scholarly journals SARS-CoV-2 variants genome analysis of Indonesian isolates and their responses to available vaccines

2022 ◽  
Author(s):  
Dyana Yurico ◽  
Michael Jeremy ◽  
Nasser Mohamed Ghassan Mohamed Adnan Shaikho ◽  
Kholis Abdurachim Audah
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Vaccine Efficacy ◽  
Whole Genome ◽  
Wild Type ◽  
Global Pandemic ◽  
Local Variant ◽  
Alpha Variant ◽  
Using Data ◽  
Almost All

Abstract Background SARS-CoV-2 is a virus that initially appeared in Wuhan, China, at the end of 2019. Since then, the virus has spread until to almost all countries resulting in a global pandemic. Over time, this virus continues to mutate and produce several other variants. In Indonesia, there are multiple variants of SARS-CoV-2 identified, as well as various local variants that are not yet considered to be ‘variants of concern’. Therefore, this investigation is intended to understand the prevalence and epidemiology of the virus, along with detecting the mutations that occur in genes associated with whole-genome-sequences (WGS) isolated in Indonesia. Result Analyses were performed to investigate SARS-CoV-2 prevalence in Indonesia using data obtained from GISAID.org. A whole-genome sequencing was performed on the random samples taken from GISAID.org utilizing the BLAST tool from NCBI. The variants identified in Indonesia are Alpha, Beta and Delta variants, as well as local variants B.1.470 and B.1.466.2. As of the end of November, it was found that there are a total of 5.348 cases of the Delta, 78 cases of the Alpha, 22 cases of the Beta, 572 cases of the local variant B.1.470, and 1.833 cases of the local variant B.1.466.2. Other cases include 219 cases of local variant B.1.1.398, 160 cases of local variant B.1.459 and 1.028 cases of the wild type. In total there are 9.260 isolated genomes collected in GISAID that are located in Indonesia. Using BLAST, WGS of Alpha, Delta, Beta, B.1.470 and B.1.466.2 variants isolated in Indonesia was compared with the wild type from Wuhan NC.045512.2. It was found that multiple mutations have occurred in the samples. The mutations identified as are H69del, V70I, N501Y, D614G, A570D, P681H, T716I, S982A, and D1118H in the Alpha variant, T19R, L452R, T478K, D614G, and D950N in the Delta variant, D215G, D614G, A701V, L241-, L242-, K417N in the Beta variant, D614G, L242F, and S12F in the B.1.470 variant and D614G, N439K, and P681R in the B.1.466.2 variant. These mutations had caused alterations in the characteristics of the virus and how it may affect vaccine efficacy. Conclusions The results from whole-genome sequencing of variants isolated in Indonesia have found that multiple mutations have occurred in genes of the SARS-CoV-2 Virus and it caused alterations in the characteristics of the virus and may affect vaccine efficacy. It should be noted that classification from the GISAID website may change overtime. The result in this paper is based on the data taken at the end of November.

scholarly journals WGS and RNA Studies Diagnose Noncoding DMD Variants in Males With High Creatine Kinase

2021 ◽  
Vol 7 (1) ◽  
pp. e554
Author(s):  
Leigh B. Waddell ◽  
Samantha J. Bryen ◽  
Beryl B. Cummings ◽  
Adam Bournazos ◽  
Frances J. Evesson ◽  
...  
Keyword(s):  
Creatine Kinase ◽  
Western Blot ◽  
Whole Genome Sequencing ◽  
Rna Sequencing ◽  
Genome Sequencing ◽  
Premature Stop Codon ◽  
Clinical Severity ◽  
Whole Genome ◽  
Wild Type ◽  
Quantitative Western Blot

ObjectiveTo describe the diagnostic utility of whole-genome sequencing and RNA studies in boys with suspected dystrophinopathy, for whom multiplex ligation-dependent probe amplification and exomic parallel sequencing failed to yield a genetic diagnosis, and to use remnant normal DMD splicing in 3 families to define critical levels of wild-type dystrophin bridging clinical spectrums of Duchenne to myalgia.MethodsExome, genome, and/or muscle RNA sequencing was performed for 7 males with elevated creatine kinase. PCR of muscle-derived complementary DNA (cDNA) studied consequences for DMD premessenger RNA (pre-mRNA) splicing. Quantitative Western blot was used to determine levels of dystrophin, relative to control muscle.ResultsSplice-altering intronic single nucleotide variants or structural rearrangements in DMD were identified in all 7 families. Four individuals, with abnormal splicing causing a premature stop codon and nonsense-mediated decay, expressed remnant levels of normally spliced DMD mRNA. Quantitative Western blot enabled correlation of wild-type dystrophin and clinical severity, with 0%–5% dystrophin conferring a Duchenne phenotype, 10% ± 2% a Becker phenotype, and 15% ± 2% dystrophin associated with myalgia without manifesting weakness.ConclusionsWhole-genome sequencing relied heavily on RNA studies to identify DMD splice-altering variants. Short-read RNA sequencing was regularly confounded by the effectiveness of nonsense-mediated mRNA decay and low read depth of the giant DMD mRNA. PCR of muscle cDNA provided a simple, yet informative approach. Highly relevant to genetic therapies for dystrophinopathies, our data align strongly with previous studies of mutant dystrophin in Becker muscular dystrophy, with the collective conclusion that a fractional increase in levels of normal dystrophin between 5% and 20% is clinically significant.

scholarly journals From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance

2021 ◽  
Author(s):  
Francisco M Ortuno ◽  
Carlos Loucera ◽  
Carlos S Casimiro-Soriguer ◽  
Jose A Lepe ◽  
Pedro Camacho Martinez ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Rate ◽  
Epidemiological Surveillance ◽  
Primary Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Wide Range ◽  
Commercial Kits ◽  
Almost All

The current SARS-CoV-2 pandemic has emphasized the utility of viral whole genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is increasingly producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and therefore useless, sequences. However, viral sequences evolve in the context of a complex phylogeny and therefore different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data. We developed impuSARS, an application that includes Minimac, the most widely used strategy for genomic data imputation and, taking advantage of the enormous amount of SARS-CoV-2 whole genome sequences available, a reference panel containing 239,301 sequences was built. The impuSARS application was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing) showing great fidelity when reconstructing the original sequences. The impuSARS application is also able to impute whole genomes from commercial kits covering less than 20% of the genome or only from the Spike protein with a precision of 0.96. It also recovers the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (< 20%). Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. impuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole genome sequencing.

scholarly journals Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 151 ◽  
Author(s):  
Robert S. de Moya ◽  
Judith K. Brown ◽  
Andrew D. Sweet ◽  
Kimberly K. O. Walden ◽  
Jorge R. Paredes-Montero ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bemisia Tabaci ◽  
Sequence Divergence ◽  
Single Copy ◽  
Economic Damage ◽  
Whole Genome ◽  
Population Structures ◽  
Genomic Studies ◽  
Using Data

The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and DNA sequence divergence. These differences allow for certain populations to become invasive and cause great economic damage in a monoculture setting. Although high mitochondrial DNA divergences have been reported between putative conspecifics of the B. tabaci species complex, there is limited data that exists across the whole genome for this group. Using data from 2184 orthologs obtained from whole genome sequencing (Illumina), a phylogenetic analysis using maximum likelihood and coalescent methodologies was completed on ten individuals of the B. tabaci complex. In addition, automatic barcode gap discovery methods were employed, and results suggest the existence of five species. Although the divergences of the mitochondrial cytochrome oxidase I gene are high among members of this complex, nuclear divergences are much lower in comparison. Single-copy orthologs from whole genome sequencing demonstrate divergent population structures among members of the B. tabaci complex and the sequences provide an important resource to aid in future genomic studies of the group.

AcornHRD: A novel tool to identify homologous recombination deficiency events in whole genome sequencing data.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15078-e15078
Author(s):  
Kai Liu ◽  
Xueyu Hao ◽  
Mengmeng Zhang ◽  
Mingwei Li ◽  
Wang Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Ovarian Cancer ◽  
Homologous Recombination ◽  
Whole Genome Sequencing ◽  
Cell Line ◽  
Cell Lines ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Wild Type ◽  
Homologous Recombination Deficiency

e15078 Background: Recently, homologous recombination deficiency (HRD) scores are associated with the efficacy of Poly‐(ADP‐Ribose)‐Polymerase (PARP) inhibition and platinum-based chemotherapy in a variety of cancers. Evaluating HRD level in patients with cancers is becoming far more important and influential, so far, there is no standard method to be used in clinical. In this study, we developed an algorithm to detect HRD from next-generation sequencing (NGS) for finding additional patients may potentially benefit from target therapy. Methods: Forty-eight patients were enrolled, including breast cancer, ovarian cancer, prostatic cancer. Fifteen cell lines with breast cancer and endometrial carcinoma were collected from Cobioer biosciences co., LTD. Forty-eight Formalin-fixed, paraffin embedded (FFPE) samples and 15 cell lines were performed by DNA extracting. We developed an HRD score algorithm, termed as AcornHRD algorithm. HRD score was analyzed by whole-genome sequencing, and GATK mutect2 software was used to detect BRCA1/2mutation by deep sequencing. Results: BRCA1/2 deleterious mutations were observed in 20 patients (41.7%). HRD was explained by deficiencies in 17 patients (85.0%) with BRCA mutation, whereas eight HRD-high tumors were non- BRCA related (28.6%). Among BRCA wild-type patients, the corresponding percentage of HRD positive patients in breast cancer, ovarian cancer and prostate cancer were 36.3%, 37.5% and 11.1%, respectively. Similar results were also verified in the cell line datasets. The findings showed that 100% (3/3) BRCA1/2 deficient cell lines are also HRD-high. Furthermore, HRD scores were highly correlated with standard results in the cell line datasets. Conclusions: We here report the NGS-based HRD scores to distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of Chinese population. AcornHRD scores were highly associated with BRCA1/2 deficiency. AcornHRD algorithm can be a useful tool to detect HRD events in clinical settings.

scholarly journals Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

2013 ◽  
Vol 31 (4) ◽  
pp. 325-330 ◽  
Author(s):  
Karl J V Nordström ◽  
Maria C Albani ◽  
Geo Velikkakam James ◽  
Caroline Gutjahr ◽  
Benjamin Hartwig ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Wild Type ◽  
Sequencing Data ◽  
Mutation Identification

scholarly journals Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Teruaki Tozaki ◽  
Aoi Ohnuma ◽  
Mio Kikuchi ◽  
Taichiro Ishige ◽  
Hironaga Kakoi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Variants ◽  
Industrial Applications ◽  
Whole Genome ◽  
X Chromosomes ◽  
Variant Discovery ◽  
Functional Variants ◽  
Thoroughbred Racehorses ◽  
Using Data

AbstractThe Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.

scholarly journals Genomic diversity of SARS-CoV-2 in Pakistan during fourth wave of pandemic

2021 ◽  
Author(s):  
Massab Umair ◽  
Aamer Ikram ◽  
Zaira Rehman ◽  
Adnan Haider ◽  
Nazish Badar ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Mutation Profile ◽  
Alpha Variant ◽  
Fourth Wave

AbstractThe emergence of different variants of concern of SARS-CoV-2 has resulted in upsurges of COVID positive cases around the globe. Pakistan is also experiencing fourth wave of COVID-19 with increasing number of positive cases. In order to understand the genomic diversity of circulating SARS-CoV-2 strains during fourth wave of pandemic in Pakistan, the current study was designed. The samples from 89 COVID-19 positive patients were subjected to whole genome sequencing using GeneStudio S5. The results showed that 99% (n=88) of isolates belonged to delta variant and only one isolate belonged to alpha variant. Among delta variant cases 26.1% (n=23) isolates were showing B.1.617.2 while 74% of isolates showing AY.4 lineage. Islamabad was found to be the most affected city with 54% (n=48) of cases, followed by Karachi (28%, n=25), and Rawalpindi (10%, n=9). AY.4 has slight difference in mutation profile compared to B.1.617.2. E156del, G142D and V26I mutations in spike and T181I in NSP6 were present in B.1.617.2 but not in AY.4. Interestingly, A446V mutation in NSP4 has been only observed in AY.4. The current study highlights the circulation of primarily delta variant (B.1.617.2 and AY.4) during fourth wave of pandemic in Pakistan.

scholarly journals Use of whole genome sequencing to complement characterisation of a typhoid fever outbreak among a Marshallese community: Oklahoma, 2015

2018 ◽  
Vol 147 ◽  
Author(s):  
L. J. Burnsed ◽  
L. D. Kovar ◽  
K. M. Angelo ◽  
E. K. Trees ◽  
J. Concepción-Acevedo ◽  
...  
Keyword(s):  
Typhoid Fever ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Relatedness ◽  
International Travel ◽  
Whole Genome ◽  
Patient Interviews ◽  
The Usa ◽  
Single Nucleotide Polymorphism Variation ◽  
Almost All

AbstractTyphoid fever is an illness caused bySalmonella entericaserotype Typhi. In developing regions, it affects an estimated 20 million people annually, causing 200 000 deaths. Although uncommon, cases occur in the USA each year, predominantly due to international travel. During February 2015, the Oklahoma State Department of Health (OSDH) detected an outbreak of typhoid fever among residents of northwestern Oklahoma. OSDH conducted case-patient interviews to identify the source and symptomatic contacts. Whole genome sequencing (WGS) was performed to characterise the genetic relatedness of isolates among the four outbreak-associated pulsed-field gel electrophoresis (PFGE) patterns. We identified 38 cases, 25 confirmed and 13 probable, in two states. WGS revealed a 0–10 single-nucleotide polymorphism variation between isolates. Although we were unable to determine the source, almost all case-patients were members of the Marshallese community that attended a common event in Oklahoma, or were contacts to a confirmed case. This is the largest outbreak of typhoid fever in the USA since 1989, and first to apply WGS to complement interpretation of PFGE results during a typhoid fever outbreak investigation. This investigation illustrates the potential risk of outbreaks among communities comprised of international populations from regions where typhoid fever remains endemic.

scholarly journals Viral loads and profile of the patients infected with SARS-CoV-2 Delta, Alpha or R.1 variants in Tokyo

2021 ◽  
Author(s):  
Chihiro Tani-Sassa ◽  
Yumi Iwasaki ◽  
Naoya Ichimura ◽  
Katsutoshi Nagano ◽  
Yuna Takatsuki ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome ◽  
Elderly Individuals ◽  
Viral Loads ◽  
Copy Numbers ◽  
Significant Difference ◽  
Rapid Spread ◽  
Alpha Variant

The rapid spread of the Delta variant of SARS-CoV-2 became a serious concern worldwide in summer 2021. We examined the copy number and variant types of all SARS-CoV-2-positive patients who visited our hospital from February to August 2021 using PCR tests. Whole genome sequencing was performed for some samples. The R.1 variant (B.1.1.316) was responsible for most infections in March, replacing the previous variant (B.1.1.214); the Alpha (B.1.1.7) variant caused most infections in April and May; and the Delta variant (B.1.617.2) was the most prevalent in July and August. There was no significant difference in copy numbers among the previous variant cases (n=29, median 3.0x104 copies/μL), R.1 variant cases (n=28, 2.1x105 copies/μL), Alpha variant cases (n=125, 4.1x105 copies/μL), and Delta variant cases (n=106, 2.4x105 copies/μL). Patients with Delta variant infection were significantly younger than those infected with R.1 and the previous variants, possibly because many elderly individuals in Tokyo were vaccinated between May and August. There was no significant difference in mortality among the four groups. Our results suggest that the increased infectivity of Delta variant may be caused by factors other than the higher viral loads. Clarifying these factors is important to control the spread of Delta variant infection.

Optimization of multiplex PCR composition to screen for SARS-CoV-2 variants of concern

2021 ◽  
Vol 4 (2) ◽  
pp. 58
Author(s):  
Maya Savira ◽  
Enikarmila Asni ◽  
Rahmat Azhari Kemal
Keyword(s):  
Whole Genome Sequencing ◽  
Multiplex Pcr ◽  
Genome Sequencing ◽  
Screening Method ◽  
Positive Control ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Screening ◽  
Single Target ◽  
Alpha Variant

Background: The ongoing COVID-19 pandemic has led to the emergence of several variants of concern. To rapidly identify those variants, screening samples for whole-genome sequencing (WGS) prioritization could be performed.  Objective: We optimized the polymerase chain reaction (PCR) screening method to identify the mutation in spike and ORF1a regions.  Methods: We adopted primers targeting mutation in spike and ORF1a region from another study. We optimized the PCR screening method using kits readily available in Indonesia. Firstly, we compared N1 and N2 primers as internal positive control. We also compared GoTaq® 1-Step RT-qPCR System and Indonesia TFRIC-19 BioCOV-19 for the multiplex reaction. We used the optimized composition to screen SARS-CoV-2 positive samples from April – June 2021. Samples with spike and/or ORF1a target failure were subjected to whole genome sequencing (WGS).  Results: The results demonstrated the N2 BioCOV-19 reaction as the optimized multiplex PCR composition for spike and ORF1a mutations screening. Whole-genome sequencing has shown that a sample with spike and ORF1a targets failure to be Alpha variant, while other samples with single target failure as non-variants of concern. Therefore, a multiplex RT-PCR composition has been optimized to detect mutation in spike and ORF1a regions. Conclusion: We have optimized a multiplex RT-PCR composition to detect mutation in spike and ORF1a regions.

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