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SARS-CoV-2 with transcription regulatory sequence motif mutation poses a greater threat

Authors:

Abstract

Objective To analyze the mutations in transcription regulatory sequences (TRSs) of coronaviruss (CoV) to provide the basis for exploring the patterns of SARS-CoV-2 transmission and outbreak. Methods A combined evolutionary and molecular functional analysis of all sets of publicly available genomic data of viruses was performed. Results A leader transcription regulatory sequence (TRS-L) usually comprises the first 60-70 nts of the 5' UTR in a CoV genome, and the body transcription regulatory sequences (TRS-Bs) are located immediately upstream of the genes other than ORF1a and 1b. In each CoV genome, the TRS-L and TRS-Bs share a specific consensus sequence, namely the TRS motif. Any changes of nucleotide residues in the TRS motifs are defined as TRS motif mutations. Mutations in the TRS-L or multiple TRS-Bs result in superattenuated variants. The spread of super-attenuated variants may cause an increase in asymptomatic or mild infections, prolonged incubation periods and a decreased detection rate of the viruses, thus posing new challenges to SARS-CoV-2 prevention and control. The super-attenuated variants also increase their possibility of long-term coexistence with humans. The Delta variant is significantly different from all the previous variants and may lead to a large-scale transmission. The Delta variant (B.1.617.2) with TRS motif mutation has already appeared and shown signs of spreading in Singapore, which, and even the Southeast Asia, may become the new epicenter of the next wave of SARS-CoV-2 outbreak. Conclusion TRS motif mutation will occur in all variants of SARS-CoV-2 and may result in super-attenuated variants. Only super-attenuated variants with TRS motif mutations will eventually lose the abilities of cross-species transmission and causing outbreaks.
新型冠状病毒SARS-CoV-2属于套式病毒目
Nidovirales冠状病毒科Coronaviridae冠状病毒
亚 科CoronavirinaeBeta 冠状病毒属的 B亚 群
Sarbecovirus。在本文中,如不特别说明,冠状病毒
指冠状病毒亚科。根据国际病毒分类委员会第9次会
议报告,冠状病毒亚科Coronaviridae分为 4个属,
别是 AlphaBetaGamma Delta 冠状病毒;Beta 冠状
病 毒 属 又 再 分 为 5个 亚 属 , Embecovirus
SarbecovirusMerbecovirusNobecovirus
Hibecovirus分别对应此前已定义ABCD4个亚
1- 2
和一个我们新定义的E亚群。SARS-CoV-2的基
因组与其他冠状病毒基因组结构相似,是一个不分节
的单股正链RNA 12 个基因共编码26个蛋白其中,
ORF1aORF1b基因各编码一个多聚蛋白,这两个多
聚蛋白 被切割成 16 成熟蛋白NSP1-16以行使功
能。此外SARS-CoV-2基因组还编4结构蛋白S
EMN6辅助蛋白3a67a7b810
TRSTRS 基序突变的新型冠状病毒威胁更大基序突变的新型冠状病毒威胁更大
贝锦龙 1徐国峰 2 2王欣钰 3丘栋安 4阮吉寿 3 2 2
1广东省农业科学院农业生物基因研究中心,广东 广州 510275南开大学 2命科学学院,
3数学科学学院,
天津 300071
4英国诺丁汉特伦特大学生物科学系,诺丁汉 NG11 8NS
SARS-CoV-2 with transcription regulatory sequence motif mutation poses a greater threat
BEI Jinlong1, XU Guofeng2, CHANG Jia2, WANG Xinyu3, QIU Dongan4, RUAN Jishou3, LI Xin2, GAO Shan2
1Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510275, China; 2College of Life Sciences,
3School of Mathematical Sciences, Nankai University, Tianjin 300071, China; 4John Van Geest Cancer Research Centre, School of Science and
Technology, Nottingham Trent University, Nottingham, NG11 8NS, United Kingdom
摘要:目的 研究冠状病毒转录调控序TRS基序突变,为深入研究冠状病毒的爆发、传播规律以及开发减毒活疫苗等提供理
论基础。方法 用进化与分子功能联合分析法,对公开的全部套目病毒基因组数据进行分析。结果 冠状病毒基因组内的前
导转录调控序列TRS-L通常由其5'端非编码区内的 60~70个核苷酸残基组成长度不同的基因体转录调控序列TRS-B
于除 ORF1a1b外的其它基因紧邻的上游,每个冠状病毒基因组的 TRS-LTRS-B共有一段特定的一致性序列,TRS
序,TRS 基序中出现的碱基变化叫做 TRS基序突变。TRS基序突变如果发生在 TRS-L或多个 TRS-B中,会形成超级减毒株。
超级减毒株的扩散,可引起无症或轻症感染者增多,潜伏时间长,以及漏检率上升等问题, SARS-CoV-2 的防控提出新的挑
战。超级减毒株还会增大与人类长期共存的概率,将长期威胁人类健康。Delta突变株与此前出现的突变株有显著不同,如果
不高度重视,可能引起大规模传播。带TRS基序突变的Delta 突变株已经在新加坡出现并有扩散趋势因此新加坡甚至东南
可能形成下一波疫情的传播中心。结论 各种SARS-CoV-2 突变株都将产生TRS 基序突变,只有带 TRS基序突变的超级减
株,才能最终失去跨物种传播和大爆发的能力。
关键词NSP15蛋白酶切位点;Delta突变株;SARS-CoV-2大流行;超级减毒株
Abstract: Objective To analyze the mutations in transcription regulatory sequences (TRSs) of coronaviruss (CoV) to provide
the basis for exploring the patterns of SARS-CoV-2 transmission and outbreak. Methods A combined evolutionary and
molecular functional analysis of all sets of publicly available genomic data of viruses was performed. Results A leader
transcription regulatory sequence (TRS-L) usually comprises the first 60- 70 nts of the 5' UTR in a CoV genome, and the body
transcription regulatory sequences (TRS-Bs) are located immediately upstream of the genes other than ORF1a and 1b. In each
CoV genome, the TRS-L and TRS-Bs share a specific consensus sequence, namely the TRS motif. Any changes of nucleotide
residues in the TRS motifs are defined as TRS motif mutations. Mutations in the TRS- L or multiple TRS-Bs result in super-
attenuated variants. The spread of super-attenuated variants may cause an increase in asymptomatic or mild infections,
prolonged incubation periods and a decreased detection rate of the viruses, thus posing new challenges to SARS-CoV-2
prevention and control. The super-attenuated variants also increase their possibility of long-term coexistence with humans.
The Delta variant is significantly different from all the previous variants and may lead to a large-scale transmission. The Delta
variant (B.1.617.2) with TRS motif mutation has already appeared and shown signs of spreading in Singapore, which, and even
the Southeast Asia, may become the new epicenter of the next wave of SARS-CoV-2 outbreak. Conclusion TRS motif mutation
will occur in all variants of SARS-CoV-2 and may result in super-attenuated variants. Only super-attenuated variants with TRS
motif mutations will eventually lose the abilities of cross-species transmission and causing outbreaks.
Keywords: NSP15 cleavage site; Delta variant; SARS-CoV-2; pandemics; super-attenuated variant
收稿日期2021-08-18
基金项目广东省自然科学基金2021A1515011072
作者简介贝锦龙副研究员硕士生导师,E-mail: beijinlong@gdaas.cn
通信作者:高 山,副教授,硕士生导师,E- mail: gao_shan@mail.nankai.
edu.cn
J South Med Univ, 2022, 42(3): 399-404 doi 10.12122/j.issn.1673-4254.2022.03.12 ··399
冠状病毒基因组的复制和转录由复制转录复合体
Replicationtranscription complex
3
其核心是RNA
依赖型RNA聚合酶RdRp也常表示为NSP12。冠状
病毒乃至整个套目病毒的一个非常重要的特征就是
在跳跃式转录,也称为不连续转录、聚合酶跳跃或模板
转换。跳跃式转录的分子机制是一个长期没有得到解
答的科学问题有研究提出Leader-body fusion模型用
以解释跳跃式转录
4
但其分子机制依然未知。直到
2021年首次报道了TRS 基序是冠状病毒的尿苷酸特异
RNA 内切酶NendoU常表示为 NSP15的酶切位
点,NSP15酶切作用是实现冠状病毒跳跃式转录的分
子基础,并提出了NSP15对冠状病毒复制和转录的负
反馈调控模型
5
。由于冠状病毒的跳跃式转录与重组
都需要依赖NSP15的酶切作用即共享一个分子机制
冠状病毒可在其生存周期中随时发生重组,成为导致
反复暴发的最主要因素
5
。在随后的研究中又发现了
NSP15蛋白酶切位点与RNA甲基化的相互关系,特别
TRS卡结构的重要作用,进一步解释了冠状病毒
制转录复合体的工作原理
3
TRS基序将冠状病毒转
录调控和重组等重要功能联系到一起因此,值得深入
研究
本研究报 道全部冠状病 毒的 TRS 基序以及多种
SARS-CoV-2突变株已出现TRS基序突变,为深入研
冠状病毒的爆发、传播规律以及开发减毒活疫苗等建
了基础;本研究采用进化与分子功能联合分析法分析
TRS 基序突变在冠状病毒进化中的作用预测
SARS-CoV-2大流行后期有可能出现带TRS突变的
级减毒株并分析了其危害,为大流行后期的防控提供
理论依据; TRS 基序突变Delta突变株已经在新加
坡出现并有扩散趋势因此新加坡东南亚可能形
心。
1材料和方法
1.1 TRS序的鉴定
NCBI RefSeqGenBank GISAID等数据库
取冠状病毒亚科和环曲病毒亚科所有病毒的基因组序
列。将下载的基因组按照亚群分类,使用 Clustal W
具进行多重比对,将结构蛋白基因SEMN对齐,
找出所有5'UTR中以及结构蛋白基因上游的TRS鉴定
每个病毒TRS-L TRS-Bs
1.2 TRS序突变的监测
通过检索国家生物信息中2019新型冠状病毒
息库https://ngdc.cncb.ac.cn/ncov/TRS-L
经典 TRS 基序 ACGAAC基因组位置为 MN908947
70-75的突变情况 GISAID 数据库获取带TRS 基序
突变SARS-CoV-2的基因组序列,通过Perl 脚本编程
再次确认TRS序突变信息并进行统计
1.3 SARS-CoV-2变株对中和抗体效力的影
通过 Outbreak.info网站对 SARS-CoV-2 S 蛋白突
变位点的频率进行统计。结合Beta冠状病毒B亚群
5个重组RC3 RC5 位于 NTD 构域中,RC6
RC7S1亚基的RBD结构域中分析各RBD突变
对中和抗体的影响。
2结果
2.1 冠状病毒跳跃式转录的分子机
如果RNA合成RdRp不间断地读取基因RNA
[记做 gRNA(+)]则合成反义基因组 RNA[记做 gRNA
(-)]如果RdRp在合成过程中遇到基因体转录调控序列
TRS-B时产生跳跃并将模板转换为前导转录调控
TRS-L则合成产物为反义亚 基因组 RNA[
sgRNAs(-)]RdRp 的连续合成完成复制以ORF1a
1b个基因的转录,RdRp的不连续合成完成其10
基因的转录,即跳跃式转录;RdRp gRNAs(- )
sgRNAs(-)为模板分别合成 gRNAs(+)sgRNAs(+)
gRNAs(+)用作 ORF1a ORF1b 翻译的模板,sgRNAs
(+)用作其它10 种蛋白质翻译的模板TRS-L通常由冠
状病毒基因组前6070个核苷酸残基位于5'端非编
码区内组成,长度不同的 TRS-B位于除 ORF1a1b
外的其它基因的紧邻上游,并调控其紧邻下游的基因;
每个冠状病毒基因组的TRS-L TRS-B共有一段特
的一致性序列,叫做转录调控序列基序简称TRS 基序
1
2.2 全部冠状病毒TRS序的鉴定
在使用NCBI公开数据进一步验 NSP15蛋白酶
切位点的过程中,我们鉴定了套目下全部病毒的经典
TRS基序2特别是确认了冠状病毒的经TRS
canonical TRS motif都是以腺苷酸残基A开始的
A最多其次是C的一致性序列这一规律。结合进化分
析的结果进一步定义如下:一个冠状病毒基因组只有
一个经典TRS基序这个 TRS 基序与该病毒所在类群
最早分化出来的祖先的TRS序最接近一般情况下
冠状病毒亚科病TRS-L中的TRS基序是经TRS
序,TRS-B中的基序可以是经TRS基序,也可以是
非经典 TRS 基序non-canonical TRS motif。非经
TRS基序与经典TRS 基序可以有几个核苷酸残基的差
异,这些差异显然来自进化过程中保留下的突变。
在鉴定环曲病毒亚科的经典TRS基序2的过
程中,我们首次发现TRS-L中的TRS基序突变,突破
了基于冠状病科数据对经典TRS基序认识最典型
的一个案例来自白鳊鱼病毒基因组RefSeq:NC_
008516现包 1其 经典 TRS 基序是
AACACAGCACTACA 1该基序长度远远大于
状病毒亚科的经典TRS基序的常见长度6~8 nt推测
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··400
此长度更接近冠状病毒祖先的经典TRS 基序的长度;
2TRS- L 中的 TRS 基序突变为非经典 TRS 基序
AACACACAACAAG1而冠状病毒亚科的所有
病毒TRS-L 中不存在TRS基序突变
2.3 TRS序突变在冠状病毒进化中的作
本研究采用此前提出的进化与分子功能联合分析
法,分析了 GenBank 数据库全部冠状病毒的基因组序
列,结果发现:1冠状病毒亚科的每一个属的所有病
只有一种经TRS高度保守只有Beta
病毒A亚群例外,它与同属的其它几个亚群的经TRS
序不 (图 12Beta 冠状病毒 B(特别是
SARS-CoV SARS-CoV-2的所有病毒基因组中的
TRS-L 和调控 4个结构基因SEMN TRS-B
的经典TRS基序均没有突变发生;3Beta冠状病毒B
亚群以外的各类群AlphaBetaGamma Delta
状病毒以Beta 冠状病毒其它亚群普遍存在至少一
调控结构基因的TRS-B 中的经TRS序突变为非
TRS基序。因此推断:TRS 基序突变导致Beta冠状
病毒 B亚群以外的各类群病毒的基因转录能力以及
NSP15调控能力降低病毒减毒后最终失去了跨物种
1 SARS-CoV-2中的跳跃式转录TRS基序
Fig1 Jumping transcription and TRS motifs in SARS-CoV-2. The elements used to represent the SARS-
CoV-2 genome (GenBank: MN908947.3) were originally used in the previous study[5]. A TRS-L usually
comprises the first 60-70 nts of the 5' UTR in a CoV genome, while TRS-Bs with varied lengths are located
immediately upstream of genes except ORF1a and 1b. In each CoV genome, the TRS- L and TRS-Bs share a
specific consensus sequence, namely the TRS motif (e.g. ACGAAC for SARS- CoV- 2). Any changes of
nucleotide residues in the TRS motifs are defined as TRS motif mutations. TRS-L: Transcription
regulatory sequence in the leader; TRS-B: Transcription regulatory sequence in the body; gRNA(+ ):
genomic RNA; gRNA(-): Antisense genomic RNA; sgRNA(+): Subgenomic RNA; sgRNA(- ): Antisense
subgenomic RNA. nsp12: RNA-dependent RNA polymerase (RdRP); nsp15: Nidoviral RNA uridylate-
specific endoribonuclease (NendoU).
2冠状病毒亚科病毒基因组中的经典TRS基序
Fig.2 Canonical TRS motifs of viruses in Coronaviridae. Embecovirus,
Sarbecovirus, Merbecovirus, Nobecovirus and Hibecovirus are also defined
as subgroups A, B, C, D and E. In the present study, we only list canonical TRS
motifs (in red color) of viruses in Coronaviridae.
http://www.j-smu.com J South Med Univ, 2022, 42(3): 399-404 ··401
传播和大爆发的能力,而仅与少量最适宿主长期共存;
不带TRS 基序突变Beta冠状病毒B亚群是冠状病毒
中毒力最强的一个分支,将长期威胁人类健康。
2.4 RBD变对中和抗体效力的影响
Beta 状病 毒 B亚群 组区 集中
ORF1a基因和S基因的S1亚基对应的基因组区域
3其中 3个重组区RC3 RC5位于 S1 亚基的 NTD
结构域对应的基因组区域另外两个RC6 RC7位于
S1基的RBD结构域对应的基因组区域RC3RC7
重组区分别对S白的67-78137-164239-262438-
452468-486位置的氨基酸。位于RBD 结构域的 RC6
RC7重组区对应的氨基酸对于病毒与宿主细胞受体
结合至关重要。而中和抗体可以通过与病毒RBD结构
域的关键氨基酸结合来阻断病毒与受体结合进而阻
病毒进入细胞
2.5 多种SARS-CoV-2突变株出TRS 基序突变
根据对SARS-CoV-2资源库中全部基因组突变信
息的实时跟踪与分析,我们发现多种突变株的基因组
已出现TRS-L 中的 TRS基序突变,这些病毒主要来自
新加坡和墨西哥等国家。根据新加坡2021 3~5月采
样的基因组数据 2我们发现有一些毒株TRS-L
中 的 经 典 TRS 基 序 ACGAAC基 因 组 位 置 为
MN90894770-75中的C突变为M表示ACS
GCY表示 TCG突变为 R表示 A
G。这些位点呈现的核苷酸残基多态MSYR
不是测序错误导致的极大可能是样本个人体内存在
了多个毒株共感染导致的。特别是我们发现了分类
Delta 突变株 B.1.617.2 型的一个新毒株GISAID
EPI_ISL_2508633的基因组TRS-L中的TRS基序突
变为ACAAAC 2。由于病毒群体的极大多样性
1白鳊鱼病毒基因组中TRS 基序
Tab.1 TRS motifs in white bream virus genome
TRS Motif
AACACACAACAAG
AACACAGCACTACA
ACACAGCACTACA
AACACTACAGCC
AACACACACCCATACA
Region
TRS-L
TRS-B
TRS-B
TRS-B
TRS-B
Position
24
21506
25194
25899
26404
Gene (Start-End)
Orf1ab (906-21523)
S (21525-25187)
M (25214-25897)
N (25915-26400)
-
All TRS motifs in the genome of white bream virus (RefSeq: NC_008516) were annotated in the present
study: The first column is the TRS motif; The second column is the region which contains the TRS motif;
The third column is the genomic position of the first nucleotide residue in the TRS motif; The fourth column
is the nearest downstream gene of the TRS motif. This virus does not has the gene E.
3 SARS-CoV-2 S蛋白的重组
Fig.3 Recombination regions in the Spike protein of SARS-CoV-2. To initiate a CoV infection, the S protein encoded by
the S gene needs to be cleaved into the S1 and S2 subunits for receptor binding and membrane fusion. RC3-7 are
recombination regions in the genomes of betacoronavirus subgroup B. Three recombination regions (RC3, RC4 and
RC5) are localized in the N-terminal domain (NTD) of the S1 subunit, while two other recombination regions (RC6 and
RC7) are localized in the receptor binding domain (RBD) of the S1 subunit. A: Only mutations in RBD regions across
SARS-CoV-2 lineages are represented, based on the data from 2,678,671 SARS-CoV-2 genomes downloaded from
outbreak. info on August 8th, 2021. B: The elements used to represent the structure of the S protein were originally
used in a previous study [10]. RBD (in blue color) and NTD (in blue color) are two domains of the S1 subunit.
AB
RC7
RC3
RC5
RC6
RC4
Mutations in the spike protein across SARS-CoV-2 lineages
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··402
于当前获得的少量样本还无法准确评TRS基序突变
对于病毒流行的影响,因此还需进一步收集数据以得
准确的结果。
GISAID数据库2020127~202156
2多种突变株出 TRS基序突
Tab.2 TRS motif mutations in several SARS-CoV-2 variants
Position/Wild
71C
72G
73A
75C
GISAID ID
EPI_ISL_1229164
EPI_ISL_1489724
EPI_ISL_2349776
EPI_ISL_2508657
EPI_ISL_2508861
EPI_ISL_462431
EPI_ISL_483591
EPI_ISL_1816969
EPI_ISL_2349852
EPI_ISL_2508633
EPI_ISL_2508830
EPI_ISL_2508981
EPI_ISL_2508907
EPI_ISL_500540
Collection date
2021/3/4
2021/3/23
2021/5/5
2021/5/14
2021/5/22
2020/3/21
2020/5/2
2021/4/23
2021/5/11
2021/5/16
2021/5/20
2021/5/27
2021/5/24
2020/6/22
Mutant
AMGAAC
ASGAAC
AMGAAC
AMGAAC
AYGAAC
ACRAAC
ACRAAC
ACRAAC
ACRAAC
ACAAAC
ACRAAC
ACRAAC
ACGWAC
ACGAAT
Strain
B.1.524
B.1.1.7
B.1.1.7
B.1.617.2
B.1.617.2
B.1.1
B.6.6
B.1.617.2
B.1.617.2
B.1.617.2
B.1.617.2
B.1.617.2
B.1.617.2
B.6.6
The first column is the position of the nucleotide residue in the SARS-CoV-2 genome (GenBank: MN908947.3)
and its wild type; The second column is the identifier of the record in the GISAID database; The third column is
the sample collection date; The fourth column is the mutant of the TRS motif ACGAAC in the TRS- L (the
mutated nucleotide residue is highlighted); The fifth column is the classification of the virus according to
GISAID. EPI_ISL_2508633 is defined as the reference genome of the Delta variant with TRS motif mutation. M
is Aor C; S is G or C; Y is T or C; R is A or G; and W is T or A.
日采样的29 205 条印度地区SARS-CoV-2的基因组几
乎不TRS 基序突变特别是在印度早期传的毒株中
未发TRS基序突变。因此,我们将EPI_ISL_2508633
指定 为带 TRS 基序突变的 Delta 突变株的参考基因
组。新突变株不仅具Delta突变株的全部特如免
疫逃而且TRS 基序突变可能已是或将发展成
超级减毒株。一步的研究显示,在带TRS序突变的
Delta 突变株中,除了 RBD 结构域中的两个重要突变
L452RRC6 T478KRC7还有最早流行的一
个突D614G此外,NTD结构域中RC4重组区有多
个突变G142DE156GF157del R158delRBD
结构域变异还要频繁
3讨论
根据跳跃式转录的分子机制,TRS基序变必然导
致冠状病毒基因的转录下降一点已得到实验验
6-8
。前期研究对冠状病毒的其它基因组特最主
要是S1/S2 交界处Furin蛋白酶切位点
2
导致的减
也进行了系统性分析
10
并发现了冠状病毒传播和爆发
的一些规律特别是:1Beta冠状病毒的祖先与其他类
群分化后形成Beta状病毒的各分支,这些支总体上
通过减毒或再次爆发得以广泛传播;2A亚群的直接
祖先Beta 冠状病毒的直接祖先分化最早,毒程度最
大,而且具有最高的多样性3BD亚群的直接祖先随
后分开伴随进一步减毒;4C亚群的直接祖先分化最
晚,仍然保留了第二Furin蛋白酶切位点因此减毒程度
很小。对比本研究与以上前期研究结果,们发现:
TRS序突变导致的减毒与Furin白酶切位点导致
减毒在冠状病毒进化中的变化趋势整体一致,特别是:
Beta状病B群所有病毒均未发TRS基序突变;
C亚群例如MERS-CoVGenkBankJX869059仅有N
基因TRS-B中的TRS 基序突变ACGAATCE亚群
例如 GenkBankNC_025217仅有 S基因的TRS-B
TRS基序突变为ACGGAAC。因此我们推断:Beta
冠状病毒BCE亚群仍然处于活跃期将长期威胁人
类健康直到这些病毒通过TRS基序突变继续减毒,
能最终失去跨物种传播和大爆发的能力
根据重组区 RC6RC7 内关键氨基酸的鉴定结
http://www.j-smu.com J South Med Univ, 2022, 42(3): 399-404 ··403
果,有研究对 2021 年初流行的 AlphaB.1.1.7Beta
B.1.351DeltaB.1.617突变株对中和抗体的影响
做了简单评估
10
Alpha 突变株的 3个主要突变69-
70DelN501YP681H均不涉RC6RC7 重组区;
Beta变株的3个主要突变K417NE484KN501Y
中,有一个E484K 涉及RC7重组区,预测会对中和抗体
的作用效果产生轻微影响作为SARS-CoV-2著名的
突变 D614G不 涉及 RC6 RC7 重组区。然而,Delta
突变株的两个突变位点L452R E484K分别位于
RC6RC7重组区内,预测会对作用效果产生重大影
响;来自南美Lambda突变株C37同时具8个主要
突变,分别位RC3G75VT76IRC4R246N247-
253DelRC6L452Q和其它区域F490SD614G
T859N因此,也对中和抗体的作用效果产生较大影
响。特别是,247-253Del 几乎导致了 RC4 的缺失。从
最早的突变 E484K 开始,Delta 突变株的双重突
L452R E484KSARS-CoV-2 已经产生了逃逸
在中和抗体的选择压力一部突变生存下来,
得进一步传播的机会,以上分析已得到后续的实验
验证
11
Delta突变株出现后,Delta 突变株与此前出
的突变株有显著不同,如果不高度重视,可能引起大规
模传播。如果Delta 突变株产生TRS 基序突变可能会
导致超级减毒株的出现,可引起无症或轻症感染者增
多,潜伏时间长,以及漏检率上升等问题,SARS-
CoV-2的防控将提出新的挑战。根据前期研究结果
10
NTD结构域RBD结构域发生过同样多的重组事件,
说明有同样大的正向选择压力因此有可能存在第二
体与NTD相互作用。
冠状病毒强大的重组能力是导致其反复爆发的最
主要因素,冠状病毒的进化历史显示了其爆发-减毒-
次爆发的规律性。减毒的来源
10
主要包RBD区域突
变、S1/S2 交界处的 Furin 蛋白酶切位点突变和 TRS
序突变等。值得注意的是,TRS基序突变与其导致的减
毒不可逆,而其它因素导致的减毒是可逆的。SARS-
CoV-2 爆发的一个重要原因就是因获得 Furin 蛋白酶
切位点而导致其传播力增强
2
。而 SARS-CoV-2爆发
不久报道 Furin 蛋白酶切位点丢失的减毒株
GISAID:EPI_ISL_417443最近出现的Omicron
12
则可能产生双重Furin蛋白酶切位点,因此获得更
大传播力。Omicron突变株,经过多次重组形成,情况
非常复 杂,但基 本上属于 RBD 域突变导致的减
株。目前尚未发现大量Omicron 突变株的基因组中存
TRS基序突变,因此,当前的Omicron突变株并不是
最终的超级减毒株。根据我们的模型包括Omicron
变株在内的各突变株都将产TRS 基序突变只有带
TRS序突变的超级减毒株才能最终失去跨物种传播
和大爆发的能力。超级减毒株通过回复突变再引起大
爆发的可能性几乎不存在,然而,如果多种超级减毒株
长期共存会形成一个庞大的基因库,可与其他非减毒
株进行重组,因此其威胁更大。
本研究分析了墨西哥20213~4月采样的大量数
据,发现大 GISAID分类为B.1.1.519型的毒株
出现了TRS 基序突变。来自新加坡和墨西哥的不同
株在相近的时段都出现TRS基序突变值得进一步深
入研究。当前的病毒核酸检测一般无法获得基因组数
据;高通量测序可以获得基因组数据,但是对于多个病
毒株的共感染样品含量高的毒株会掩盖含量低的减
株,最后得到的一致性序列会丢失很多重要的信息。
此,希望疾控部门监测上传的基因组数据特别是高通
量测序数据中的 TRS基序突变,以便及早应对可能
现的超级减毒株。带TRS基序突变的B.1.1.7突变株已
经向日本GISAIDEPI_ISL_2771613 和 德 国
GISAIDEPI_ISL_2759898扩散 TRS基序突变
B.1.617.2 突变株已经向印度尼西亚GISAID
EPI_ISL_2931745 )和 英 国GISAIDEPI_ISL_
2852198扩散这些再次证了的部测。
参考文献:
1] 陈嘉源,施劲,栋安,. 2019新型冠状病毒基因组的生物息学
分析J.生物信息学, 2020, 18(2): 96-102.
2] 李 ,段广有,张 伟,. 2019新型冠状病毒S蛋白可能存在Furin
蛋白酶切位点J.生物信息学, 2020, 18(2): 103-8.
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complex of SARS-CoV-2 functions in leader-to-body fusionJ.
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6Graham RL, Deming DJ, Deming ME, et al. Evaluation of a
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8Sola I, Moreno JL, Zúñiga S, et al. Role of nucleotides immediately
flanking the transcription-regulating sequence core in coronavirus
subgenomic mRNA synthesisJ. J Virol, 2005, 79(4): 2506-16.
9Liu C, Chen Z, Hu Y, et al. Complemented palindromic small RNAs
first discovered from SARS coronavirusJ. Genes, 2018, 9(9): 442-6.
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Betacoronavirus provides insights into SARS and COVID-19
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the SARS-CoV-2 Omicron variant in southern AfricaJ. Nature,
2022: 2022Jan7.
编辑:林 萍
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··404
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  • 施劲松 陈嘉源
  • 丘栋安
陈嘉源, 施劲松, 丘栋安, et al. 2019 新型冠状病毒基因组的生物信息学分析 [J]. 生物信息学, 2020, 18(02): 96-102.
  • 段广有 李鑫
  • 张伟
李鑫, 段广有, 张伟, et al. 2019 新型冠状病毒 S 蛋白可能存在 Furin 蛋白酶切位点 [J]. 生物信息学, 2020, 18(02): 103-108.