scholarly journals Molecular detection of dugbe orthonairovirus in cattle and their infesting ticks (Amblyomma and Rhipicephalus (Boophilus)) in Nigeria

2021 ◽  
Vol 15 (11) ◽  
pp. e0009905
Author(s):  
Oluwafemi Babatunde Daodu ◽  
Albert Eisenbarth ◽  
Ansgar Schulz ◽  
Julia Hartlaub ◽  
James Olukayode Olopade ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Local Government ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Prototype Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Similarity ◽  
North Central ◽  
Tick Burden

Dugbe orthonairovirus (DUGV), a tick-borne zoonotic arbovirus, was first isolated in 1964 in Nigeria. For over four decades, no active surveillance was conducted to monitor the spread and genetic variation of DUGV. This study detected and genetically characterized DUGV circulating in cattle and their infesting ticks (Amblyomma and Rhipicephalus (Boophilus)) in Kwara State, North-Central Nigeria. Blood and or ticks were collected from 1051 cattle at 31 sampling sites (abattoirs and farms) across 10 local government areas of the State. DUGV detection was carried out by RT-qPCR, and positive samples sequenced and phylogenetically analysed. A total of 11824 ticks, mostly A. variegatum (36.0%) and R. (B.) microplus (63.9%), were obtained with mean tick burden of 12 ticks/cattle. Thirty-four (32 A. variegatum and two R. (B.) microplus) of 4644 examined ticks were DUGV-positive, whereas all of the cattle sera tested negative for DUGV genome. Whole genome sequence (S, M and L segments) and phylogenetic analyses indicate that the positive samples shared up to 99.88% nucleotide identity with and clustered around the Nigerian DUGV prototype strain IbAr 1792. Hence, DUGV with high similarity to the previously characterised strain has been detected in Nigeria. To our knowledge, this is the first report of DUGV in North-Central Nigeria and the most recent information after its last surveillance in 1974.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

scholarly journals A multisite genomic epidemiology study of Clostridioides difficile infections in the U.S. supports differential roles of healthcare versus community spread for two common strains

2020 ◽  
Author(s):  
Arianna Miles-Jay ◽  
Vincent B. Young ◽  
Eric G. Pamer ◽  
Tor C. Savidge ◽  
Mini Kamboj ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Clinical Care ◽  
Whole Genome Sequence ◽  
P Value ◽  
Whole Genome ◽  
Epidemiology Study ◽  
Genomic Epidemiology ◽  
Clostridioides Difficile ◽  
Healthcare Associated ◽  
The U.S

ABSTRACTClostridioides difficile is the leading cause of healthcare-associated infectious diarrhea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare transmission, and that the primary sites of C. difficile transmission may be strain dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs. community spread for two of the most common C. difficile strains in the U.S.: sequence type (ST) 1 (associated with Ribotype 027) and ST2 (associated with Ribotype 014/020). Isolates recovered from stool specimens collected during standard clinical care at three geographically distinct U.S. medical centers between 2010 and 2018 underwent whole genome sequencing and phylogenetic analyses. ST1 and ST2 isolates both displayed some evidence of phylogenetic clustering by study site, but clustering was stronger and more apparent in ST1, consistent with our healthcare-based study more comprehensively sampling local transmission of ST1 compared to ST2 strains. Analyses of pairwise single nucleotide variant (SNV) distance distributions were also consistent with more evidence of healthcare transmission of ST1 compared to ST2, with 44% of ST1 isolates being within 2 SNVs of another isolate from the same geographic collection site compared to 5.5% of ST2 isolates (p-value = <0.001). Conversely, ST2 isolates were more likely to have close genetic neighbors across disparate geographic sites compared to ST1 isolates, further supporting non-healthcare routes of spread for ST2 and highlighting the potential for misattributing genomic similarity among ST2 isolates to recent healthcare transmission. Finally, we estimated a lower evolutionary rate for the ST2 lineage compared to the ST1 lineage using Bayesian timed phylogenomic analyses, and hypothesize that this may contribute to observed differences in geographic concordance among closely related isolates. Together, these findings suggest that ST1 and ST2, while both common causes of C. difficile infection in hospitals, show differential reliance on community and hospital spread. This conclusion supports the need for strain-specific criteria for interpreting genomic linkages and emphasizes the importance of considering differences in the epidemiology of circulating strains when devising interventions to reduce the burden of C. difficile infections.DATA SUMMARYAll whole genome sequence data was uploaded to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under Bioproject accessions PRJNA595724, PRJNA561087, and PRJNA594943. Metadata that comply with patient privacy rules are included in the Supplementary Materials.

scholarly journals Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

2019 ◽  
Author(s):  
Xin Zhou ◽  
Lu Zhang ◽  
Ziming Weng ◽  
David L. Dill ◽  
Arend Sidow
Keyword(s):  
Genetic Variation ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Sequence Data ◽  
Association Studies ◽  
Cost Effective ◽  
Whole Genome Sequence ◽  
Personal Genome ◽  
Whole Genome ◽  
Nucleotide Polymorphisms

AbstractVariant discovery in personal, whole genome sequence data is critical for uncovering the genetic contributions to health and disease. We introduce a new approach, Aquila, that uses linked-read data for generating a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. Assemblies cover >95% of the human reference genome, with over 98% in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased VCF file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective evolution of whole-genome reconstruction that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.

scholarly journals Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

2019 ◽  
Author(s):  
Paul J. Galewski ◽  
J. Mitchell McGrath
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
Demographic History ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Crop Type ◽  
Crop Types ◽  
Well Differentiated

Abstract Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet). Crop improvement and management activities are segregated by crop type, preserving unique genome diversity and differentiation, with occasional introgressions between diverged lineages for specific traits. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including table, leaf (chard), fodder, and sugar beet. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between populations based on identity-by-state and shared genetic variation among lineages. Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history inferences for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between the table and chard groups, perhaps the result of less intensive selection for their end use.

scholarly journals Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

2020 ◽  
Author(s):  
Paul J. Galewski(New Corresponding Author) ◽  
J. Mitchell McGrath(Former Corresponding Author)
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
Demographic History ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Crop Type ◽  
Crop Types ◽  
Well Differentiated

Abstract Background: Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and organization. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including the familiar table, leaf (chard), fodder, and sugar beet crop types. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between accessions based on identity-by-state metrics and shared genetic variation among lineages. Results: Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. Conclusions: A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between table and sugar groups, perhaps the result of less intensive selection for end use.

scholarly journals Whole Genome and Phenotypic Characterization of Novel QnrB19-positive Salmonella Nigeria serovars from Food Animals in Ilorin, North-central, Nigeria.

2021 ◽  
Author(s):  
Ibrahim Adisa Raufu ◽  
Olayiwola Akeem Ahmed ◽  
Abdulfatai Aremu ◽  
Jessica C Chen ◽  
James A Ameh ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Antimicrobial Agents ◽  
Farm Animals ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Whole Genome ◽  
Single Mutation ◽  
North Central ◽  
Phenotypic Resistance ◽  
Food Animals

Abstract Background: Non-typhoidal Salmonella are major foodborne pathogens, posing serious challenges to public health and food safety worldwide. Salmonellosis in humans is commonly associated with the consumption of contaminated food, water, and direct contact with infected animals. This study aimed to characterize the distribution, diversity, virulence genotypes and antibiotic resistance of Salmonella enterica subsp. enterica serovar Nigeria, isolated from farm animals in north central Nigeria.Results: We recovered 9 different S. enterica ser. Nigeria isolates from our sampling, eight from pig and one from chicken. The antimicrobial susceptibility testing against 15 antimicrobial agents showed variable resistance profiles. Whole genome sequence (WGS) analysis revealed that all 9 isolates contained a single mutation parC (T57S) substitution in addition to qnrB19, expected to confer decreased susceptibility to ciprofloxacin and tet(A) expected to confer resistance to tetracycline. Furthermore, two plasmid targets were also detected in all the strains, Col(pHAD28) and IncQ1. MLST analysis showed that all 9 isolates exhibited only one sequence type, (ST-4911) irrespective of the source of isolation. A SNP-based phylogeny indicates that the 9 isolates are highly related and lack other close relatives in the pathogen detection database.Forty core (housekeeping) and accessory virulence genes were identified from different virulence loci including Salmonella Pathogenicity Islands, virulence associated plasmids (pSV), chromosomes and fimbriae. Conclusion: This study provided valuable information on the resistance determinants, virulence genes, phenotypic resistance profiles, plasmids and multilocus sequence typing (MLST) of Salmonella Nigeria from food animals by WGS. Highlighting the significance of poultry and pig to the spread and emergence of Salmonella Nigeria in this region of Nigeria, therefore, there is the need for consumer's education and enlightenments on the importance of proper handling and preparation of food, this will reduce the potential risk of transmission of this pathogen.

scholarly journals Molecular Characteristics of Human Adenovirus Type 3 Circulating in Parts of China During 2014–2018

2021 ◽  
Vol 12 ◽  
Author(s):  
Yali Duan ◽  
Baoping Xu ◽  
Changchong Li ◽  
Yixiao Bao ◽  
Shuhua An ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Phylogenetic Analyses ◽  
Hypervariable Region ◽  
Human Adenovirus ◽  
Adenovirus Type ◽  
Prototype Strain ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Penton Base ◽  
Type 3

Human adenoviruses (HAdVs) are important pathogens causing respiratory infections; 3.5–11% of childhood community-acquired pneumonia is associated with HAdV infection. Human adenovirus type 3 (HAdV-3), leading to severe morbidity and mortality, is one of the most prevalent genotype among adenoviruses responsible for acute respiratory infections (ARIs) in children in China. To identify the genetic variation of HAdV-3 in children with ARIs in China, a molecular epidemiological study was conducted. A total of 54 HAdV-3 isolated strains were obtained from children with ARIs in Beijing, Wenzhou, Shanghai, Shijiazhuang, Hangzhou, Guangzhou, and Changchun from 2014 to 2018. Thirty-two strains of which were selected for whole-genome sequencing, while the hexon, penton base, and fiber genes were sequenced for remaining strains. Bioinformatics analysis was performed on the obtained sequences. The phylogenetic analyses based on whole-genome sequences, major capsid protein genes (hexon, penton base, and fiber), and early genes (E1, E2, E3, and E4) showed that the HAdV-3 strains obtained in this study always clustered together with the reference strains from Chinese mainland, while the HAdV-3 prototype strain formed a cluster independently. Compared with the prototype strain, all strains possessed nine amino acid (AA) substitutions at neutralization antigenic epitopes of hexon. The homology models of the hexon protein of the HAdV-3 prototype and strain BJ20160214 showed that there was no evident structural change at the AA mutation sites. Two AA substitutions were found at the Arg-Gly-Asp (RGD) loop and hypervariable region 1 (HVR1) region of the penton base. A distinct AA insertion (20P) in the highly conserved PPPSY motif of the penton base that had never been reported before was observed. Recombination analysis indicated that partial regions of protein IIIa precursor, penton base, and protein VII precursor genes among all HAdV-3 strains in this study were from HAdV-7. This study showed that the genomes of the HAdV-3 strains in China were highly homologous. Some AA mutations were found at antigenic sites; however, the significance needs further study. Our data demonstrated the molecular characteristics of HAdV-3 circulating in China and was highly beneficial for further epidemiological exploration and the development of vaccines and drugs against HAdV-3.

Chachezhania sediminis sp. nov., isolated from marine sediment

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Jihye Baek ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung-Sook Lee ◽  
Ampaitip Sukhoom ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The Republic

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain (CAU 1508T) was isolated from marine sediment collected in the Republic of Korea. Growth was observed at 10–45 °C (optimum, 30 °C), pH 4.0–11.0 (optimum, pH 6.0–8.0) and with 0–8.0 % (w/v) NaCl (optimum, 2–4 %). The isolate formed a monophyletic clade in the phylogenetic analyses using 16S rRNA gene and whole-genome sequences, exhibiting the highest similarity to Chachezhania antarctica SM1703T (96.5 %), and representing a distinct branch within the genus Chachezhania (family Rhodobacteraceae ). Its whole genome sequence was 5.59 Mb long, with a G+C content of 65.7 mol% and 2183 predicted genes belonging to six functional categories. The average nucleotide identity and digital DNA–DNA hybridization values between CAU 1508T and C. antarctica SM1703T were 79.1 and 22.2 %, respectively. The predominant cellular fatty acids were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two unidentified phospholipids and one unidentified aminophospholipid. The sole isoprenoid quinone was ubiquinone 10. Phenotypic phylogenetic properties supported the classification of CAU 1508T as representing a novel species of the genus Chachezhania , with the proposed name Chachezhania sediminis sp. nov. The type strain is CAU 1508T (=KCTC 62999T=NBRC 113697T).

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