages of a slaughterhouse. These isolates exhibited resistance to at least three classes of antimicrobials, including tigecycline. The majority of them, seven E. coli and three A. simiae, represent separate clonal groups. Notably, the seven E. coli isolates belonged to ST761, a common ST carrying the tet(X4) gene that has been identified in 39 isolates from animals, meat, wastewater and humans from seven Chinese provinces. All 46 tet(X4)-positive E. coli ST761 strains from various sources have a close phylogenetic relationship (0-72 SNPs), with a high nucleotide sequence similarity of resistance genes and the tet(X4)-carrying IncX1-IncFIA(HI1)-IncFIB(K) hybrid plasmid, indicating a clonal relationship of tet(X4)-positive E. coli ST761 among animals, food, the environment and humans. The clonal relationship of tet(X4)-positive E. coli ST761 between humans and animals poses a previously underestimated threat to public health. To the best of our knowledge, this is the first description of tet(X4)-positive A. simiae.

Characterization of erm(B)-carrying Campylobacter Spp. of retail chicken meat origin

The erm(B) gene in Campylobacter Spp., conferring resistance to macrolides, is of great concern worldwide. In this study, the prevalence of erm(B) in Campylobacter of retail chicken meat origin was investigated and the characterization of erm(B)-harboring Campylobacter isolates was analyzed. Antimicrobial susceptibility testing was performed to determine the susceptibility of Campylobacter isolates. Whole-genome sequencing and analysis were used to characterize sequence type (ST) and genetic context of erm(B). Natural transformation was conducted to evaluate transferability of the erm(B) gene. A total of 16 (11.8%) Campylobacter isolates were obtained from 136 samples collected from retail chicken meat, amongst which five erm(B)-positive isolates were identified as Campylobacter coli belonging to ST3753 (n=4) and ST825 (n=1). A total of 22 Campylobacter Spp. were erm(B)-positive in GenBank database; all isolates were collected in China except for one Campylobacter jejuni isolate. Diverse STs were involved in these erm(B)-carrying isolates. Comparison analysis indicated that 11 types of genetic environment for erm(B) were identified, mostly associated with multidrug-resistance genomic islands (MDRGIs). The genetic context of erm(B) in C. coli of retail chicken meat origin showed high nucleotide sequence similarity with that of C. coli from humans. This is the first report of prevalence and characterization for erm(B) in Campylobacter of retail chicken meat origin. The genetic context of erm(B) in C. coli isolates from retail chicken meat is highly homologous with that of C. coli from humans; this impies the possibility of zoonotic transmission of erm(B) in Campylobacter, which presents a threat to public health.

Analysis of Nucleotide Sequences Similarity and Protein Prediction of Some Resistance Genes in Escherichia coli Isolated from Iraqi Patients with Urinary Tract Infections.

Antibiotic resistance leads to a dramatic increase in the morbidity and mortality caused by infectious diseases. Even though estimates vary widely, the economic cost of antimicrobial-resistantbacteria is on a rise. The current aimed to identify the antimicrobial resistance of Escherichia coli (E. coli). In fact, this study focused on the recent deep-learning methods (sequencing) to investigate E. coli antibiotic resistance and their protein sequences. To evaluate antibiotic resistance, the sequencing method could be considered the method of choice. The E. coli was identified by either specific biochemical tests or polymerase chain reaction (PCR) using the 16S rRNA gene. The results of aadA1 gene sequences demonstrated 10 nucleic acid substitutions throughout, as compared to the reference NCBI database (MG385063). Out of the 10 nucleic acid substitutions, 9 missense effects were observed. While the dfrA1 gene sequences illustrated 20 nucleic acid substitutions throughout, compared to the reference NCBI database (KY706080), out of the 20 nucleic acid substitutions, 8 missense effects were observed. Furthermore, the sul1 gene sequences displayed 20 nucleic acid substitutions throughout, in comparison with the reference NCBI database (CP069561), and out of the 20 nucleic acid substitutions, 12 missense effects were detected. The cat1 gene sequences showed 14 nucleic acid substitutions throughout, compared to the reference NCBI database (NC017660), and out of the 14 nucleic acid substitutions, 8 missense effects were observed. The precise point (Missense) mutation in four genes (aadA1, dfrA1, sul1, and cat1) in the expected sequence is interpreted to be the target site of a site-specific recombination mechanism that led to antibiotics resistance in E. coli isolates.

Occurrence and Molecular Phylogeny of Economically Relevant Viruses Infecting Honey Bees (Apis mellifera L.) of Bingöl Province, Turkey

Abstract In this study, we conducted a six-month survey to evaluate the current status of three common honey bee viruses (black queen cell virus [BQCV], acute bee paralysis virus [ABPV], and sacbrood virus [SBV]) in Turkey’s Bingöl region and revealed their phylogenetic relationships with the same types of viruses in other parts of the world. We randomly sampled 384 worker honey bees from a total of 128 apiaries from different locations of this region. Molecular tests confirmed the presence of SBV and BQCV, with infection rates of 7.03% and 11.7%, respectively, but ABPV could not be detected in any of the surveyed apiaries. In addition, double infection was detected in an apiary with an infection rate of 0.78%. The sequences of a partial polyprotein gene region of a randomly selected isolate from each detected virus were collected and registered in GenBank under the accession numbers MZ357971 and MZ357972 for SBV and MZ357974 for BQCV. The nucleotide sequence similarity of Turkish BQCV and SBV isolates was 75.71–96.58% and 85.96–92.98%, respectively. A comparison of the phylogenetic tree of Bingöl honey bee viral genomes with other isolates from around the world revealed that Bingöl SBV isolates were closely related to another Turkey isolate while Bingöl BQCV isolate to France, Italy, Australia, and Brazil isolates. To our knowledge, the presence and phylogenetic affinity of SBV and BQCV viruses detected in the present study is the first recording for Turkey’s Bingöl province.

Whole-Genome Analysis Reveals That Bacteriophages Promote Environmental Adaptation of Staphylococcus aureus via Gene Exchange, Acquisition, and Loss.

The study of bacteriophages is experiencing a resurgence owing to their antibacterial efficacy, lack of side effects, and low production cost. Nonetheless, the interactions between Staphylococcus aureus bacteriophages and their hosts remain unexplored. In this study, whole-genome sequences of 188 S. aureus bacteriophages—20 Podoviridae, 56 Herelleviridae, and 112 Siphoviridae—were obtained from the National Center for Biotechnology Information (NCBI, USA) genome database. A phylogenetic tree was constructed to estimate their genetic relatedness using single-nucleotide polymorphism analysis. Comparative analysis was performed to investigate the structural diversity and ortholog groups in the subdividing clusters. Mosaic structures and gene content were compared in relation to phylogeny. Phylogenetic analysis revealed that the bacteriophages could be distinguished into three lineages (I–III), including nine subdividing clusters and seven singletons. The subdividing clusters shared similar mosaic structures and core ortholog clusters, including the genes involved in bacteriophage morphogenesis and DNA packaging. Notably, several functional modules of bacteriophages 187 and 2368A shared more than 95% nucleotide sequence identity with prophages in the S. aureus strain RJ1267 and the Staphylococcus pseudintermedius strain SP_11306_4, whereas other modules exhibited little nucleotide sequence similarity. Moreover, the cluster phages shared similar types of holins, lysins, and DNA packaging genes and harbored diverse genes associated with DNA replication and virulence. The data suggested that the genetic diversity of S. aureus bacteriophages was likely due to gene replacement, acquisition, and loss among staphylococcal phages, which may have crossed species barriers. Moreover, frequent module exchanges likely occurred exclusively among the subdividing cluster phages. We hypothesize that during evolution, the S. aureus phages enhanced their DNA replication in host cells and the adaptive environment of their host.

The membrane associated NAC transcription factors ANAC060 and ANAC040 are functionally redundant in the inhibition of seed dormancy in Arabidopsis thaliana.

The NAC family of transcription factors is involved in plant development and various biotic and abiotic stresses. The Arabidopsis thaliana ANAC genes ANAC060, ANAC040, and ANAC089 are highly homologous based on protein and nucleotide sequence similarity. These three genes are predicted to be membrane bound transcription factors (MTFs) containing a conserved NAC domain, but divergent C-terminal regions. The anac060 mutant shows increased dormancy when compared with the wild type. Mutations in ANAC040 lead to higher seed germination under salt stress, and a premature stop codon in ANAC089 Cvi allele results in seeds exhibiting insensitivity to high concentrations of fructose. Thus, these three homologous MTFs confer distinct functions, although all related to germination. To investigate whether the differences in function are caused by a differential spatial or temporal regulation, or by differences in the coding sequence (CDS), we performed swapping experiments in which the promoter and CDS of the three MTFs were exchanged. Seed dormancy and salt and fructose sensitivity analyses of transgenic swapping lines in mutant backgrounds showed that there is functional redundancy between ANAC060 and ANAC040, but not between ANAC060 and ANAC089.

Detection and phylogenetic analysis of carp edema virus in common carp (Cyprinus Carpio) in Iran; 2020–2021

Carp edema virus (CEV), a member of the family Poxviridae, is the etiologic agent of carp edema virus disease, also known as the koi sleepy disease (KSD). The disease is important across the world because it increases mortality rates in common carp and koi carp. From autumn 2020 to spring 2021, gills and internal organs were collected from suspected common carps cultured in twenty Iranian farms in Khuzestan, Gilan, and Mazandaran provinces. The presence of CEV was confirmed by molecular diagnosis. PCR was performed using specific primers to amplify the p4a gene, and positive samples were subsequently sequenced. Phylogenetic analysis assigned them to CEV genogroup I, and they shared high nucleotide sequence similarity with CEVs from Italy, Hungary, Iraq, Poland, the United States, and the Czech Republic. The results confirmed the presence of CEV in Iranian freshwater aquaculture after five years of observing clinical symptoms strongly reminiscent of CEV disease. The results also warned of the spread of the virus throughout the continent and point to the need to implement restrictions on the fish trade. Further studies are needed to determine the full-genome sequences of circulating viruses in order to provide insights into the epidemiology of fish viruses in Iran and the region.

Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family.

In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host–pathogen pairs were derived from the same sampling location—the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4–25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.

Molecular Characterization and Pathogenesis of H6N6 Low Pathogenic Avian Influenza Viruses Isolated from Mallard Ducks (Anas platyrhynchos) in South Korea.

The subtype H6N6 has been identified worldwide following the increasing frequency of avian influenza viruses (AIVs). These AIVs also have the ability to bind to human-like receptors, thereby increasing the risk of animal-human transmission. In September 2019, an H6N6 avian influenza virus—KNU2019-48 (A/Mallard (Anas platyrhynchos)/South Korea/KNU 2019-48/2019(H6N6))—was isolated from Anas platyrhynchos in South Korea. Phylogenetic analysis results revealed that the hemagglutinin (HA) gene of this strain belongs to the Korean lineage, whereas the neuraminidase (NA) and polymerase basic protein 1 (PB1) genes belong to the Chinese lineage. Outstanding internal proteins such as PB2, polymerase acidic protein, nucleoprotein, matrix protein, and non-structural protein belong to the Vietnamese lineage. Additionally, a monobasic amino acid (PRIETR↓GLF) at the HA cleavage site; non-deletion of the stalk region (residue 59–69) in the NA gene; and E627 in the PB2 gene indicate that the KNU2019-48 isolate is a typical low-pathogenic avian influenza (LPAI) virus. The nucleotide sequence similarity analysis of HA revealed that the highest homology (97.18%) of this isolate is to that of A/duck/Jiangxi/01.14 NCJD125-P/2015(H6N6), and the amino acid sequence of NA (97.38%) is closely related to that of A/duck/Fujian/10.11_FZHX1045-C/2016 (H6N6). An in vitro analysis of the KNU2019-48 virus shows a virus titer of not more than 2.8 Log10 TCID 50/mL until 72 h post-infection, whereas in the lungs, the virus is detected at 3 dpi (days post-infection). The isolated KNU2019-48 (H6N6) strain is the first reported AIV in Korea, and the H6 subtype virus has co-circulated in China, Vietnam, and Korea for half a decade. Overall, our study demonstrates that Korean H6N6 strain PB1-S375N, PA-A404S, and S409N mutations are infectious in humans and might contribute to the enhanced pathogenicity of this strain. Therefore, we emphasize the importance of continuous and intensive surveillance of the H6N6 virus not only in Korea but also worldwide.

Molecular characterization of a novel Conyza canadensis-infecting begomovirus in China

A novel monopartite begomovirus was found in naturally infected Conyza canadensis plants exhibiting typical begomovirus-induced yellow vein symptoms in Yunnan Province of China. Analysis of two obtained full-length viral genome sequences showed that they shared 99.8% nucleotide (nt) sequence similarity, and both consisted of 2733 nts (GenBank accession no. OK120264 and OK120266, respectively). Further analysis showed that these two sequences shared the highest nt sequence similarity (78.9%) with tomato yellow leaf curl Vietnam virus (TYLCVV) (EU189150). In the assayed C. canadensis plants, a betasatellite of 1,341 nts (Accession no. OK120265 and OK120267, respectively) was also found, and it shared 98.1% sequence similarity with malvastrum yellow vein betasatellite (MaYVB) (JX679254). Based on the current classification criteria for begomoviruses, we consider that the two obtained viral isolates are a novel begomovirus, and named it as conyza yellow vein virus (CoYVV). Our further analysis result showed that CoYVV is likely originated from a recombination event between tomato yellow leaf curl Yunnan virus (TYLCYnV) and tomato yellow leaf curl China virus (TYLCCNV). To investigate the effect of CoYVV infection in plant, we constructed two infectious clones (i.e., pCoYVV and pMaYVB), and inoculated them individually or together to Nicotiana benthamiana plants through agro-infiltration. The result showed that the plants co-inoculated with CoYVV and MaYVB developed yellow vein and downward leaf-curling symptoms, whereas the plants inoculated with CoYVV alone showed no clear virus-like symptoms. Virus infection in the inoculated N. benthamiana plants was confirmed through polymerase chain reaction (PCR). The result of quantitative PCR (qPCR) showed that in the presence of MaYVB, the accumulation level of CoYVV DNA was significantly increased compared to that in the plants infected with CoYVV alone.

POLYPHASIC TAXONOMY ANALYSE OF COMAMONAS TESTOSTERONІ RESISTANT ТО HEXACHLOROBENZENE

Based on the analysing phenotypic and genotypic properties, the taxonomic position of isolates # 46 and # 47 was established and assigned to the species Comamonas testosteronі UCM B-400 and UCM B-401. Isolates were selected from the soil with organochlorine wastes landfill of chemical enterprises in Kalush, Ivano-Frankivsk region, Ukraine. The strains are resistant to high hexachlorobenzene concentrations. According to morphological, cultural and biochemical properties, the studied strains are related to typical members of the Comamonadaceae family, they are motile gram-negative rods, aerobic, chemoorganotrophic. Saturated and unsaturated fatty acids with a carbon chain length from C10 to C18 were found in composition of cellular lipids. The qualitative and quantitative composition of marker hydroxy acids, namely: 2 hydroxyhexadecane (C16: 0 2OH) and 3 hydroxydecane (C10: 0 3OH) in the lipids of the strains ranged from 2-5%, which corresponded to their content in the representatives of the Comamonas genus. Phylogenetic analysing the nucleotide sequences of the 16S rRNA gene revealed the affinity of isolates # 46 (97.77%) and # 47 (98.05%) with a similar nucleotide sequence of a typical strain of Comamonas testosteroni LMG 1800. The 16S rRNA nucleotide sequences of Comamonas testosteroni UCM B-400 and UCM B-401 were placed in GenBank under the numbers SUB9376895 Comamonas_testosteroni_46 MW861636 and SUB9376895 Comamonas_testosteroni_47 MW861637.

Incidence and Distribution of Barley yellow dwarf virus Infecting Oats in Korea

A survey of Barley yellow dwarf virus (BYDV) was conducted in major oat-growing areas of Korea in 2020. BYDV is an economically important pathogen of cereal crops that can be transmitted by aphids. The present study evaluated the genetic composition of BYDV in oat from eight geographical areas in Korea. Multiplex reverse transcription-polymerase chain reaction was used to screen 322 oat leaf samples for six BYDV strains (PAV, MAV, SGV, PAS, RPV, and RMV). The 125 samples (~39%) tested positive for BYDV. BYDV-PAV, BYDV-SGV, BYDV-PAS, and BYDV-RPV were detected from oat in different areas. Most of the BYDV-infected samples were assigned to subgroup I (n=112). The results indicate that BYDV-PAV could be dominant throughout Korea. Also, the phylogenetic analysis of coat protein sequences indicated that 23 BYDV isolates from Korea could be separated into two clades, which exhibited high nucleotide sequence similarity. In conclusion, the present survey provides a BYDV infection assessment for domestic oat varieties in Korea and basic information for the development of BYDV control measures in Korea’s oat industry.

Molecular characterization and phylogenetic analysis of acute bee paralysis virus collected from some important beekeeping provinces of Iran

Viruses are the most infectious agents in honey bees (Apis mellifera L.). Acute bee paralysis virus (ABPV) is one of the honey bee viruses. ABPV is a small single-stranded RNA virus. The aim of this study is molecular detection of the aforementioned viruses and phylogenetic analysis of ABPV in Iran. Samples were taken from 89 suspected apiaries of four important beekeeping provinces (Mazandaran, Khorasan Razavi, Hormozgan, and Kurdistan). ABPV was detected in the samples with RT-PCR and sequencing was confirmed for all positive samples. In this research, we studied the phylogenetic analysis of ABPV. Nucleotide sequence analyses were used to identify ABPV and phylogenetic analysis was 94.5% to 98.9% identical to the reference strains. IR-APV-GMG-1 and IR-APV-GMG-3 showed maximum nucleotide sequence similarity to Hungary 1 (accession number: AF486072) from Hungary, but IR-APV-GMG-2 had no similarity to reference strains, forming a distinct group. The phylogenetic tree for the molecular relationship between the above viruses was drawn. This study of the phylogenetic analysis of ABPV indicates the presence of this virus and reveals its similarity to European-origin-related viruses.

RECOMBINANT ANTIBODY PRODUCTION BY CLONING OF Pepper yellow leaf curl Indonesia virus (PepYLCIV) COAT PROTEIN GENE

Pepper yellow leaf curl Indonesia virus (PepYLCIV) is an important pathogen on chili cultivation and is transmitted through the seed. Serological tests are sensitive, accurate, efficient and it has been widely used for the detection of seed-transmitted plant viruses. This study aimed to produce PepYLCIV recombinant protein as a material to produce recombinant antibodies PepYLCIV. DNA was extracted from infected chili leaves collected from Congkrang, Muntilan, Central Java verified using primer PepYLCIV-BamHI and PepYLCIV-EcoRI and produced an amplicon at 840 bp. The amplified fragments were cloned into the pET32a then transformed to Escherichia coli BL21. The percentage of nucleotide sequence identity and sequence of amino acid, PepYLCIV CK-6 isolates had the highest similarity of nucleotide and amino acid sequences to of chili isolates from Bandung. The expressed recombinant protein was obtained with IPTG concentration 0,5 mM and harvested at 6 hours after IPTG induction. SDS PAGE analysis of the recombinant plasmid Begomovirus CK-6 showed that the coat protein size was about 29 kDa. Immunization was carried out on rabbits by injecting 150 µg of recombinant protein 4 times with an interval of 1 week to produce crude antiserum and pure antiserum capable of detecting PepYLCIV in chili and Ageratum conyzoides using I-ELISA and DIBA tests.

Outbreak of neuropathogenic equid herpesvirus 1 causing abortions in Yili horses of Zhaosu, North Xinjiang, China

BackgroundEHV-1 is one of the most serious viral pathogens that frequently cause abortion in horses around the world. However, so far, relatively little information is available on EHV-1 infections as they occur in China. In January 2021, during an abortion storm which occurred in Yili horses at the Chinese State Studs of Zhaosu (North Xinjiang, China), 43 out of 800 pregnant mares aborted.ResultsPCR detection revealed the presence of EHV-1 in all samples as the possible cause of all abortions, although EHV-4, EHV-2 and EHV-5 were also found to circulate in the aborted fetuses. Furthermore, the partial ORF33 sequences of the 43 EHV-1 shared 99.3–100% and 99.0–100% similarity in nucleotide and amino acid sequences respectively. These sequences not only indicated a highly conserved region but also allowed the strains to group into six clusters. In addition, based on the predicted ORF30 nucleotide sequence, it was found that all the strains carried a guanine at the 2254 nucleotide position (aspartic acid at position 752 of the viral DNA polymerase) and were, therefore, identified as neuropathogenic strains.ConclusionThis study is the first one that establishes EHV-1 as the cause of abortions in Yili horses, of China. Further characterization of the ORF30 sequences revealed that all the EHV-1 strains from the study carried the neuropathogenic genotype. Totally, neuropathogenic EHV-1 infection in China’s horse population should be concerned although the virus only detected in Yili horse abortions.

First isolation and genomic characterization of bovine parechovirus from faecal samples of cattle in Japan

A novel picornavirus was isolated from the faeces of a diarrhoeic cow using MA-104 cells at the third blind passage. This virus, named Den1/2021/JPN, was completely sequenced using total RNA from the cell culture supernatant by deep sequencing. The genome of Den1/2021/JPN had a standard picornavirus genome organisation with conserved picornaviral motifs. The 5' untranslated region harboured a type-II internal ribosomal entry site. Den1/2021/JPN was most closely related to a bovine parechovirus (Bo_ParV) named cow/2018/4, which has been recently identified in publicly available databases. Phylogenetic analyses and pairwise sequence comparison revealed that Den1/2021/JPN and Bo_ParV cow/2018/4 clustered with parechoviruses and were most closely related to Parechovirus E identified in birds of prey, exhibiting nucleotide sequence similarity of 64.2-64.5 %, 58.6-59.7 % and 66.3-66.4 % in the polyprotein, P1 and 2C+3 CD coding regions, respectively. This study presents the first report on the isolation of Bo_ParV. Den1/2021/JPN and Bo_ParV cow/2018/4, which are candidates for a novel species in the genus Parechovirus.

Genetic and biological characteristics of species A rotaviruses detected in common shrews suggest a distinct evolutionary trajectory.

Species A rotaviruses (RVAs) are important aetiological agents of severe diarrhoea in young children. They are also widely distributed in mammals and birds, and increasing evidence indicates the possibility of zoonotic transmission of RVA strains between animals and humans. Moreover, reassortment of the eleven segments of the RVA genome can result in rapid biological changes and may influence pathogenic properties. Here, the nearly complete genome of an RVA strain from a common shrew (Sorex araneus) was sequenced, which showed high nucleotide sequence similarity to additionally determined partial sequences from common shrew RVAs but only very low identity (below 68 per cent) to RVAs from other animal species and humans. New genotypes were assigned to most genome segments of the novel common shrew RVA strain KS14/269, resulting in the genome constellation G39-P[55]-I27-R26-C22-M22-A37-N26-T26-E30-H26. Phylogenetic analyses clustered the common shrew RVAs as ancestral branches of other mammalian and avian RVAs for most of the genome segments, which is in contrast to the phylogeny of the hosts. Nevertheless, conserved sequences typical for all RVAs were identified at the 5ʹ- and 3ʹ- non-coding segment termini. To explore whether the common shrew RVA can exchange genetic material with other mammalian RVAs by reassortment, a reverse genetics system based on the simian RVA strain SA11 was used. However, no viable reassortants could be rescued by exchanging the VP4-, VP6-, or VP7-encoding genome segment alone or in combinations. It can be concluded that highly divergent RVAs are present in common shrews, indicating an evolution of these viruses largely separated from other mammalian and avian RVAs. The zoonotic potential of the virus seems to be low but needs to be further analysed in future.

Rabies outbreak in black-backed jackals (Canis mesomelas), South Africa, 2016

Rabies, a fatal and vaccine-preventable disease, is endemic throughout Africa. In 2016, a rabies outbreak occurred in black-backed jackals (Canis mesomelas) along the western boundary of Gauteng Province, South Africa. We investigated the possible drivers of the 2016 outbreak and established its origin. Using spatio-temporal locations of cases, we applied logistic regression and Geographic Information System techniques to investigate environmental covariates driving occurrences of emerging rabies cases in Gauteng Province. About 53.8% of laboratory-confirmed lyssaviruses in Gauteng Province in 2016 originated from jackals. Phylogenetic trees reconstructed from a partial region of the glycoprotein gene of these and historical rabies viruses (RABVs) demonstrated the lyssaviruses to be of canid origin with 97.7% nucleotide sequence similarity. The major cluster comprised jackal RABVs from the 2012 KwaZulu/Natal outbreak and the 2016 outbreak in Gauteng Province. The second cluster was composed of both jackal and dog RABVs. Both clusters correlated with independent RABV introductions into Gauteng by dogs and jackals, respectively. This study demonstrated an expansion of a jackal rabies cycle from north-west Province into Gauteng Province during the 2016 dry period, as jackals ranged widely in search for food resources leading to increased jackal-dog interactions, reminiscent of the intricate links of domestic and wildlife rabies cycles in South Africa.