Characterization of the different expressed RNAseq variants in SARS-CoV-2 infected patients

A recent study posted to the medRxiv* preprint server analyzed the ribonucleic acid sequencing (RNAseq) variants of coronavirus disease 2019 (COVID-19) patients and healthy donors.

Study: RNAseq analysis reveals prominent and distinct expressed variants that are related to disease severity in SARS-CoV-2 infected patients with mild-to-severe disease. Image Credit: tilialucida/Shutterstock
Study: RNAseq analysis reveals prominent and distinct expressed variants that are related to disease severity in SARS-CoV-2 infected patients with mild-to-severe disease. Image Credit: tilialucida/Shutterstock

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major public health concern worldwide. To date, COVID-19 has caused more than 482 million cases and 6.12 million deaths globally. Understanding the expressed variants that underpin a wide range of SARS-CoV-2 presentations is important in combating the COVID-19 pandemic. Analyzing what causes SARS-CoV-2 to present differently among populations and how to control the pandemic could be aided by identifying the expressed RNA variants.

However, SARS-CoV-2 being a new virus, it is yet to be determined what defines the expressed RNAseq variants in convalescent, healthy, moderately infected, severely infected, and COVID-19 patients admitted to the intensive care unit (ICU).

About the study

In the present work, the researchers characterized the different expressed RNAseq variants among the recovered, ICU-admitted, moderately infected, and severely infected COVID-19 patients. The scientists postulated that COVID-19 leads to the expression of distinct RNA variants. They performed bulk RNA sequencing from SARS-CoV-2-positive patients with diverse clinical outcomes, COVID-19 convalescents, and healthy donors in several medical facilities in the United States of America (USA), Georgia, and Atlanta. The team analyzed the expression of host RNA variants to discover more about COVID-19 and its pathogenesis.

Peripheral blood mononuclear cells (PBMCs) samples were procured from 34 healthy donors and 16 severely infected, eight ICU admitted, eight moderately infected, and two convalescents COVID-19 patients. The bulk RNA sequencing data and the identifier PRJNA639275 were retrieved from the Sequence Reads Archive (SRA). 

Cutadapt version 3.7 and Fast Quality Control (FastQC) version 0.11.9 were used for adaptor trimming and to evaluate the read quality, respectively. The splice aware genome aligner named STAR was used to compare the reads to the reference genome, i.e., Homosapien genome assembly 38 (hg38). The Genome Analysis Tool Kit (GATK) was used to identify variants employing the rnavar pipeline, a component of the nf-core pipelines.

Findings and discussions

The results indicated that the healthy controls displayed distinct expressed RNA variants versus the COVID-19 patients irrespective of the status of the SARS-CoV-2 infection. Surprisingly, the authors found that the SARS-CoV-2-recovered individuals and healthy cohorts' data clustered together. The present study data were heterogeneous as some healthy controls were grouped with the COVID-19 patients. This might be because of false-negative findings that misclassified these participants as healthy while they were asymptomatic SARS-CoV-2-infected patients.

It was observed that the state of COVID-19 does not affect the expressed RNA variants in SARS-CoV-2-positive patients with moderate disease, severe disease, and admitted to the ICU. The male (36) and female (32) participants had an identical response to COVID-19, and the expressed RNA variants.

The expressed RNA variants' abundance in healthy and COVID-19 patients differed significantly. The ICU-admitted, severe, and moderate SARS-CoV-2-positive patients demonstrated an equivalent abundance of expressed RNA variants following the viral infection. Additionally, COVID-19-recovered and healthy controls' data clustered together, indicating that once the SARS-CoV-2-infected individual recovers, their transcriptome profile switches back to the healthy state.

Nevertheless, the expression profiles of the expressed RNA variants among patients with severe SARS-CoV-2 infection revealed a distinct pattern. Some variants were more numerous in one group of critically infected patients and less plentiful in another. Female and male patients had the same variant expression after SARS-CoV-2 infection.

The COVID-19-recovered, ICU-admitted, severe, and moderate patients displayed diverse sets of distinct single nucleotide polymorphism (SNP) variants that separate these patients from the healthy controls. Among SARS-CoV-2-recovered, ICU-admitted, moderately infected, and severely infected individuals, six, 35, 33, and seven distinct RNAseq variants were discovered, respectively. Surprisingly, the top expressed variants overlapped across the severely infected and ICU-admitted COVID-19 patients, indicating that the expressed SNP variants in ICU patients also describe critically infected individuals.

Conclusions

The study findings indicated that the SARS-CoV-2-recovered, severely infected, moderately infected, and ICU admitted individuals had distinct sets of RNAseq variants. COVID-19 convalescents demonstrated the same expressed RNA variant sets similar to that of healthy people. On the contrary, the COVID-19 patients and healthy controls exhibited different sets of expressed variants, which were the patient phenotype characteristics. These unique expressed variants in COVID-19 patients could be potential targets for SARS-CoV-2 therapies. 

Overall, the present findings will be beneficial in the development of COVID-19 test kits and classifying SARS-CoV-2-infected people to improve the control and management of COVID-19. Further, it offers a list of SARS-CoV-2 RNA variants and relevant genes which can inform the COVID-19 drug development and discovery studies.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Shanet Susan Alex

Written by

Shanet Susan Alex

Shanet Susan Alex, a medical writer, based in Kerala, India, is a Doctor of Pharmacy graduate from Kerala University of Health Sciences. Her academic background is in clinical pharmacy and research, and she is passionate about medical writing. Shanet has published papers in the International Journal of Medical Science and Current Research (IJMSCR), the International Journal of Pharmacy (IJP), and the International Journal of Medical Science and Applied Research (IJMSAR). Apart from work, she enjoys listening to music and watching movies.

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