Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East

Tayoun, Ahmad Abou; Loney, Tom; Khansaheb, Hamda; Ramaswamy, Sathishkumar; Harilal, Divinlal; Deesi, Zulfa; Varghese, Rupa; Suwaidi, Hanan Al; Alkhajeh, Abdulmajeed; AlDabal, Laila; Uddin, Mohammed; Hamoudi, Rifat; Halwani, Rabih; Senok, Abiola; Hamid, Qutayba; Nowotny, Norbert; Alsheikh‐Ali, Alawi A.

doi:10.1101/2020.05.06.080606

Cited by 16 publications

(20 citation statements)

References 10 publications

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“…This study was approved by the Total RNA Library kit from Illumina (San Diego, CA, USA) as previously described. 12,13,14 Libraries were then sequenced using the NovaSeq SP Reagent kit (2 X 150 cycles) from Illumina (San Diego, CA, USA) to generate a minimum of 15M reads per sample (Supplementary Table 1).…”

Section: Patient Cohort and Ethics Statementmentioning

confidence: 99%

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Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes

Jain

Ramaswamy

Harilal

et al. 2020

Preprint

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Characterizing key molecular and cellular pathways involved in COVID-19 is essential for disease prognosis and management. We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify a molecular signature associated with disease severity. Specifically, we identify globally dysregulated immune related pathways, such as cytokine-cytokine receptor signaling, complement and coagulation cascades, JAK-STAT, and TGF-β signaling pathways in all, though to a higher extent in patients with severe symptoms. The excessive release of cytokines and chemokines such as CCL2, CCL22, CXCL9 and CXCL12 and certain interferons and interleukins related genes like IFIH1, IFI44, IFIT1 and IL10 were significantly higher in patients with severe clinical presentation compared to mild and moderate presentations. Moreover, early induction of the TGF-β signaling pathway might be the primary cause of pulmonary fibrosis in patients with severe disease. Differential gene expression analysis identified a small set of regulatory genes that might act as strong predictors of patient outcome. Our data suggest that rapid transcriptome analysis of nasopharyngeal swabs can be a powerful approach to quantify host molecular response and may provide valuable insights into COVID-19 pathophysiology.

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Section: Patient Cohort and Ethics Statementmentioning

confidence: 99%

“…described 12. Briefly, mild cases were asymptomatic or had mild non-life-threatening symptoms, while moderate cases presented with symptoms (such as persistent fever) requiring medical attention and/or hospitalization.…”

mentioning

confidence: 99%

Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes

Jain

Ramaswamy

Harilal

et al. 2020

Preprint

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“…The COVID-19 pandemic has rapidly spread around the globe during the first six months of 2020. The causative coronavirus, SARS-CoV-2, is the subject of many studies using genomic analysis providing key insights into viral diversity across cities 1 , provinces 2-5 , countries 6-11 , and globally 12 . SARS-CoV-2 has an estimated mutation rate of 0.71-1.40×10 −3 13 , which translates to 21-42 mutations per year.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 phylogeny during the early outbreak in the Basel area, Switzerland: import and spread dominated by a single B.1 lineage variant (C15324T)

Stange

Mari

Roloff

et al. 2020

Preprint

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Background: The first local case of SARS-CoV-2 in Basel, Switzerland, was detected on February 26th 2020. We present a phylogenetic cross-sectional study and explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. Methods: We sequenced SARS-CoV-2 samples from naso-oropharyngeal swabs and generated 468 high quality genomes and called variants with our COVID-19 Genome Analysis Pipeline (COVGAP). We analysed viral genetic diversity using PANGOLIN taxonomic lineages. For identification of introduction and dissemination events across the Basel area a time-calibrated phylogeny was inferred including global SARS-CoV-2 genomes. Findings: Our samples exhibit low lineage diversity compared to neighbouring countries. Lineage B.1 (82.7%), detected from March 2nd, dominated infections in Basel. A large clade within B.1 contains 69.1% of our samples, all of which carry the SNP C15324T, suggesting local transmission in spreading events. We have located the geographic origin of this mutation in our tri-national region. The remaining genomes map broadly over the global phylogenetic tree, evidencing several events of introduction from and/or dissemination to other regions of the world. Further, we have identified several transmission events within families. Interpretation: Molecular surveillance of SARS-CoV-2 by phylogenetic reconstruction in the Basel area provides important insights into local transmission (spreading events and family transmission). This phylogenetic analysis enriches epidemiological and contact tracing data, allowing connection of seemingly unconnected events and drawing conclusions, which can be used to inform public health interventions. Funding: No dedicated funding was used for this work.

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“…Genome-based studies of the SARS-CoV-2 variants in different geographical regions identified multiple introductions associated with international travel routes (for example, (Bugembe et al 2020, Tayoun et al 2020, Worobey et al 2020). The introductions to the UK (>1400 events) have been recorded to early February and throughout that month (20% of transmission lineages) with the majority (80%) being established in March (Plessis et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

Lycett¹,

Hughes²,

McHugh³

et al. 2021

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The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health Service (NHS), a ‘lockdown’ was introduced on 23rd March 2020 with a restriction of people’s movements. To augment the public health efforts a large-scale genome epidemiology effort (as part of the COVID-19 Genomics UK (COG-UK) consortium) resulted in the sequencing of over 5000 SARS-CoV-2 genomes by 18th August 2020 from Scottish cases, about a quarter of the estimated number of cases at that time. Here we quantify the geographical origins of the first wave introductions into Scotland from abroad and other UK regions, the spread of these SARS-CoV-2 lineages to different regions within Scotland (defined at the level of NHS Health Board) and the effect of lockdown on virus ‘success’. We estimate that approximately 300 introductions seeded lineages in Scotland, with around 25% of these lineages composed of more than five viruses, but by June circulating lineages were reduced to low levels, in line with low numbers of recorded positive cases. Lockdown was, thus, associated with a dramatic reduction in infection numbers and the extinguishing of most virus lineages. Unfortunately since the summer cases have been rising in Scotland in a second wave, with >1000 people testing positive on a daily basis, and hospitalisation of COVID-19 cases on the rise again. Examining the available Scottish genome data from the second wave, and comparing it to the first wave, we find that while some UK lineages have persisted through the summer, the majority of lineages responsible for the second wave are new introductions from outside of Scotland and many from outside of the UK. This indicates that, while lockdown in Scotland is directly linked with the first wave case numbers being brought under control, travel-associated imports (mostly from Europe or other parts of the UK) following the easing of lockdown are responsible for seeding the current epidemic population. This demonstrates that the impact of stringent public health measures can be compromised if following this, movements from regions of high to low prevalence are not minimised.

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Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East

Cited by 16 publications

References 10 publications

Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes

Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes

SARS-CoV-2 phylogeny during the early outbreak in the Basel area, Switzerland: import and spread dominated by a single B.1 lineage variant (C15324T)

Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

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