Molecular Genetic Analysis of the Causative Agents of COVID-19–Associated Bacterial Pneumonia in Hospitals of Rostov-on-Don

Introduction: Hospital-acquired bacterial superinfections in COVID-19 patients are one of the main reasons of a severer course of the disease, a higher risk of adverse outcomes, and, consequently, a longer hospital stay. Much attention is, therefore, paid to the study of genetic markers enabling identification of clonal relationships between different isolates of the causative agents of bacterial co-infections, which, in their turn, help distinguish between hospital- and community-acquired cases of infectious diseases. Objective: To study the genetic diversity and clonal relationships of A. baumannii and P. aeruginosa isolated from patients with a novel coronavirus disease (COVID-19) in Rostov-on-Don. Materials and methods: We tested biological specimens from 217 in- and outpatients with community-acquired pneumonia in the city of Rostov-on-Don. Whole-genome sequencing of A. baumannii and P. aeruginosa strains was performed using a MiSeq sequencer (Illumina, USA). SNP markers were selected using proprietary software written in Java and Python. Cluster analysis and dendrogram construction were performed using the author's software using the UPGMA method. The MEGA 5 software was used to build the dendrogram. Results: We established the spectrum of bacteria causing the development of secondary infection associated with COVID-19. Results of the whole-genome sequencing of 10 pneumonia pathogens isolated from patients with the novel coronavirus disease revealed clonality of individual strains. The nosocomial origin of two isolates of P. aeruginosa and two of A. baumannii was demonstrated and confirmed by the analysis of their plasmid composition. Secondary bacterial infection in COVID-19 patients may be attributed to the pathological development of the dominant microflora of the upper respiratory tract mucosa, which provides normal biocenosis in healthy people, or non-compliance with basic principles of hospital hygiene and infection control precautions. Conclusion: The research helped determine the etiological structure of pneumonia in patients with COVID-19. Whole-genome sequencing and the following bioinformatic analysis revealed the nosocomial origin of a number of strains of P. aeruginosa and A. baumanii.

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Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2

International Journal of Molecular Sciences ◽

10.3390/ijms20215442 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5442

Author(s):

Motonori Tomita ◽

Shiho Yazawa ◽

Yoshimasa Uenishi

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rice Variety ◽

Kernel Weight ◽

Snp Markers ◽

Recurrent Parent ◽

Whole Genome ◽

Isogenic Line ◽

Chromosome 2 ◽

Single Nucleotide

Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F3 plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F2 and all BCnF2 generations, large, medium, and small grain segregated in a 1:2:1 ratio, indicating that the large grain is controlled by a single allele. Mapping by using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers with small grain homozygous segregants in the F2 of Nipponbare × Inochinoichi, revealed linkage with around 7.7 Mb markers from the distal end of the short arm of chromosome 2. Whole-genome sequencing on a large grain isogenic Koshihikari (BC4F2) using next-generation sequencing (NGS) identified a single nucleotide deletion in GW2 gene, which is located 8.1 Mb from the end of chromosome 2, encoding a RING protein with E3 ubiquitin ligase activity. The GW2-integrated isogenic Koshihikari showed a 34% increase in thousand kernel weight compared to Koshihikari, while retaining a taste score of 80. We further developed a large grain/semi-dwarf isogenic Koshihikari integrated with GW2 and the semidwarfing gene d60, which was found to be localized on chromosome 2. The combined genotype secured high yielding while providing robustness to withstand climate change, which can contribute to the New Green Revolution.

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Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses

BMC Genomics ◽

10.1186/s12864-020-07265-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

E. A. Hisey ◽

H. Hermans ◽

Z. T. Lounsberry ◽

F. Avila ◽

R. A. Grahn ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Wide Association Study ◽

Secondary Infection ◽

Whole Genome Sequencing Data ◽

Incomplete Penetrance ◽

Whole Genome ◽

Genome Wide ◽

A Genome

Abstract Background Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, or, if secondary infection occurs, may lead to loss of the eye. Friesian horses represent the vast majority of reported cases of equine distichiasis, and as the breed is known to be affected with inherited monogenic disorders, this condition was hypothesized to be a simply inherited Mendelian trait. Results A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. An additive single locus mixed linear model (EMMAX) approach identified a 1.83 Mb locus on ECA5 and a 1.34 Mb locus on ECA13 that reached genome-wide significance (pcorrected = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10− 5, cases: n = 5 and controls: n = 37). A 371 kb run of homozygosity (ROH) on ECA13 was found in 13 of the 14 cases, providing evidence for a recessive mode of inheritance. Haplotype analysis (hapQTL) narrowed the region of association on ECA13 to 163 kb. Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). Functional annotation data supports a tissue-specific regulatory role of this locus. This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10− 13). Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder. Conclusions This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. Further functional analysis in relevant tissues from cases and controls will help to clarify the precise role of this deletion in normal and abnormal eyelash development and investigate the hypothesis of incomplete penetrance.

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Whole-genome sequencing and de novo assembly of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in Vietnam

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/18/2/15082 ◽

2020 ◽

Vol 18 (2) ◽

pp. 197-208

Author(s):

Le Tung Lam ◽

Nguyen Trung Hieu ◽

Nguyen Hong Trang ◽

Ho Thi Thuong ◽

Tran Huyen Linh ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sanger Sequencing ◽

De Novo ◽

Whole Genome ◽

Smrt Sequencing ◽

Sequencing Technology ◽

High Quality ◽

Long Read ◽

Novel Coronavirus

The pandemic COVID-19 caused by the virus SARS-CoV-2 has devastated countries worldwide, infecting more than 4.5 million people and leading to more than 300,000 deaths as of May 16th, 2020. Whole-genome sequencing (WGS) is an effective tool to monitor emerging strains and provide information for intervention, thus help to inform outbreak control decisions. Here, we reported the first effort to sequence and de novo assemble the whole genome of SARS-CoV-2 using PacBio’s SMRT sequencing technology in Vietnam. We also presented the annotation results and a brief analysis of the variants found in our SARS-CoV-2 strain, which was isolated from a Vietnamese patient. The sequencing was successfully completed and de novo assembled in less than 30 hours, resulting in one contig with no gap and a length of 29,766 bp. All detected variants as compared to the NCBI reference were highly accurate, as confirmed by Sanger sequencing. The results have shown the potential of long read sequencing to provide high quality WGS data to support public health responses and advance understanding of this and future pandemics.

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Complex Characteristics of Yersinia pestis Strains Isolated in the Sarydzhaz and Upper-Naryn High-Mountain Foci in 2019–2020

Problems of Particularly Dangerous Infections ◽

10.21055/0370-1069-2021-2-114-122 ◽

2021 ◽

pp. 114-122

Author(s):

L. M. Kukleva ◽

A. K. Dzhaparova ◽

E. G. Oglodin ◽

E. A. Naryshkina ◽

Ya. M. Krasnov ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Yersinia Pestis ◽

Genome Sequencing ◽

Biochemical Properties ◽

Molecular Genetic Analysis ◽

Tien Shan ◽

Laboratory Animals ◽

High Mountain ◽

Whole Genome

The aim of the study was a comprehensive analysis of the phenotypic and genetic properties of Yersinia pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci of the Tien Shan in 2019–2020; determination of the present-day population structure and areal of these highly virulent strains of the plague pathogen.Materials and methods. Studies of biochemical properties (fermentation of carbohydrates, nutritional requirements), virulence (in vitro and in laboratory animals), molecular-genetic analysis and whole genome sequencing of Y. pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci in 2019–2020 have been carried out. We used Y. pestis strains from the foci of the Tien Shan and Pamir-Alai dated 1928–2016 for the comparison. Whole genome sequencing was performed using the Ion S5 XL System. Phylogenetic analysis was performed on the basis of 1443 identified core SNPs in 36 Y. pestis strains of various phylogenetic lines included in the analysis. The construction of dendrograms was carried out using the Maximum Likelihood algorithm, PHYML program, HKY85 model.Results and discussion. It is established that all Y. pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci in 2019–2020 belong to the 0.ANT5 phylogenetic branch of the ancient biovar of the main subspecies. Genome-wide sequencing revealed the presence of two 0.ANT5 clones, the first of which consists of strains from the basin of the river Kooylu in the Sarydzhaz focus, dated 2020. The second powerful clone includes the strains of 2012–2020 isolated in the Sarydzhaz and Upper-Naryn foci. The high virulence of the isolated strains has been shown. It was concluded that further study of the territories of the highmountain foci of the Tien Shan and Pamir-Alai is necessary to establish the current boundaries of the 0.ANT5 areal, as well as to identify the circulation areas of Y. pestis of other phylogenetic lineages.

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WHOLE-GENOME SEQUENCING AND DE NOVO ASSEMBLY OF A 2019 NOVEL CORONAVIRUS (SARS-COV-2) STRAIN ISOLATED IN VIETNAM

10.1101/2020.06.12.149377 ◽

2020 ◽

Author(s):

Le Tung Lam ◽

Nguyen Trung Hieu ◽

Nguyen Hong Trang ◽

Ho Thi Thuong ◽

Tran Huyen Linh ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sanger Sequencing ◽

De Novo ◽

Whole Genome ◽

Smrt Sequencing ◽

Sequencing Technology ◽

Zoonotic Virus ◽

Long Read ◽

Novel Coronavirus

ABSTRACTThe pandemic COVID-19 caused by the zoonotic virus SARS-CoV-2 has devastated countries worldwide, infecting more than 4.5 million people and leading to more than 300,000 deaths. Whole genome sequencing (WGS) is an effective tool to monitor emerging strains and provide information for intervention, thus help to inform outbreak control decisions. Here, we reported the first effort to sequence and de novo assemble the whole genome of SARS-CoV-2 using PacBio’s SMRT sequencing technology in Vietnam. We also presented the annotation results and a brief analysis of the variants found in our SARS-CoV-2 strain, which was isolated from a Vietnamese patient. The sequencing was successfully completed and de novo assembled in less than 30 hours, resulting in one contig with no gap and a length of 29,766 bp. All detected variants as compared to the NCBI reference were highly accurate as confirmed by Sanger sequencing. The results have shown the potential of long read sequencing to provide high quality WGS data to support public health responses, and advance understanding of this and future pandemics.

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