Genomic and phenotypic characterization of Multisystem Inflammatory Syndrome in Children (MIS-C): a prospective multicenter study from the Middle East

ImportanceClinical, genetic and laboratory characteristics of patients with multisystem inflammatory syndrome in children (MIS-C) in the Middle East have not yet been documented. ObjectiveTo uncover rare genetic variants contributing to MIS-C in patients of primarily Arab and Asian origin. Design, Setting, and ParticipantsA prospective multicenter cohort study was conducted between September 2020 and August 2021 in the United Arab Emirates and Jordan. Forty-five patients meeting the case definition of MIS-C, and a matched control group of twenty-five healthy children with a confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, were recruited. Whole Exome Sequencing (WES) in all 70 participants was performed to identify rare likely deleterious variants in patients with MIS-C and to correlate genetic findings with the clinical course of illness. ExposuresSARS-CoV-2 Main Outcomes and MeasuresFever, organ system complications, laboratory biomarkers, WES findings, treatments, and clinical outcomes. Mann-Whitney U test was used to assess the association between genetic variations and MIS-C attributes. Fishers exact test was used to compute the genetic burden in MIS-C relative to controls. ResultsIn 45 MIS-C patients (23 boys [51.1%]; average age, 7 years [range, 2-14 years]), key inflammatory markers were significantly dysregulated in all patients. Mucocutaneous and gastrointestinal manifestations were reported in 80% (95% CI 66% to 89%) while cardiac and neurological findings were reported in 49% (95% CI 35% to 63%) and 31% (95% CI 19.5% to 45.6%) of patients, respectively. Rare, likely deleterious heterozygous variants in immune-related genes including TLR3, TLR6, IFNAR2, IL22RA2, IFNB1, and IFNA6, were identified in 19 patients (42.2%, 95% CI 29% to 56.7%), of whom seven had more than one variant. There was significant enrichment of genetic variants in patients relative to the control group (29 versus 3, P<.0001). Those variants were significantly associated with earlier onset of disease (31.5%, 95% CI 15.4% to 54% of patients with versus 7.7%, 95% CI 2% to 24% without genetic findings were < 3 years) and resistance to treatment (42%, 95% CI 23% to 64% of patients with versus 11.5%, 95% CI 4% to 29% of patients without genetic findings received two doses of IVIG). Conclusions and RelevanceRare, likely deleterious genetic variants contribute to MIS-C onset and management. Key PointsO_ST_ABSQuestionC_ST_ABSWhat are the clinical, genetic, and laboratory characteristics of multisystem inflammatory syndrome in children (MIS-C) of the Middle East? FindingsIn this prospective study of 45 MIS-C patients of primarily Arab and Asian origins, we show that the clinical course was consistent with that of previously characterized patients from other backgrounds. However, we find an enrichment of rare, likely deleterious immune-related genetic variants, in MIS-C patients, and an association of genetic status with MIS-C onset and resistance to treatment. MeaningComprehensive genetic profiling of MIS-C patients of diverse ancestries is essential to characterize the genetic contribution to this disease.

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

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-{beta} 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-{beta} 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.

SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

BackgroundWith the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical and cost considerations of cWGS should be addressed before it can be widely implemented. MethodsWe performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. ResultsWe show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains. ConclusionsSARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.

Whole genome and phylogenetic analysis of SARS-CoV-2 strains from the index and early patients with COVID-19 in Dubai, United Arab Emirates, 29 January to 18 March 2020

International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel hub in the Middle East, we establish SARS-CoV-2 full genome sequences from the index and early COVID-19 patients in the UAE. The genome sequences are analysed in the context of virus introductions, chain of transmissions, and possible links to earlier strains from other regions of the world. Phylogenetic analysis showed multiple spatiotemporal introductions of SARS-CoV-2 into the UAE from Asia, Europe, and the Middle East during the early phase of the pandemic. We also provide evidence for early community-based transmission and catalogue new mutations in SARS-CoV-2 strains in the UAE. Our findings contribute to the understanding of the global transmission network of SARS-CoV-2.

Molecular characterization of rotavirus strains circulating in Oman in 2005.

Limited genotyping data are available for rotavirus strains in the Middle East. In this study, we investigated the molecular epidemiology of human rotavirus strains circulating in the Sultanate of Oman during 2005. Rotavirus was detected in 178 (57.4%) of 310 of the diarrheal stools of young children <5 years admitted to hospitals and outpatients clinics. Polyacrylamide gel electrophoresis demonstrated the cocirculation of 8 strains, although 2 strains predominated across the Sultanate. Genotyping revealed the presence of human rotavirus strains of types G1P[8], G2P[4], and G3P[8]. Several strains exhibited unusual combinations of G and P genotypes and RNA electropherotypes, indicating the likelihood of natural reassortment events occurring with a high frequency. In addition, the unusual P[10] genotype was identified among the rotavirus strains, in combination with the G1 type.