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 Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Genomic Surveillance and Phylodynamic Analyses Reveal the Emergence of Novel Mutations and Co-mutation Patterns Within SARS-CoV-2 Variants Prevalent in India

2021 ◽  
Vol 12 ◽  
Author(s):  
Nupur Biswas ◽  
Priyanka Mallick ◽  
Sujay Krishna Maity ◽  
Debaleena Bhowmik ◽  
Arpita Ghosh Mitra ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Time Course ◽  
West Bengal ◽  
Genomic Diversity ◽  
Viral Population ◽  
Whole Genome ◽  
Novel Mutations ◽  
Frequent Mutations ◽  
Time Periods

Identification of the genomic diversity and the phylodynamic profiles of prevalent variants is critical to understand the evolution and spread of SARS-CoV-2 variants. We performed whole-genome sequencing of 54 SARS-CoV-2 variants collected from COVID-19 patients in Kolkata, West Bengal during August–October 2020. Phylogeographic and phylodynamic analyses were performed using these 54 and other sequences from India and abroad that are available in the GISAID database. We estimated the clade dynamics of the Indian variants and compared the clade-specific mutations and the co-mutation patterns across states and union territories of India over the time course. Frequent mutations and co-mutations observed within the major clades across time periods do not show much overlap, indicating the emergence of newer mutations in the viral population prevailing in the country. Furthermore, we explored the possible association of specific mutations and co-mutations with the infection outcomes manifested in Indian patients.

scholarly journals Whole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Xuebing Wang ◽  
Haijian Zhou ◽  
Dongke Chen ◽  
Pengcheng Du ◽  
Ruiting Lan ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Chronically Ill ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Corynebacterium Striatum

ABSTRACT Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 C. striatum isolates obtained from 14 September 2017 to 29 March 2018 in a hospital in Beijing, China, were analyzed by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was conducted on 91 isolates. Nearly all isolates (96.3%, 183/190) were MDR. The highest resistance rate was observed for ciprofloxacin (99.0%, 190/192), followed by cefotaxime (90.6%, 174/192) and erythromycin (89.1%, 171/192). PFGE separated the 192 isolates into 79 pulsotypes, and differences in core genome single-nucleotide polymorphisms (SNPs) partitioned the 91 isolates sequenced into four clades. Isolates of the same pulsotype were identical or nearly identical at the genome level, with some exceptions. Two dominant subclones, clade 3a, and clade 4a, were responsible for the hospital-wide dissemination. Genomic analysis further revealed nine resistance genes mobilized by eight unique cassettes. PFGE and whole-genome sequencing revealed that the C. striatum isolates studied were the result mainly of predominant clones spreading in the hospital. C. striatum isolates in the hospital progressively acquired resistance to antimicrobial agents, demonstrating that isolates of C. striatum may adapt rapidly through the acquisition and accumulation of resistance genes and thus evolve into dominant and persistent clones. These insights will be useful for the prevention of C. striatum infection in hospitals.

scholarly journals Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

2019 ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

scholarly journals Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Benjamin Morga ◽  
Maude Jacquot ◽  
Camille Pelletier ◽  
Germain Chevignon ◽  
Lionel Dégremont ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Analyses ◽  
Genomic Diversity ◽  
Microbial Pathogens ◽  
Whole Genome ◽  
Site Mutation ◽  
Herpesvirus Type ◽  
New Variant ◽  
Genomic Regions

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.

scholarly journals Author Correction: Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sarbashis Das ◽  
B. M. Fredrik Pettersson ◽  
Phani Rama Krishna Behra ◽  
Amrita Mallick ◽  
Martin Cheramie ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mycobacterium Marinum ◽  
Genomic Diversity ◽  
Whole Genome

scholarly journals Molecular Typing of Invasive Staphylococcus aureus from the Emerging Infections Program (EIP) Using Whole-Genome Sequencing

2020 ◽  
Vol 41 (S1) ◽  
pp. s71-s72
Author(s):  
Davina Campbell ◽  
Gillian McAllister ◽  
Kelly Jackson ◽  
Isaac See ◽  
Alison Halpin ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Reference Method ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Emerging Infections ◽  
Convenience Sample ◽  
Genomic Markers ◽  
Sequence Types

Background: The CDC has performed surveillance for invasive Staphylococcus aureus (iSA) infections through the Emerging Infections Program (EIP) since 2004. SCCmec and spa typing for clonal complex (CC) assignment and genomic markers have been used to characterize isolates. In 2019, whole-genome sequencing (WGS) of isolates began, allowing for high-resolution assessment of genomic diversity. Here, we evaluate the reliability of SCCmec typing, spa typing, and CC assignment using WGS data compared to traditional methods to ensure that backwards compatibility is maintained. Methods:S. aureus isolates were obtained from a convenience sample of iSA cases reported through the EIP surveillance system. Overall, 78 iSA isolates with diverse spa repeat patterns, CCs, SCCmec types, and antimicrobial susceptibility profiles were sequenced (MiSeq, Illumina). Real-time PCR and Sanger sequencing were used as the SCCmec and spa typing reference methods, respectively. spa-MLST mapping (Ridom SpaServer) served as the reference method for CC assignment. WGS assembly and multilocus sequence typing (MLST) were performed using the CDC QuAISAR-H pipeline. WGS-based MLST CCs were assigned using eBURST and SCCmec types using SCCmecFinder. spa types were assigned from WGS assemblies using BioNumerics. For isolate subtyping, previously published and validated canonical single-nucleotide polymorphisms (canSNPs) as well as the presence of the Panton-Valentine leukocidin (PVL) toxin and arginine catabolic mobile element (ACME) virulence factor were assessed for all genome assemblies. Results: All isolates were assigned WGS-based spa types, which were 100% concordant (78 of 78) with Sanger-based spa typing. SCCmecFinder assigned 91% of isolates (71 of 78) SCCmec types, which were 100% concordant with reference method results. Also, 7 isolates had multiple cassettes predicted or an incomplete SCCmec region assembly. Using WGS data, 96% (75 of 78) of isolates were assigned CCs; 3 isolates had unknown sequence types that were single-locus variants of established sequence types. Overall, 70 isolates had CCs assigned by the reference method; 100% (70 of 70) concordance was observed with WGS-based CCs. Analysis of canSNPs placed 42% (33 of 78) of isolates into CC8, with 17 (52%) of these isolates classified as USA300. PVL and ACME were not accurate markers for inferring the USA300 subtype as 24% (4 of 17) of isolates did not contain these markers. Conclusions:S. aureus CCs, SCCmec, and spa types can be reliably determined using WGS. Incorporation of canSNP analysis represents a more efficient method for CC8 assignment than the use of genomic markers alone. WGS allows for the replacement of multiple typing methods for increased laboratory efficiency, while maintaining backward compatibility with historical typing nomenclature.Funding: NoneDisclosures: None

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.

scholarly journals Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity

2021 ◽  
Author(s):  
Jon Lucas Boatwright ◽  
Sirjan Sapkota ◽  
Hongyu Jin ◽  
James Schnable ◽  
Zachary Brenton ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phenotypic Diversity ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Evolutionary Divergence ◽  
Whole Genome ◽  
Linear Predictor ◽  
Association Panel ◽  
Genomic Marker

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions with distinct histories of evolutionary divergence and local adaptation. We report the whole-genome sequencing (WGS) of 400 sorghum [Sorghum bicolor (L.) Moench] accessions from the Sorghum Association Panel (SAP) at an average coverage of 38X (25X-72X), enabling the development of a high-density genomic-marker set of 43,983,694 variants including SNPs (~38 million), indels (~5 million), and CNVs (~170,000). We observe slightly more deletions among indels and a much higher prevalence of deletions among copy number variants compared to insertions. This new marker set enabled the identification of several putatively novel genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5 kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has been and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

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