Increased Transmissibility of SARS-CoV-2 Alpha Variant (B.1.1.7) in Children: Three Large Primary School Outbreaks Revealed by Whole Genome Sequencing in the Netherlands

Abstract BackgroundVariant of concern (VOC) SARS-CoV-2 alpha variant (B.1.1.7) was the dominant strain in the Netherlands between March 2021 – June 2021. We describe three primary school outbreaks due to the alpha variant using whole genome sequencing with evidence of large-scale transmission among children, teachers and their household contacts. MethodAll outbreaks described were investigated by the South Limburg Public Health Service, the Netherlands. A case was defined as an individual with a real-time polymerase chain reaction test or antigen test positive for SARS-CoV-2. Whole genome sequencing was performed on random samples from at least one child and one teacher of each affected class.ResultsPeak attack rates in classes were 53%, 33% and 39%, respectively. Specific genotypes were identified for each school across a majority of affected classes. Attack rates were high among staff members, likely to promote staff-to-children transmission. Cases in some classes were limited to children, indicating child-to-child transmission. At 39%, the secondary attack rate (SAR) in household contacts of infected children was remarkably high, similar to SAR in household contacts of staff members (42%). SAR of household contacts of asymptomatic children was only 9%. Conclusion Our findings suggest increased transmissibility of the alpha variant in children compared to preceding non-VOC variants, consistent with a substantial rise in the incidence of cases observed in primary schools and children aged 5-12 since the alpha variant became dominant in March 2021. Lack of mandatory masking, insufficient ventilation and lack of physical distancing also probably contributed to the school outbreaks. The rise of the delta variant (B.1.617.2) since July 2021 which is estimated to be 55% more transmissible than the alpha variant, provides additional urgency to adequate infection prevention in school settings.

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SARS-CoV-2 whole-genome sequencing for informed public health decision making and outbreak tracking and tracing in the Netherlands

BioStudies database ◽

10.6019/s-bsst662 ◽

2021 ◽

Keyword(s):

Public Health ◽

Decision Making ◽

The Netherlands ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Public Health Decision ◽

Health Decision Making ◽

Health Decision

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Characterization and whole genome sequencing of closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands

PLoS ONE ◽

10.1371/journal.pone.0219795 ◽

2019 ◽

Vol 14 (7) ◽

pp. e0219795 ◽

Cited By ~ 1

Author(s):

Redmar R. van den Berg ◽

Serge Dissel ◽

Michel L. B. A. Rapallini ◽

Coen C. van der Weijden ◽

Ben Wit ◽

...

Keyword(s):

The Netherlands ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Multidrug Resistant ◽

Poultry Meat ◽

Whole Genome

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Genomic diversity of SARS-CoV-2 in Pakistan during fourth wave of pandemic

10.1101/2021.09.30.21264343 ◽

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.

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Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.50.1900130 ◽

2019 ◽

Vol 24 (50) ◽

Cited By ~ 5

Author(s):

Rana Jajou ◽

Thomas A Kohl ◽

Timothy Walker ◽

Anders Norman ◽

Daniela Maria Cirillo ◽

...

Keyword(s):

The Netherlands ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Repeat Unit ◽

Genetic Distances ◽

Variable Number ◽

Pairwise Distance ◽

Reference Database ◽

Whole Genome ◽

The Impact

Background Whole genome sequencing (WGS) is a reliable tool for studying tuberculosis (TB) transmission. WGS data are usually processed by custom-built analysis pipelines with little standardisation between them. Aim To compare the impact of variability of several WGS analysis pipelines used internationally to detect epidemiologically linked TB cases. Methods From the Netherlands, 535 Mycobacterium tuberculosis complex (MTBC) strains from 2016 were included. Epidemiological information obtained from municipal health services was available for all mycobacterial interspersed repeat unit-variable number of tandem repeat (MIRU-VNTR) clustered cases. WGS data was analysed using five different pipelines: one core genome multilocus sequence typing (cgMLST) approach and four single nucleotide polymorphism (SNP)-based pipelines developed in Oxford, United Kingdom; Borstel, Germany; Bilthoven, the Netherlands and Copenhagen, Denmark. WGS clusters were defined using a maximum pairwise distance of 12 SNPs/alleles. Results The cgMLST approach and Oxford pipeline clustered all epidemiologically linked cases, however, in the other three SNP-based pipelines one epidemiological link was missed due to insufficient coverage. In general, the genetic distances varied between pipelines, reflecting different clustering rates: the cgMLST approach clustered 92 cases, followed by 84, 83, 83 and 82 cases in the SNP-based pipelines from Copenhagen, Oxford, Borstel and Bilthoven respectively. Conclusion Concordance in ruling out epidemiological links was high between pipelines, which is an important step in the international validation of WGS data analysis. To increase accuracy in identifying TB transmission clusters, standardisation of crucial WGS criteria and creation of a reference database of representative MTBC sequences would be advisable.

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Viral loads and profile of the patients infected with SARS-CoV-2 Delta, Alpha or R.1 variants in Tokyo

10.1101/2021.09.21.21263879 ◽

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.

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Optimization of multiplex PCR composition to screen for SARS-CoV-2 variants of concern

Acta Biochimica Indonesiana ◽

10.32889/actabioina.58 ◽

2021 ◽

Vol 4 (2) ◽

pp. 58

Author(s):

Maya Savira ◽

Enikarmila Asni ◽

Rahmat Azhari Kemal

Keyword(s):

Whole Genome Sequencing ◽

Multiplex Pcr ◽

Genome Sequencing ◽

Screening Method ◽

Positive Control ◽

Whole Genome ◽

Rt Pcr ◽

Pcr Screening ◽

Single Target ◽

Alpha Variant

Background: The ongoing COVID-19 pandemic has led to the emergence of several variants of concern. To rapidly identify those variants, screening samples for whole-genome sequencing (WGS) prioritization could be performed. Objective: We optimized the polymerase chain reaction (PCR) screening method to identify the mutation in spike and ORF1a regions. Methods: We adopted primers targeting mutation in spike and ORF1a region from another study. We optimized the PCR screening method using kits readily available in Indonesia. Firstly, we compared N1 and N2 primers as internal positive control. We also compared GoTaq® 1-Step RT-qPCR System and Indonesia TFRIC-19 BioCOV-19 for the multiplex reaction. We used the optimized composition to screen SARS-CoV-2 positive samples from April – June 2021. Samples with spike and/or ORF1a target failure were subjected to whole genome sequencing (WGS). Results: The results demonstrated the N2 BioCOV-19 reaction as the optimized multiplex PCR composition for spike and ORF1a mutations screening. Whole-genome sequencing has shown that a sample with spike and ORF1a targets failure to be Alpha variant, while other samples with single target failure as non-variants of concern. Therefore, a multiplex RT-PCR composition has been optimized to detect mutation in spike and ORF1a regions. Conclusion: We have optimized a multiplex RT-PCR composition to detect mutation in spike and ORF1a regions.

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Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school

Scientific Reports ◽

10.1038/s41598-021-99080-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pippa Scott ◽

Ji Zhang ◽

Trevor Anderson ◽

Patricia C. Priest ◽

Stephen Chambers ◽

...

Keyword(s):

Staphylococcus Aureus ◽

New Zealand ◽

Primary School ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Ad Hoc ◽

Epidemiological Studies ◽

Whole Genome ◽

Typing Method ◽

Allelic Differences

AbstractEpidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of “allelic differences”. We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.

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Whole genome sequencing of macrolide resistant Streptococcus pneumoniae serotype 19A sequence type 416

10.21203/rs.3.rs-15521/v1 ◽

2020 ◽

Author(s):

Petra Spanelova ◽

Vladislav Jakubu ◽

Lucia Malisova ◽

Martin Musilek ◽

Jana Kozakova ◽

...

Keyword(s):

Czech Republic ◽

Streptococcus Pneumoniae ◽

The Netherlands ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Illumina Miseq ◽

Sequence Type ◽

Macrolide Resistance ◽

Whole Genome ◽

Recent Origin

Abstract Background: The resistance of Streptococcus pneumoniae to macrolides is becoming an increasingly important issue and thus it is important to understand the genetics related to adaptation of this species to the widespread use of antibiotics in Europe. The 58 isolates of S. pneumoniae belonging to sequence type 416 and serotype 19A and to several different phenotypes originated from Italy, Portugal and Czech Republic were thus sequenced on Illumina MiSeq. The aim of the study was to describe the relation between isolates in this collection and the Netherlands15B-37 clone, which belongs to serotype 15B and sequence type 199. The association of sequence type 416 with macrolide resistance was also investigated. Results: Investigation of genes associated with serotype confirmed common recent origin of inquired isolates in the serotype switch between 15B and 19A serotypes. The genes associated with the macrolide resistance are to be quite variable even within closely genetically relative isolates. Conclusions: This tendency to interchange and modification of genes associated with macrolide resistance and surrounding sequences could lead to adaptation to different circumstances and thus to accelerate spreading of this sequence type in regions with high macrolide consumption.

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