scholarly journals SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

2021 ◽  
Author(s):  
Juliana D Siqueira ◽  
Livia R Goes ◽  
Brunna M Alves ◽  
Pedro S de Carvalho ◽  
Claudia Cicala ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cancer Patients ◽  
Disease Severity ◽  
Healthcare Workers ◽  
Viral Population ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Consensus Sequences ◽  
Vulnerable Patients

Abstract Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.

scholarly journals SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution

2020 ◽  
Author(s):  
Juliana D. Siqueira ◽  
Livia R. Goes ◽  
Brunna M. Alves ◽  
Pedro S. de Carvalho ◽  
Claudia Cicala ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cancer Patients ◽  
Disease Severity ◽  
Deep Sequencing ◽  
Healthcare Workers ◽  
Adverse Outcomes ◽  
Genomic Diversity ◽  
Consensus Sequences ◽  
The Impact

AbstractNumerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (HCW; non-cancer controls) by deep sequencing and investigated the within-host viral quasispecies of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers (HCW) from the Brazilian Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants (iSNVs) were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%). Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to HCW (p = 0.009). Intrahost genetic diversity in cancer patients was independent of SARS-CoV-2 Ct values, and was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Such a feature may explain, at least in part, the more adverse outcomes to which cancer/COVID-19 patients experience.Author SummaryCancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. In this study, phylogenetic and variation analysis of SARS-CoV-2 genomes from cancer patients and non-cancer healthcare workers at the Brazilian National Cancer Institute were characterized by deep sequencing. Viral genomes showed signatures characteristic of Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. Despite most genomes in patients and healthcare workers belonging to the same lineage, intrahost variability was higher in cancer patients when compared to non-cancer counterparts. The intrahost genomic diversity analysis presented in our study highlights the relaxed evolution of SARS-CoV-2 in a vulnerable population of cancer patients. The high number of minor variations can result in the selection of immune escape variants, resistance to potential drugs, and/or increased pathogenicity. The impact of this higher intrahost variability over time warrants further investigation.

scholarly journals Clonal propagation history shapes the intra-cultivar genetic diversity in ‘Malbec’ grapevines

2020 ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Red Wines ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Diversity Pattern ◽  
History Of ◽  
Potential Impact ◽  
Whole Genome Resequencing

AbstractGrapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on ‘Malbec’. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four ‘Malbec’ clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey ‘Malbec’ genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped ‘Malbec’ extant genetic diversity pattern.

scholarly journals Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Lucy Crooks ◽  
Johnathan Cooper-Knock ◽  
Paul R. Heath ◽  
Ahmed Bouhouche ◽  
Mostafa Elfahime ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Population ◽  
European Ancestry ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Moroccan Population ◽  
African Populations

Abstract Background Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. The ancestry of present-day Moroccans is unknown and may be substantially different from Africans found South of the Sahara desert, Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans and suggested that North African individuals may be genetically distinct from previously studied African populations. Results We present SNVs discovered by whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G and were not in the extensive gnomAD database. We summarise the SNVs by genomic position, type of sequence gene context and effect on proteins encoded by the sequence. Analysis of the overall genomic information of the Moroccan individuals to individuals from 1000G supports the Moroccan population being distinct from both sub-Saharan African and European populations. Conclusions We conclude that Moroccan samples are genetically distinct and lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of novel SNVs and aid in functional characterisation of the genome.

Genetic diversity among Canadienne, Brown Swiss, Holstein and Jersey cattle based on mitochondrial D-loop sequence variation

2003 ◽  
Vol 83 (1) ◽  
pp. 39-44 ◽  
Author(s):  
C. Hansen ◽  
J. N. B. Shrestha ◽  
R. J. Parker ◽  
G. H. Crow ◽  
P. J. McAlpine ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Bos Taurus ◽  
Sequence Divergence ◽  
Single Nucleotide ◽  
Brown Swiss ◽  
Jersey Cattle ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Polymorphisms creating 36 unique haplotypes were observed with in breeds at 55 sites in the displacement loop (D-loop) region of the mitochondrial DNA (mtDNA) consisting of 814 bp. The majority (56%) of the differences observed were the result of nucleotide substitution events with 19 transitions, 12 transversions, 11 deletions, 12 insertions and 1 inversion. In all cases, the insertions and deletions were of a single nucleotide. Canadienne cattle were found to have 60% unique haplotypes within the population compared to 89% in Brown Swiss, 90% in Holstein and 100% in Jersey cattle, possibly reflecting the narrow genetic base in the Canadienne breed. The degree of sequence divergence in the D-loop region of mtDNA was based on samples from 20 Canadienne, 9 Brown Swiss, 10 Holstein and 10 Jersey cattle and a phylogenetic analysis showed that these cattle (Bos taurus) were not evolutionarily distinct. All four breeds grouped together when a strict consensus tree was generated. Intra-breed variability proved to be high for the Canadienne, Holstein and Jersey breeds (57–73%) but not the Brown Swiss breed (29%). The Canadienne and Brown Swiss (45%), and Brown Swiss and Holstein (43%) showed the lowest degree of inter-breed variability. The greatest variability among the four breeds was between Canadienne and Jersey (80%) cattle. These findings question the validity of phenotypic assessment of genetic diversity, such as Canadienne cattle being described as “Black Jersey”. Key words: Genetic distance, phylogenetic analysis, D-loop sequence, cattle

scholarly journals Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11015
Author(s):  
Rita Feghali ◽  
Georgi Merhi ◽  
Aurelia Kwasiborski ◽  
Veronique Hourdel ◽  
Nada Ghosn ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Consensus Sequence ◽  
Unknown Origin ◽  
International Travel ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Genetic Lineages ◽  
Consensus Sequences

Background In December 2019, the COVID-19 pandemic initially erupted from a cluster of pneumonia cases of unknown origin in the city of Wuhan, China. Presently, it has almost reached 94 million cases worldwide. Lebanon on the brink of economic collapse and its healthcare system thrown into turmoil, has previously managed to cope with the initial SARS-CoV-2 wave. In this study, we sequenced 11 viral genomes from positive cases isolated between 2 February 2020 and 15 March 2020. Methods Sequencing data was quality controlled, consensus sequences generated, and a maximum-likelihood tree was generated with IQTREE v2. Genetic lineages were assigned with Pangolin v1.1.14 and single nucleotide variants (SNVs) were called from read files and manually curated from consensus sequence alignment through JalView v2.11 and the genomic mutational interference with molecular diagnostic tools was assessed with the CoV-GLUE pipeline. Phylogenetic analysis of whole genome sequences confirmed a multiple introduction scenario due to international travel. Results Three major lineages were identified to be circulating in Lebanon in the studied period. The B.1 (20A clade) was the most prominent, followed by the B.4 lineage (19A clade) and the B.1.1 lineage (20B clade). SNV analysis showed 15 novel mutations from which only one was observed in the spike region.

scholarly journals Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing

2020 ◽  
Author(s):  
Lucy Crooks ◽  
Johnathan Cooper-Knock ◽  
Paul R. Heath ◽  
Ahmed Bouhouche ◽  
Elmostafa El Fahime ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Population ◽  
European Ancestry ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Moroccan Population ◽  
African Populations

Abstract Background Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs), which have predominately focused on individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The more recent African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans, showed that North Africa individuals are expected to show genetic differences from previously studied African populations. Results We present single nucleotide variant (SNV) results from whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G. We provide a summary of the SNVs by genomic position, gene context and effect on protein coding. Comparison of genome-wide information of the Moroccan individuals to individuals from 1000G by principal component analysis revealed a substantial genomic distinction between the Moroccan population and sub-Saharan African populations. Conclusions We conclude that Moroccan samples lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of new SNVs and aid in functional characterisation of the genome.

scholarly journals Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic

2021 ◽  
Author(s):  
P.W.G. Mallon ◽  
F. Crispie ◽  
G. Gonzalez ◽  
W. Tinago ◽  
A.A. Garcia Leon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Disease Severity ◽  
Genome Sequencing ◽  
Population Level ◽  
Whole Genome ◽  
Multiple Introductions ◽  
Relative Contribution ◽  
The Impact

AbstractBackgroundWhole-genome sequencing (WGS) of SARS-CoV-2 laboratory-confirmed cases can provide insights into viral transmission and genetic diversity at a population level. However, less is known about the impact of non-pharmaceutical interventions (NPIs), including ‘lockdowns’, on circulating SARS-CoV-2 lineages and variants of concern, the relative contribution of travel to re-emergence of pandemic waves within communities or how different lineages and variants contribute to disease severity.MethodsWe have conducted an analysis within a prospective, multicentre observational study of individuals attending four hospitals in the South-East of Ireland with COVID-19. Samples underwent WGS from which lineages and variants were assigned, lineage frequency was plotted over time and phylogenetic analysis was employed to determine the origin of variants detected post-lockdown. Univariate and multivariate analyses assessed relationships between viral lineage/variant and COVID-19 disease severity.ResultsWe analysed 225 genome sequences across two SARS-CoV-2 waves, 134 (59.6%) from wave 1 (March to June) and 91 (40.4%) from wave 2 (July to December), representing 15.2% of COVID-19 admissions to these hospitals during the sampling periods. Four variants (B.1.1.162, B1.1.70, B.1.1.267 and B.1.1) comprised 68% of variants detected during wave 1. Of these variants, only a single B.1.1.70 sequence was detected in wave 2, while the B.1.177 lineage emerged and contributed to 82.3% of lineages detected. Phylogenetic analysis suggested multiple introductions of wave 2 variants from outside Ireland. We found no consistent association between SARS-CoV-2 lineages and disease severity.ConclusionsThese data suggest elimination of common SARS-CoV-2 lineages from hospitalised cases associated with effective NPIs and that importation of new viral variants through travel was a significant contributor to the re-emergence of the pandemic in the second wave in Ireland. Our findings highlight the importance of genomic surveillance in identifying circulating viral genetic diversity and variants of concern and, also, modelling the disease burden of SARS-CoV-2.

scholarly journals A fully phased accurate assembly of an individual human genome

2019 ◽  
Author(s):  
David Porubsky ◽  
Peter Ebert ◽  
Peter A. Audano ◽  
Mitchell R. Vollger ◽  
William T. Harvey ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Consensus Sequence ◽  
Error Rates ◽  
Single Individual ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Consensus Sequences ◽  
Oxford Nanopore ◽  
Genome Assemblies

The prevailing genome assembly paradigm is to produce consensus sequences that “collapse” parental haplotypes into a consensus sequence. Here, we leverage the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing (Strand-seq)1,2 and combine them with high-fidelity (HiFi) long sequencing reads3, in a novel reference-free workflow for diploid de novo genome assembly. Employing this strategy, we produce completely phased de novo genome assemblies separately for each haplotype of a single individual of Puerto Rican origin (HG00733) in the absence of parental data. The assemblies are accurate (QV > 40), highly contiguous (contig N50 > 25 Mbp) with low switch error rates (0.4%) providing fully phased single-nucleotide variants (SNVs), indels, and structural variants (SVs). A comparison of Oxford Nanopore and PacBio phased assemblies identifies 150 regions that are preferential sites of contig breaks irrespective of sequencing technology or phasing algorithms.

scholarly journals Population genetic analysis of Indian SARS-CoV-2 isolates reveals a unique phylogenetic cluster

2020 ◽  
Author(s):  
Dhruv Das ◽  
V.S.S.N.R Akkipeddi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Polymorphism ◽  
Population Genetic ◽  
Vaccine Development ◽  
Viral Population ◽  
Population Genetic Analysis ◽  
Phylogenetic Cluster ◽  
Indian Study ◽  
Novel Virus

AbstractThe SARS-CoV-2 pandemic originated from Wuhan, China in December 2019 raised an alarming situation all over the globe. Sequencing of this novel virus provides an opportunity to evaluate the genetic polymorphism present in the viral population. Herein, we analysed 173 sequences isolated from Indian patients and performed SNP linkage, clustering and phylogenetic analysis to understand the local genetic diversity. We found that the SNP linkages that lead to the identification of some global clades, do not hold true for the local clade classification. In addition to the unique cluster, established by another Indian study, we identified a new cluster (I-20D) that encompasses 28% of the analysed sequences. This cluster is defined by two linked variations – C22444T and C28854T. A detailed study of such polymorphisms can be useful for drug and vaccine development.

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