SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

Download Full-text

SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

10.1101/2021.02.11.21251589 ◽

2021 ◽

Cited By ~ 2

Author(s):

Ana Rita Goncalves Cabecinhas ◽

Tim Roloff ◽

Madlen Stange ◽

Claire Bertelli ◽

Michael Huber ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Implementation Process ◽

Amplicon Sequencing ◽

World Health ◽

Whole Genome ◽

Diagnostic Systems ◽

Early Introduction ◽

Specific Pcr ◽

Health Organization

AbstractThe rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations by the European Center for Disease Prevention and Control (ECDC) and World Health Organization (WHO) for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological definitions based on travel history and the S gene dropout in certain diagnostic systems. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 3492 VoCs have been identified since the detection of the first Swiss case in October 2020, with 1370 being B1.1.7, 61 B.1.351, and none P.1. The remaining 2061 cases of VoCs have been described without further lineage specification. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

Download Full-text

6 Translating genomics for clinical benefit

Postgraduate Medical Journal ◽

10.1136/postgradmedj-2019-fpm.6 ◽

2019 ◽

Vol 95 (1130) ◽

pp. 686.3-686

Author(s):

Mark Caulfield

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Medicine ◽

Health Gain ◽

Annual Review ◽

Whole Genome ◽

Department Of Health ◽

Data Points ◽

Genome Analyses ◽

The Uk

The UK 100,000 Genomes Project has focussed on transforming genomic medicine in the National Health Service using whole genome sequencing in rare disease, cancer and infection. Genomics England partnering with the NHS established 13 Genomic Medicine Centres, the NHS whole genome sequencing centre and the Genomics England Clinical Interpretation Partnership (3337 researchers from 24 countries). We sequenced the 100,000th genome on the 5th December 2019 and completed an initial analysis for participants in July 2019. Alongside these genomes we have assembled a longitudinal life course dataset for research and diagnosis including 2.6 billion clinical data points for the 3000 plus researchers to work on to drive up the value of the genomes for direct healthcare. In parallel we have partnered the NHS to establish one of the world’s most advanced Genomic Medicine Service where we re-evaluated 300,000 genomic tests and upgraded 25% of tests to newer technologies with an annual review. The Department of Health have announced the ambition to undertake 5 million genome analyses over the next 5 years focused on new areas tractable to health gain.

Download Full-text

In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms

American Journal of Epidemiology ◽

10.1093/aje/kwaa025 ◽

2020 ◽

Vol 189 (8) ◽

pp. 841-849

Author(s):

Fermín Acosta ◽

Ana Fernández-Cruz ◽

Sandra R Maus ◽

Pedro J Sola-Campoy ◽

Mercedes Marín ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Outbreak Strain ◽

Single Nucleotide ◽

Specific Pcr ◽

Extensively Drug Resistant ◽

Polymerase Chain

Abstract In 2013–2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011–2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.

Download Full-text

Next generation whole genome sequencing of Plasmodium falciparum using NextSeq500 technology in India

10.1101/068676 ◽

2016 ◽

Author(s):

Alassane Mbengue ◽

Pragya Namdev ◽

Tarkeshwar Kumar ◽

Kasturi Haldar ◽

Souvik Bhattacharjee

Keyword(s):

Plasmodium Falciparum ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Immune Evasion ◽

Malaria Elimination ◽

Protozoan Parasite ◽

Amplicon Sequencing ◽

Whole Genome ◽

Next Generation ◽

New Genes

AbstractPlasmodium falciparum is a protozoan parasite that causes the deadliest form of human malaria. Although, malaria burdens worldwide have decreased substantially over the last decade (WHO, 2014), genetic variation and adaptation by parasite strains against drugs and vaccines present significant challenges for the elimination of malaria (Ariey et al., 2014; Neafsey et al., 2015). India has formally launched a malaria elimination campaign (NVBDCP, 2016). Therefore, early in-country detection of drug resistance and/or immune evasion will be important for the program. Presently, the majority of surveillance methods in India detect a limited number of known polymorphisms (Campino et al., 2011; Chatterjee et al., 2016; Daniels et al., 2008; Mishra et al., 2015; Neafsey et al., 2012; Neafsey et al., 2008). A recently reported amplicon sequencing method enables targeted re-sequencing of a panel of genes (Rao et al., 2016). However, the capacity to identify new genes of resistance/immune evasion by whole genome sequencing (WGS) through next generation sequencing (NGS) in India, has remained elusive. Here we report the first WGS of P. falciparum strain performed by Eurofins Genomics India Pvt. Ltd at its Bengaluru division within 40 days of sample submission. Our data establish that timely, commercial WGS through NGS in India can be applied to P. falciparum to greatly empower the malaria elimination agenda in India.

Download Full-text

Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0008796 ◽

2020 ◽

Vol 14 (11) ◽

pp. e0008796 ◽

Cited By ~ 1

Author(s):

Catherine N. Wilson ◽

Caisey V. Pulford ◽

James Akoko ◽

Blanca Perez Sepulveda ◽

Alexander V. Predeus ◽

...

Keyword(s):

Lymph Node ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Mesenteric Lymph Node ◽

Zoonotic Transmission ◽

Whole Genome ◽

Foodborne Disease ◽

Mesenteric Lymph ◽

The Uk

Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.

Download Full-text

Reliability of Spike Gene Target Failure for ascertaining SARS-CoV-2 lineage B.1.1.7 prevalence in a hospital setting

10.1101/2021.04.12.21255084 ◽

2021 ◽

Author(s):

José Afonso Guerra-Assunção ◽

Paul A. Randell ◽

Florencia A. T. Boshier ◽

Michael A. Crone ◽

Juanita Pang ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Lower Cost ◽

Hospital Setting ◽

Qpcr Assay ◽

Spike Protein ◽

Whole Genome ◽

Gene Target ◽

Spike Gene ◽

The Uk

AbstractThe appearance of the SARS-CoV-2 lineage B.1.1.7 in the UK in late 2020, associated with faster transmission, sparked the need to find effective ways to monitor its spread. The set of mutations that characterise this lineage include a deletion in position 69 and 70 of the spike protein, which is known to be associated with Spike Gene Target Failure (SGTF) in a commonly used three gene diagnostic qPCR assay. The lower cost and faster turnaround times compared to whole genome sequencing make the use of qPCR for monitoring of the variant spread an attractive proposition. However, there are several potential issues with this approach. Here we use 826 SARS-CoV-2 samples collected in a hospital setting as part of the Hospital Onset COVID Infection (HOCI) study where qPCR was used for viral detection, followed by whole genome sequencing (WGS), to identify the factors to consider when using SGTF to infer lineage B.1.1.7 prevalence in a hospital setting, with potential implications for locations where this variant has recently been introduced.

Download Full-text

Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

10.1101/236786 ◽

2017 ◽

Author(s):

Kimon Lemonidis ◽

Talal S. Salih ◽

Stephanie J. Dancer ◽

Iain S. Hunter ◽

Nicholas P. Tucker

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Sequence Type ◽

Whole Genome ◽

Vancomycin Resistant Enterococcus ◽

Phylogenetic Comparison ◽

Vancomycin Resistant ◽

The Uk ◽

Increased Susceptibility

AbstractMulti-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two closely located hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains across both hospitals, while the fifth was of a multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested VanA-type pstS-null VREfm strains (5 English and 18 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.

Download Full-text

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples

10.1101/094789 ◽

2016 ◽

Cited By ~ 5

Author(s):

Antonina A. Votintseva ◽

Phelim Bradley ◽

Louise Pankhurst ◽

Carlos del Ojo Elias ◽

Matthew Loose ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antibiotic Susceptibility ◽

Point Of Care ◽

Low Cost ◽

Illumina Miseq ◽

Turnaround Time ◽

Reference Laboratory ◽

Whole Genome ◽

Specific Pcr

AbstractRoutine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near point of care.We demonstrate a low-cost DNA extraction method for TB WGS direct from patient samples. We initially evaluated the method using the Illumina MiSeq sequencer (40 smear-positive respiratory samples, obtained after routine clinical testing, and 27 matched liquid cultures). M. tuberculosis was identified in all 39 samples from which DNA was successfully extracted. Sufficient data for antibiotic susceptibility prediction was obtained from 24 (62%) samples; all results were concordant with reference laboratory phenotypes. Phylogenetic placement was concordant between direct and cultured samples. Using an Illumina MiSeq/MiniSeq the workflow from patient sample to results can be completed in 44/16 hours at a cost of £96/£198 per sample.We then employed a non-specific PCR-based library preparation method for sequencing on an Oxford Nanopore Technologies MinION sequencer. We applied this to cultured Mycobacterium bovis BCG strain (BCG), and to combined culture-negative sputum DNA and BCG DNA. For the latest flowcell, the estimated turnaround time from patient to identification of BCG was 6 hours, with full susceptibility and surveillance results 2 hours later. Antibiotic susceptibility predictions were fully concordant. A critical advantage of the MinION is the ability to continue sequencing until sufficient coverage is obtained, providing a potential solution to the problem of variable amounts of M. tuberculosis in direct samples.

Download Full-text

The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak

European Respiratory Journal ◽

10.1183/13993003.02313-2017 ◽

2018 ◽

Vol 51 (6) ◽

pp. 1702313 ◽

Cited By ~ 13

Author(s):

Maeve K. Lalor ◽

Nicola Casali ◽

Timothy M. Walker ◽

Laura F. Anderson ◽

Jennifer A. Davidson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Epidemiological Methods ◽

Whole Genome ◽

Transmission Network ◽

Drug Resistant ◽

Nucleotide Polymorphisms ◽

The Uk ◽

Epidemiological Information

We used whole-genome sequencing (WGS) to delineate transmission networks and investigate the benefits of WGS during cluster investigation.We included clustered cases of multidrug-resistant (MDR) tuberculosis (TB)/extensively drug-resistant (XDR) TB linked by mycobacterial interspersed repetitive unit variable tandem repeat (MIRU-VNTR) strain typing or epidemiological information in the national cluster B1006, notified between 2007 and 2013 in the UK. We excluded from further investigation cases whose isolates differed by greater than 12 single nucleotide polymorphisms (SNPs). Data relating to patients' social networks were collected.27 cases were investigated and 22 had WGS, eight of which (36%) were excluded as their isolates differed by more than 12 SNPs to other cases. 18 cases were ruled into the transmission network based on genomic and epidemiological information. Evidence of transmission was inconclusive in seven out of 18 cases (39%) in the transmission network following WGS and epidemiological investigation.This investigation of a drug-resistant TB cluster illustrates the opportunities and limitations of WGS in understanding transmission in a setting with a high proportion of migrant cases. The use of WGS should be combined with classical epidemiological methods. However, not every cluster will be solvable, regardless of the quality of genomic data.

Download Full-text

Intragenic DOK7 deletion detected by whole-genome sequencing in congenital myasthenic syndromes

Neurology Genetics ◽

10.1212/nxg.0000000000000152 ◽

2017 ◽

Vol 3 (3) ◽

pp. e152 ◽

Cited By ~ 2

Author(s):

Yoshiteru Azuma ◽

Ana Töpf ◽

Teresinha Evangelista ◽

Paulo José Lorenzoni ◽

Andreas Roos ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Congenital Myasthenic Syndromes ◽

Specific Pcr ◽

Number Variation ◽

Allele Specific ◽

Exercise Induced ◽

Allele Specific Pcr ◽

Myasthenic Syndromes

Objective:To identify the genetic cause in a patient affected by ptosis and exercise-induced muscle weakness and diagnosed with congenital myasthenic syndromes (CMS) using whole-genome sequencing (WGS).Methods:Candidate gene screening and WGS analysis were performed in the case. Allele-specific PCR was subsequently performed to confirm the copy number variation (CNV) that was suspected from the WGS results.Results:In addition to the previously reported frameshift mutation c.1124_1127dup, an intragenic 6,261 bp deletion spanning from the 5′ untranslated region to intron 2 of the DOK7 gene was identified by WGS in the patient with CMS. The heterozygous deletion was suspected based on reduced coverage on WGS and confirmed by allele-specific PCR. The breakpoints had microhomology and an inverted repeat, which may have led to the development of the deletion during DNA replication.Conclusions:We report a CMS case with identification of the breakpoints of the intragenic DOK7 deletion using WGS analysis. This case illustrates that CNVs undetected by Sanger sequencing may be identified by WGS and highlights their relevance in the molecular diagnosis of a treatable neurologic condition such as CMS.

Download Full-text