Whole-genome sequencing of SARS-COV-2 reveals a substantially lower frequency of the UK variant than previously announced in Libya

A cluster-5 variant was detected in September 2020 in minks and humans in Denmark and currently classified as Alpha or B.1.1.7 strain. This variant presents several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The national center for disease control (NCDC) announced on 24th February 2021 the discovery of B.1.1.7 strain in Libya using a reverse-transcriptase PCR assay for S-gene target failure (SGTF) and reported that 25% of the tested samples were UK variant. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes S gene drop out in RT-PCR; characteristic of the UK variant (B.1.1.7). This letter discusses our whole genome sequencing results of positive SARS-COV-2 samples with SGTF collected between 25th February - 4th March 2021 in Libya.

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S Gene Target Failure (SGTF) in Commercial Multiplex RT-PCR assay as indicator to detect SARS-CoV-2 VOC B.1.1.7 lineage in Tamil Nadu, India

10.1101/2021.12.14.21251883 ◽

2021 ◽

Author(s):

Vidhya N M ◽

Kumaresan A ◽

Kalaivani V ◽

Rajesh Kumar A ◽

Gurunathan Subramanian ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tamil Nadu ◽

Immune Escape ◽

Whole Genome ◽

Rt Pcr ◽

Pcr Assay ◽

Gene Target ◽

S Gene ◽

Significant Public Health

Emergence of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) Variants of Concern (VOC) possessing improved virulence, transmissibility and/or immune-escape capabilities has raised significant public health concerns. In order to identify VOCs, WHO recommends Whole-Genome Sequencing approach, which is costly and involves longer completion time. Hence, potential role of commercial multiplex RT-PCR kit to screen variants rapidly is being attempted in this study. A total of 1200 suspected COVID samples from different districts of Tamil Nadu State (India) were screened with Thermo TaqPath RT-PCR kit and Altona Realstar RT-PCR Assay kit. Among 1200 screened, S-gene target failure (SGTF) phenomenon were identified in 112 samples while testing with TaqPath RT-PCR Kit. 100% concordant results were observed between SGTF phenomenon and whole-genome sequencing (WGS) results in detecting SARS-CoV-2 VOC B.1.1.7. TaqPath RT-PCR assay testing can be utilized by laboratories to screen rapidly the VOC B.1.1.7 variants, thus enabling early detection of B.1.1.7 variant infection and transmission in population. This in turn will pave way to implement suitable preventive measures by appropriate authorities to control the transmission of the viral variant.

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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.

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Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

Eurosurveillance ◽

10.2807/1560-7917.es.2021.26.3.2100008 ◽

2021 ◽

Vol 26 (3) ◽

Author(s):

Antonin Bal ◽

Gregory Destras ◽

Alexandre Gaymard ◽

Karl Stefic ◽

Julien Marlet ◽

...

Keyword(s):

Whole Genome ◽

Rt Pcr ◽

Pcr Assay ◽

Gene Target ◽

S Gene

We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69–V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.

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Two-step strategy for the identification of SARS-CoV-2 variants co-occurring with spike deletion H69-V70, Lyon, France, August to December 2020

10.1101/2020.11.10.20228528 ◽

2020 ◽

Cited By ~ 2

Author(s):

Antonin Bal ◽

Gregory Destras ◽

Alexandre Gaymard ◽

Hadrien Regue ◽

Quentin Semanas ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

False Negative ◽

False Negative Result ◽

Whole Genome ◽

Rt Pcr ◽

Pcr Assay ◽

Large Scale Screening

AbstractThe spike deletion H69-V70 (ΔH69/ΔV70) has been recently detected in a SARS-CoV-2 variant under investigation in England (VUI 202012/01) as well as in cluter-5 variant detected both in minks and humans in Denmark. Herein we report the implementation of a two-step strategy enabling to detect SARS-CoV-2 variants carrying H69-V70 deletion. We found that this deletion resulted in a false negative result for the spike target of a three-target RT-PCR assay (TaqPath kit). From August 3rd to December 20th, 59/9,266 (0.6%) of positive tests displayed a S negative profile (negative for S target and positive for N & ORF1ab targets). Among the 59 samples without detection of the S target, 36 were available for whole genome sequencing (WGS). The most frequent S mutations co-occurring with ΔH69/ΔV70 were S477N & D614G (21/36 samples). The co-occurrence of N439K and D614G mutations was found in 10/36 samples. The complete combination of S mutations detected in VUI 202012/01 or in cluster-5 variant was not found. The data presented herein emphasize that the TaqPath RT-PCR assay enables a rapid, large-scale screening of ΔH69/ΔV70 variants. Samples with S negative profiles should be further addressed to national referral laboratories for SARS-CoV-2 WGS. This 2-step strategy is currently being reinforced in France as national diagnostic platforms have mainly implemented the TaqPath RT-PCR kit.

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False COVID-19 cases due to contamination by inactivated virus vaccine

Clinical Infectious Diseases ◽

10.1093/cid/ciab684 ◽

2021 ◽

Author(s):

Kelvin Kai-Wang To ◽

Xin Li ◽

David Christopher Lung ◽

Jonathan Daniel Ip ◽

Wan-Mui Chan ◽

...

Keyword(s):

Public Health ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Virus Vaccine ◽

False Positive ◽

Spike Protein ◽

Whole Genome ◽

Rt Pcr ◽

Health Measures ◽

Respiratory Specimens

Abstract A false-positive SARS-CoV-2 RT-PCR result can lead to unnecessary public-health measures. We report two individuals whose respiratory specimens were contaminated by inactivated SARS-CoV-2 vaccine strain(CoronaVac), likely at vaccination premises. Incidentally, whole-genome sequencing of CoronaVac showed adaptive deletions on the spike protein, which do not result in observable changes of antigenicity.

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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.

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First detection and report of SARS-CoV-2 Spike protein N501Y mutations in Oklahoma USA

10.1101/2021.01.26.21250584 ◽

2021 ◽

Author(s):

Sai Narayanan ◽

Girish Patil ◽

Sunil More ◽

Jeremiah Saliki ◽

Anil Kaul ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Spike Protein ◽

Whole Genome ◽

S Gene ◽

Pathogen Dynamics ◽

Geographical Locations

AbstractWe describe the detection of SARS-CoV-2 (VOC)B.1.1.7 lineage in Oklahoma, USA. Various mutations in the S gene and ORF8 with similarity to the genome of B.1.1.7 lineage were detected in 4 of the 6 genomes sequenced and reported here. The sequences have been made available in GISAID. Presence of novel lineages indicate the need for frequent whole genome sequencing to better understand pathogen dynamics in different geographical locations.

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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.

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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.

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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.

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