Introgression v1 | ScienceGate

GATK Nuclear variant discovery and consensus assembly v1

10.17504/protocols.io.bqzgmx3w ◽

2020 ◽

Author(s):

Graham Etherington

Keyword(s):

Great Britain ◽

Genome Sequencing ◽

Range Expansion ◽

Legal Protection ◽

Population Level ◽

Population Increase ◽

Whole Genome ◽

Mustela Putorius ◽

Variant Discovery ◽

Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as ‘pure’ polecats.

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Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain.

10.1101/2021.12.20.473448 ◽

2021 ◽

Author(s):

Graham John Etherington ◽

Adam Ciezarek ◽

Rebecca Shaw ◽

Johan Michaux ◽

Elizabeth Croose ◽

...

Keyword(s):

Great Britain ◽

Cognitive Function ◽

Legal Protection ◽

Population Level ◽

Population Increase ◽

Whole Genome ◽

Population Recovery ◽

Ural Mountains ◽

Mustela Putorius ◽

Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which occurs across much of Europe east to the Ural Mountains. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as pure polecats. We quantify this introgression and find introgressed genes under selection that may assist in cognitive function and sight.

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Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa027 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Peter Higgins ◽

Cooper A Grace ◽

Soon A Lee ◽

Matthew R Goddard

Keyword(s):

Saccharomyces Cerevisiae ◽

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Range Expansion ◽

Copy Number ◽

Small Scale ◽

Whole Genome ◽

Copy Number Changes ◽

The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

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Multiplex SARS-CoV-2 Genotyping PCR for Population-Level Variant Screening and Epidemiologic Surveillance

10.1101/2021.04.20.21255480 ◽

2021 ◽

Cited By ~ 1

Author(s):

Hannah Wang ◽

Jacob A. Miller ◽

Michelle Verghese ◽

Mamdouh Sibai ◽

Daniel Solis ◽

...

Keyword(s):

Public Health ◽

Nucleic Acid ◽

Whole Genome Sequencing ◽

San Francisco ◽

Genome Sequencing ◽

High Throughput ◽

Population Level ◽

Nucleic Acid Amplification ◽

Whole Genome ◽

Epidemiologic Surveillance

ABSTRACTBackgroundEmergence of SARS-CoV-2 variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a spike genotyping nucleic acid amplification test (NAAT) could facilitate high-throughput variant surveillance.MethodsWe designed and analytically validated a one-step multiplex allele-specific reverse transcriptase polymerase chain reaction (RT-qPCR) to detect three non-synonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2 positive specimens from our San Francisco Bay Area population.ResultsBetween December 1, 2020 and March 1, 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K+N501Y mutations. The assay had near-perfect (98-100%) concordance with whole-genome sequencing in a validation subset of 229 specimens, and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed rapid emergence of L452R in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021.ConclusionsWe developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.Summary / Key PointsEmergence of SARS-CoV-2 variants with concerning phenotypes is of public health interest. We developed a multiplex genotyping RT-qPCR to rapidly detect L452R, E484K, and N501Y with high sequencing concordance. This high-throughput alternative to resource-intensive sequencing enabled surveillance of L452R emergence.

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

10.1101/2021.02.09.21251402 ◽

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.

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Refining the evolutionary time machine: an assessment of whole genome amplification using single historical Daphnia eggs

10.1101/2021.04.19.440325 ◽

2021 ◽

Author(s):

Christopher James O'Grady ◽

Vignesh Dhandapani ◽

John K. Colbourne ◽

Dagmar Frisch

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Amplification ◽

Natural Populations ◽

Population Level ◽

Freshwater Ecosystems ◽

Whole Genome ◽

Exogenous Dna ◽

Genome Amplification ◽

Dormant Eggs

Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimised workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10y and 300y old. Resulting genome coverage breadth in most samples was ~70%, including those from >100y old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with SNPs in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300y). The mtDNA provides an additional source for evolutionary studies of these populations. We provide an optimised workflow for WGA followed by whole genome sequencing including steps to minimise exogenous DNA.

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Multiplex SARS-CoV-2 Genotyping RT-PCR for Population-Level Variant Screening and Epidemiologic Surveillance

Journal of Clinical Microbiology ◽

10.1128/jcm.00859-21 ◽

2021 ◽

Author(s):

Hannah Wang ◽

Jacob A. Miller ◽

Michelle Verghese ◽

Mamdouh Sibai ◽

Daniel Solis ◽

...

Keyword(s):

Nucleic Acid ◽

Whole Genome Sequencing ◽

San Francisco ◽

Genome Sequencing ◽

High Throughput ◽

Population Level ◽

Nucleic Acid Amplification ◽

Spike Protein ◽

Whole Genome ◽

Epidemiologic Surveillance

Emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a nucleic acid amplification test (NAAT) to genotype mutations in the viral spike protein could facilitate high-throughput variant surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase polymerase chain reaction (RT-qPCR) to detect three non-synonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2 positive specimens from our San Francisco Bay Area population. Between December 1, 2020 and March 1, 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K+N501Y mutations. The assay had perfect (100%) concordance with whole-genome sequencing in a validation subset of 229 specimens, and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed rapid emergence of L452R in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. We developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.

Download Full-text