scholarly journals A36 Analysis of CHIKV evolution during the Caribbean outbreak, 2013–5, using complete genome sequences

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
T E Hoornweg ◽  
H Vennema ◽  
J H J Reimerink
Keyword(s):  
Amino Acid ◽  
High Speed ◽  
Reference Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Chikungunya Fever ◽  
Caribbean Islands ◽  
The Caribbean ◽  
Dutch Caribbean

Abstract Chikungunya virus (CHIKV) is a re-emerging, mosquito-borne alphavirus that causes chikungunya fever, a febrile illness characterized by severe acute and persistent arthralgia. At the end of 2013, autochthonous CHIKV transmission was detected for the first time in the Americas, on the Caribbean island of Saint Martin. Subsequently, CHIKV rapidly spread through the Caribbean Islands and onto the American mainland, causing millions of cases of chikungunya fever. During the outbreak, the Dutch National Institute of Health performed diagnostics on patient samples originating from the six Caribbean islands that belong to the Kingdom of the Netherlands. Using a subset of PCR-positive patient samples, we aimed to retrospectively analyze the 2013–5 CHIKV outbreak on the Dutch Caribbean islands using whole-genome sequences. Twenty-five CHIKV-positive sera were selected for next-generation sequencing based on viral load, location, and date of sampling. Sera were subjected to high speed centrifugation, filtration, and nuclease treatment to reduce the amount of background sequences from human and bacterial origin. Total RNA was extracted, primed with random nanomers for reverse transcription, after which dsDNA was produced and purified. Libraries were created using Nextera XT library preparation kit, and samples were run on a MiSeq desktop sequencer. Reads were trimmed and mapped to a reference sequence using the CLC Genomics workbench. To date, eight full-genome sequences were obtained, originating from four different islands and dating from the start of the outbreak (December 2013) to April 2015, when the outbreak was waning. High similarity (>99%) between sequences was found; nevertheless, all genome sequences were unique with a minimum of three SNPs differentiating one sequence from another. Thirty-three unique single nucleotide polymorphisms (SNPs) were identified, of which 29 were located in the coding regions of the genome. Eight SNPs were informative, and ten SNPs led to amino acid changes. Of the amino acid changes, nine were located in the non-structural proteins (1× nsP1, 5× nsP2, and 3× nsP3), and one was located in E2. In conclusion, we report the first whole-genome sequences of CHIKV isolates from the 2013 to 2015 outbreak that originated from the Dutch Caribbean islands. Sequencing of the remaining samples is still in progress.

scholarly journals Chikungunya Fever in Japan Imported from the Caribbean Islands

2016 ◽  
Vol 69 (2) ◽  
pp. 151-153 ◽  
Author(s):  
Kazuo Imai ◽  
Eri Nakayama ◽  
Takuya Maeda ◽  
Kei Mikita ◽  
Yukiko Kobayashi ◽  
...  
Keyword(s):  
Chikungunya Fever ◽  
Caribbean Islands ◽  
The Caribbean

scholarly journals Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Sara Jones ◽  
Raji Prasad ◽  
Anjana S. Nair ◽  
Sanjai Dharmaseelan ◽  
Remya Usha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Analysis ◽  
Influenza A ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
H1n1 Pandemic ◽  
Genome Sequences ◽  
Influenza A H1n1 ◽  
Virus Isolates ◽  
New Mutations

ABSTRACT We report here the whole-genome sequence of six clinical isolates of influenza A(H1N1)pdm09, isolated from Kerala, India. Amino acid analysis of all gene segments from the A(H1N1)pdm09 isolates obtained in 2014 and 2015 identified several new mutations compared to the 2009 A(H1N1) pandemic strain.

scholarly journals Whole-Genome Sequences of Six Listeria monocytogenes Strains Isolated from Food

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Jule Anna Horlbog ◽  
Hyein Jang ◽  
Gopal Gopinath ◽  
Roger Stephan ◽  
Claudia Guldimann
Keyword(s):  
Listeria Monocytogenes ◽  
Amino Acid ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Milk Products ◽  
Stop Codons

Here, we report the whole-genome sequences of six Listeria monocytogenes strains isolated from meat and milk products in Switzerland. All of these strains carry premature stop codons or amino acid deletions in inlA.

scholarly journals Within-Host Variations of Human Papillomavirus Reveal APOBEC Signature Mutagenesis in the Viral Genome

2018 ◽  
Vol 92 (12) ◽  
pp. e00017-18 ◽  
Author(s):  
Yusuke Hirose ◽  
Mamiko Onuki ◽  
Yuri Tenjimbayashi ◽  
Seiichiro Mori ◽  
Yoshiyuki Ishii ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cervical Cancer ◽  
Deep Sequencing ◽  
Viral Genome ◽  
Reference Sequence ◽  
Characteristic Change ◽  
Whole Genome ◽  
Cervical Carcinogenesis ◽  
Genome Sequences ◽  
Host Genetic

ABSTRACTPersistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied by the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here, we explored within-host genetic diversity of HPV by performing deep-sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52, and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC) and were deep sequenced. After constructing a reference viral genome sequence for each specimen, nucleotide positions showing changes with >0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1,n= 56; CIN2/3,n= 68; ICC,n= 27), with various numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the trinucleotide context encompassing substituted bases revealed that TpCpN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions.IMPORTANCEHPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep-sequencing analyses, we show for the first time a comprehensive snapshot of the within-host genetic diversity of high-risk HPVs during cervical carcinogenesis. Quasispecies harboring minor nucleotide variations in viral whole-genome sequences were extensively observed across different grades of CIN and cervical cancer. Among the within-host variations, C-to-T transitions, a characteristic change mediated by cellular APOBEC cytosine deaminases, were predominantly detected throughout the whole viral genome, most strikingly in low-grade CIN lesions. The results strongly suggest that within-host variations of the HPV genome are primarily generated through the interaction with host cell DNA-editing enzymes and that such within-host variability is an evolutionary source of the genetic diversity of HPVs.

scholarly journals Genetic Determinants of Biofilm Formation and Antibiotic Resistance of Helicobacter Pylori using Whole Genome Sequencing

2021 ◽  
Author(s):  
Kartika Afrida Fauzia ◽  
Hafeza Aftab ◽  
Muhammad Miftahussurur ◽  
Langgeng Agung Waskito ◽  
Vo Phuoc Tuan ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Antibiotic Resistance ◽  
Biofilm Formation ◽  
Cross Sectional Study ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Genome Sequences ◽  
Cross Sectional ◽  
H Pylori

Abstract The nucleotide polymorphisms (SNPs) associated with the biofilm formation phenotype of Helicobacter pylori were investigated. Fifty-six H. pylori isolates from Bangladeshi patients were included in this cross-sectional study. Crystal violet was used to classify the phenotypes into high- and low-biofilm formers. Whole genome sequences were analyzed using the “Antimicrobial Resistance Identification By Assembly” (ARIBA) pipeline. The results indicated 19.6% high- and 81.4% low-biofilm formers. These phenotypes were not related to specific clades in the phylogenetic analysis. Biofilm formation was significantly associated with SNPs of alpA, alpB, cagE, cgt, csd4, csd5, futB, gluP, homD, and murF (P < 0.05). Among the SNPs reported in alpB, strains encoding the N156K, G160S, and A223V mutations were high-biofilm formers. Mutations associated with antibiotic resistance can be detected. This study revealed the potential role of SNPs to biofilm formation, and propose a method to detect mutation in antibiotic resistance and biofilm from whole genome sequences.

scholarly journals Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences

2020 ◽  
Author(s):  
Babatunde Olarenwaju Motayo ◽  
Olukunle Oluwapamilerin Oluwasemowo ◽  
Paul Akiniyi Akinduti ◽  
Babatunde Adebiyi Olusola ◽  
Olumide T Aerege ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Spike Protein ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Amino Acid ◽  
Protein Variant ◽  
Health Crisis ◽  
Most Recent Common Ancestor

ABSTRACTThe ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 × 10−4 high posterior density HPD (4.132 × 10−4 to 4.134 × 10−4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.

scholarly journals Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species

2021 ◽  
Vol 11 ◽  
Author(s):  
Ingrid Hänel ◽  
Eva Müller ◽  
Belén González Santamarina ◽  
Herbert Tomaso ◽  
Helmut Hotzel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Foodborne Pathogens ◽  
Antimicrobial Susceptibility ◽  
Amino Acid Change ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Phenotypic Analysis ◽  
Phenotypic Resistance ◽  
Reference Strains

Aliarcobacter cibarius and Aliarcobacter thereius are two rarely detected Aliarcobacter species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic Campylobacter species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus Aliarcobacter is part of the Campylobacteraceae family and includes the species Aliarcobacter butzleri, Aliarcobacter cryaerophilus, Aliarcobacter skirrowii, and the rarely described Aliarcobacter cibarius, Aliarcobacter faecis, Aliarcobacter lanthieri, Aliarcobacter thereius, and Acrobarter trophiarum. Aliarcobacter are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of Aliarcobacter cibarius and Aliarcobacter thereius. They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted in silico known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In Aliarcobacter butzleri, the nucleotide sequence of the gyrA gene (DQ464331) can show a signature mutation resulting in an amino acid change T85&gt;I. Acrobarter cibarius and Acrobarter thereius showed the same gene as assessed by similarity annotation of the mutations 254C&gt;G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant Aliarcobacter thereius isolate was associated with the amino acid change T85&gt;I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.

scholarly journals Plasmid diversity among genetically related Klebsiella pneumoniae blaKPC-2 and blaKPC-3 isolates collected in the Dutch national surveillance

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Antoni P. A. Hendrickx ◽  
◽  
Fabian Landman ◽  
Angela de Haan ◽  
Dyogo Borst ◽  
...  
Keyword(s):  
The Netherlands ◽  
Klebsiella Pneumoniae ◽  
Antibiotic Resistance Genes ◽  
Transport Systems ◽  
Sequencing Analysis ◽  
Caribbean Islands ◽  
Long Read ◽  
The Caribbean ◽  
Dutch Caribbean ◽  
Generation Sequencing

Abstract Carbapenemase-producing Klebsiella pneumoniae emerged as a nosocomial pathogen causing morbidity and mortality in patients. For infection prevention it is important to track the spread of K. pneumoniae and its plasmids between patients. Therefore, the major aim was to recapitulate the contents and diversity of the plasmids of genetically related K. pneumoniae strains harboring the beta-lactamase gene blaKPC-2 or blaKPC-3 to determine their dissemination in the Netherlands and the former Dutch Caribbean islands from 2014 to 2019. Next-generation sequencing was combined with long-read third-generation sequencing to reconstruct 22 plasmids. wgMLST revealed five genetic clusters comprised of K. pneumoniae blaKPC-2 isolates and four clusters consisted of blaKPC-3 isolates. KpnCluster-019 blaKPC-2 isolates were found both in the Netherlands and the Caribbean islands, while blaKPC-3 cluster isolates only in the Netherlands. Each K. pneumoniae blaKPC-2 or blaKPC-3 cluster was characterized by a distinct resistome and plasmidome. However, the large and medium plasmids contained a variety of antibiotic resistance genes, conjugation machinery, cation transport systems, transposons, toxin/antitoxins, insertion sequences and prophage-related elements. The small plasmids carried genes implicated in virulence. Thus, implementing long-read plasmid sequencing analysis for K. pneumoniae surveillance provided important insights in the transmission of a KpnCluster-019 blaKPC-2 strain between the Netherlands and the Caribbean.

scholarly journals Whole-genome analysis of two bovine rotavirus C strains: Shintoku and Toyama

2013 ◽  
Vol 94 (1) ◽  
pp. 128-135 ◽  
Author(s):  
Junichi Soma ◽  
Hiroshi Tsunemitsu ◽  
Takeshi Miyamoto ◽  
Goro Suzuki ◽  
Takashi Sasaki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
High Identity ◽  
Rotavirus A ◽  
Bovine Rotavirus ◽  
Epidemiological Impact

Rotavirus C (RVC) has been detected frequently in epidemic cases and/or outbreaks of diarrhoea in humans and animals worldwide. Because it is difficult to cultivate RVCs serially in cell culture, the sequence data available for RVCs are limited, despite their potential economical and epidemiological impact. Although whole-genome sequences of one porcine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nucleotide sequences for five as-yet underresearched genes, including the NSP4 gene, from a cultivable bovine RVC, the Shintoku strain, identified in Hokkaido Prefecture, Japan, in 1991. In addition, we elucidated the ORF sequences of all segments from another bovine RVC, the Toyama strain, detected in Toyama Prefecture, Japan, in 2010, in order to investigate genetic divergence among bovine RVCs. Comparison of segmental nucleotide and deduced amino acid sequences among RVCs indicates high identity among bovine RVCs and low identity between human and porcine RVCs. Phylogenetic analysis of each gene showed that the two bovine RVCs belong to a cluster distinct from human and porcine RVCs. These data demonstrate that RVCs can be classified into different genotypes according to host species. Moreover, RVC NSP1, NSP2 and VP1 amino acid sequences contain a unique motif that is highly conserved among rotavirus A (RVA) strains and, hence, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.

scholarly journals Genome-wide association study of HIV whole genome sequences validated using drug resistance

2016 ◽  
Author(s):  
Robert A. Power ◽  
Siva Davaniah ◽  
Anne Derache ◽  
Eduan Wilkinson ◽  
Frank Tanser ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Amino Acid ◽  
High Throughput Sequencing ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Sequences ◽  
Gag Protein ◽  
Genome Wide

AbstractGenome-wide association studies (GWAS) have considerably advanced our understanding of human traits and diseases. With the increasing availability of whole genome sequences (WGS) for pathogens, it is important to establish whether GWAS of viral genomes could reveal important biological insights. Here we perform the first proof of concept viral GWAS examining drug resistance (DR), a phenotype with well understood genetics.We performed a GWAS of DR in a sample of 343 HIV subtype C patients failing 1st line antiretroviral treatment in rural KwaZulu-Natal, South Africa. The majority and minority variants within each sequence were called using PILON, and GWAS was performed within PLINK. HIV WGS from patients failing on different antiretroviral treatments were compared to sequences derived from individuals naive to the respective treatment.GWAS methodology was validated by identifying five associations on a genetic level that led to amino acid changes known to cause DR. Further, we highlighted the ability of GWAS to identify epistatic effects, identifying two replicable variants within amino acid 68 of the reverse transcriptase protein previously described as potential fitness compensatory mutations. A possible additional DR variant within amino acid 91 of the matrix region of the Gag protein was associated with tenofovir failure, highlighting the ability of GWAS to identify variants outside classical candidate genes. Our results also suggest a polygenic component to DR.These results validate the applicability of GWAS to HIV WGS data even in relative small samples, and emphasise how high throughput sequencing can provide novel and clinically relevant insights. Further they suggested that for viruses like HIV, population structure was only minor concern compared to that seen in bacteria or parasite GWAS. Given the small genome length and reduced burden for multiple testing, this makes HIV an ideal candidate for GWAS.

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