Paper intensive reading (三十一)：Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

Title: Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

Author: Zijie Shen , Yan Xiao, Lu Kang, Wentai Ma...

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 101300, China;

09 March 2020

Summary
An elevated level of viral diversity was found in some SARS-CoV-2 infected patients, indicating the risk of rapid evolution of the virus. Although no evidence for the transmission of intra-host variants was found, the risk should not be overlooked.

Abstract:
Background A novel coronavirus (SARS-CoV-2) has infected more than 75,000 individuals and spread to over 20 countries. It is still unclear how fast the virus evolved and how the virus interacts with other microorganisms in the lung.
Methods We have conducted metatranscriptome sequencing for the bronchoalveolar lavage fluid of eight SARS-CoV-2 patients, 25 community-acquired pneumonia (CAP) patients, and 20 healthy controls.支气管肺泡灌洗液
Results The median number of intra-host variants was 1-4 in SARS-CoV-2 infected patients, which ranged between 0 and 51 in different samples. The distribution of variants on genes was similar to those observed in the population data (110 sequences). However, very few intra-host variants were observed in the population as polymorphism, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. ？？？Although current evidence did not support the transmission of intra-host variants in a person-to-person spread, the risk should not be overlooked. The microbiota in SARS-CoV-2 infected patients was similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria.
Conclusion SARS-CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intra-host variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.

Outline

1. Introduction

2. Results

2.1 Data summary

2.2 Intra-host variants in the genome of SARS-CoV-2

2.3 No evidence for transmission of intra-host variants between samples

2.4 Missing microbiota signature associated with SARS-CoV-2 infection

3. Discussion

4. Methods.

4.1 Subjects and samples collection

4.2 Metatranscriptome sequencing

4.3 Data availability

4.4 Data processing and taxonomic assignments

4.5 Intra-individual variants detection

4.6 Statistical analysis.

正文摘要

肺泡灌洗液上metatranscriptome sequencing
    In our study, we conducted metatranscriptome sequencing on bronchoalveolar lavage fluid (BALF) samples from 8 subjects with Coronavirus disease 2019 (COVID-19, the disease caused by SARS-CoV-2) patients. 

    宿主体内变体的数量很大，说明进化很快
    We found that the number of intra-host variants ranged from 0 to 51 with a median number of 4, suggesting a high evolution rate of the virus. 

    这篇paper虽然有metatranscriptome sequencing，但是并没有太描述这个方法的作用，感觉就是测了RNA，然后分析多样性而已，