Okendo Javan, Okanda David
Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road Observatory, Cape Town, 7925 South Africa.
Research, Innovations, and Academics Unit, Tunacare Services Health Providers Limited, Nairobi, Kenya.
Egypt J Med Hum Genet. 2022;23(1):84. doi: 10.1186/s43042-022-00299-5. Epub 2022 Apr 28.
Severe acute respiratory syndrome (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate, and those admitted to the intensive care unit (ICU) is yet to be presented. We characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals.
The bulk RNA sequencing data with identifier PRJNA639275 were downloaded from Sequence Reads Archive (SRA). The individuals were divided into: (1) healthy, = 34, moderate, = 8, convalescent, = 2, severe, = 16, and ICU, = 8. Fastqc version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. STAR was used to align reads to the reference genome, and GATK best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines.
Our analysis demonstrated that different sets of unique RNAseq variants characterize convalescent, moderate, severe, and those admitted to the ICU. The data show that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as the healthy controls. We showed that the healthy and SARS-CoV-2-infected individuals display different sets of expressed variants characteristic of the patient phenotype.
The individuals with severe, moderate, those admitted to the ICU, and convalescent display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance the management and control of SARS-CoV-2 infection in our population.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）仍然是全球重大的公共卫生挑战。SARS-CoV-2是一种新型病毒，对于在健康、康复、重症、中度以及入住重症监护病房（ICU）的患者中，哪些构成了表达的RNA序列变体，目前尚无相关研究报道。我们对健康、重症、中度、ICU和康复个体中不同的表达RNA序列变体进行了特征分析。
从序列读取存档库（SRA）下载了标识符为PRJNA639275的批量RNA测序数据。个体被分为：（1）健康组，n = 34；中度组，n = 8；康复组，n = 2；重症组，n = 16；ICU组，n = 8。分别使用Fastqc 0.11.9版本和Cutadapt 3.7版本评估读取质量并进行接头修剪。使用STAR将读取序列与参考基因组进行比对，并遵循GATK最佳实践，使用nf-core管道中的rnavar管道调用变体。
我们的分析表明，康复、中度、重症和入住ICU的个体具有不同的独特RNA序列变体集。数据显示，从SARS-CoV-2感染中康复的个体与健康对照具有相同的表达变体集。我们表明，健康个体和感染SARS-CoV-2的个体表现出不同的表达变体集，这些变体集是患者表型的特征。
重症、中度、入住ICU和康复的个体表现出独特的变体集。本研究的结果将为检测试剂盒的开发和SARS-CoV-2患者的分类提供信息，以加强我国人群中SARS-CoV-2感染的管理和控制。
