这个问题由 @拍照稀烂帮帮主 绝对最靠谱。
我不太了解病毒变异的实时动态。不过从“很久没有听到新变异”的角度,Nature最近发了一篇新闻,可能会提供一个不同的视角。
Why call it BA.2.12.1? A guide to the tangled Omicron family (nature.com)
第一句是这样说的。
For the foreseeable future, the coronavirus SARS-CoV-2 will continue evolving into new variants that lead to waves of infections. 在可以预见的未来,新冠都将继续进化出新的变异,带来一波又一波的新感染。
对,这是新闻,不是经过评议的文章。但不代表这话就听不得,没道理。评议可以同行匿名做,也可以就这样公开做,很多期刊已经开始公开评议内容了。有异议的尽管提。
In 2020 and 2021, the World Health Organization (WHO) announced the emergence of variants of concern by giving them names from the Greek alphabet. But this year, Omicron has remained in the spotlight, with members of its family — subvariants — fuelling surges as they evade antibodies that people have generated from previous infections and vaccines. For example, the Omicron subvariant BA.2.12.1 is gaining ground in North America, now accounting for about 26% of the SARS-CoV-2 genomes submitted to the GISAID data initiative, and BA.4 and BA.5 are spreading rapidly in South Africa, comprising more than 90% of genomes sequenced. 2020年以来,世卫组织通过用希腊字母命名的方式来宣示需密切关注的新变异株(VOC)。但今年以来,关注的全是Omicron和其家族内层出不穷的免疫逃逸亚型。例如,BA2.12.1已占北美流行的26%,而BA.4和BA.5已经在南非超过90%。
Given the subvariants’ increasing dominance, Nature spoke to researchers to make sense of the current wonky names, and to learn why the WHO hasn’t given them Greek monikers that could spur policymakers to take stronger action. 既然亚型这么多,Nature询问相关研究人员现行命名的意义,以及为什么世卫给新的变种希腊字母名称以取得政策制定者更高的关注。
SARS-CoV-2 acquires mutations as it replicates in cells. Technically, this means that millions of variants probably arise every day. But the majority of mutations don’t improve the virus’s ability to survive and reproduce, and so these variants are lost to time — outcompeted by fitter versions. 新冠通过在细胞内复制积累突变。这就意味着每天都会产生数以百万的突变体。但绝大多数突变并不会提高病毒的生存或复制能力,因此这些变异会遭到淘汰。
A small portion of variants do, however, gain traction. When this happens, researchers conducting genomic surveillance flag samples that all have the same set of distinct mutations. To find out whether these samples constitute a new branch on the SARS-CoV-2 family tree, they contact bioinformaticians who have established nomenclature systems for the virus. One popular group, called Pango, consists of about two dozen evolutionary biologists and bioinformaticians who compare the samples’ sequences with hundreds of others using phylogenetic software. 但是,少数突变体会留下。研究者需要对这样的情况进行基因组学监控,通过相同的变异发现流行株,然后由生物信息学家进行进化分析,从而确定病毒的命名。一个由二十余位进化生物学家和生物信息学家组成的团队,Pango,就在进行这样工作。
The group’s name derives from a software program called Pangolin, originally created by bioinformatician Áine O’Toole at the University of Edinburgh, UK. If the analysis suggests that the new samples derived from the same recent common ancestor, it means that they are a distinct lineage on the coronavirus tree. In determining whether to name the lineage, Pango considers whether the variants have appeared more frequently over time, and whether their mutations are in regions of the virus that might give it a competitive edge. At this point, a lineage label doesn’t indicate risk. Rather, it allows scientists to keep an eye on a variant and learn more. 团队名字来自于一个由爱丁堡大学(不是上海)生物信息学家Aine O'Toole开发的叫作Pangolin的软件。如果分析认为新的样品来自于进化树的某个节点,就意味着新冠又产生了新的分支。决定是否为新分支命名时,Pango需要考虑该突变体是否会持续流行,以及其突变所在位置是否会带来竞争优势。目前来看,分支的标示并不意味着风险。更多只是让科学家保持关注。
“We want to name everything that jumps out at us at an early stage so that we can define it and track it, and see if it is growing quickly relative to other lineages,” says Andrew Rambaut, an evolutionary biologist at the University of Edinburgh and a member of Pango. “You probably won’t hear of most of the lineages we name,” he says, because they couldn’t compete with other versions of SARS-CoV-2 and have disappeared. 爱丁堡大学的进化生物学家,也是Pango成员Andrew Rambaut说:“我们想要为每一个早期出现的变异体命名以便持续观察其是否具有生存优势。你可能没机会听说绝大多数我们命名的突变体,因为它们都被淘汰消失了。”
When naming a variant, the Pango committee uses a hierarchical system that indicates the variant’s evolutionary history and when it was detected relative to others. The initial letters in the name reflect when Pango gave the lineage a label, following in a sequence from A to Z, then from AA to AZ, BA to BZ, and so on. Separated by a full stop, the next numbers indicate the order of branches from that lineage. For example, BA.1, BA.2, BA.3, BA.4 and BA.5 are the first five branches descending from an original Omicron ancestor. And BA.2.12.1 is the 12th lineage to branch off from BA.2, and then the first named branch on that 12th bush. All subvariants are variants, but researchers use the former term when they want to imply that the lineages belong to a larger grouping, such as Omicron. 命名变异体时,Pango委员会使用一个层级系统来表示变异体的进化历史和发现的次序。首字母是谱系的标示,从A到Z排列。然后是AA到AZ,BA到BZ,以此类推。后缀用句点分隔的数字代表在该谱系内的分支次序。例如BA.1,BA.2,BA.3,BA.4和BA.5是Omicron始祖率先分化的五个分支。而BA.2.12.1表示从BA.2分化出的第十二个谱系中第一个被命名的分支。所有的亚型都是不同的变异体,但研究者沿用旧标示以表示所有谱系都来自于Omicron。
If a variant evades the immune system much more effectively than others in circulation, causes more severe disease or is much more transmissible, the WHO might determine it to be a ‘variant of concern’ and change its name to a Greek letter (see ‘Evolution of a virus’). For instance, the multiple concerning mutations in a variant labelled as B.1.1.529 last year, coupled with its rapid rise, prompted the WHO to change its name to Omicron in November 2021. Whereas Pango’s technical names are meant to help researchers track SARS-CoV-2 evolution, the WHO’s system places a priority on the ease of communication to the public. 如果变异体可以更有效地免疫逃逸,或具有更高的致病性,或更强力的传播力,世卫组织可能会决定这是一个新的VOC,并将其名称改为希腊字母。例如,去年一个具有多个突变的变异体B.1.1.529快速兴起,导致世卫在11月将其名称改为Omicron。一言以蔽之,Pango的命名更多是为研究者追踪病毒的进化服务,而世卫的命名系统更重视与公众交流的便利性。
Given all these variants, is SARS-CoV-2 evolving more rapidly than other viruses?
Not necessarily, Rambaut says. Researchers are finding an incredible amount of diversity in SARS-CoV-2, but they’re also sequencing this virus at an unprecedented rate. A record 11 million SARS-CoV-2 genomes have been uploaded to the popular GISAID data platform since January 2020. By contrast, researchers have uploaded about 1.6 million sequences of the influenza virus to GISAID’s EpiFlu database since May 2008. 既然有这么多变异体,这说明新冠的进化比其它病毒更快吗?Rambaut说不一定。研究者发现新冠有很多变异体,但对新冠变异的关注也是前所未有的。自2020年1月以来已经有一千一百余万组新冠基因组数据上传到GISAID数据平台。与之相比,自2008年5月以来,只有约一百六十万流感基因组上传到GISAID数据库。
Still, Rambaut says, many questions remain about how SARS-CoV-2 is evolving, because sequencing is nearly absent in some parts of the world, and some countries with raging outbreaks are scaling back genomic surveillance. Rambaut说,还有很多关于新冠进化的问题需要解决。世界某些地方的测序资料是几乎空白的,而有些爆发流行的地区正在减少基因组学的监控。
Could Omicron’s subvariants, such as BA.4, eventually receive Greek names?
Yes, although it hasn’t happened yet. Some researchers argue that the Omicron subvariants currently fuelling surges, such as BA.4 and BA.2.12.1, deserve simpler names to aid communication with governments and the public at a time when regard for COVID-19 control measures, such as face masks, is waning. They also point out that unlike Delta’s subvariants — which were not discussed much in the media — BA.4 and BA.2.12.1 can overcome immunity provided by earlier infections with other Omicron subvariants. This was unexpected, says Houriiyah Tegally, a bioinformatician at the Centre for Epidemic Response and Innovation in Stellenbosch, South Africa. “Everyone thought that only new variants would cause new waves, but now that we’re seeing that Omicron can do it, maybe we should adapt the system of naming,” she suggests. Omicron的亚型如BA.4有没有可能最终获得希腊字母命名?有可能,不过目前尚未提上日程。一些研究者认为Omicron的亚型如BA.4和BA.2.12.1在掀起流行的浪潮,应该获得更简单的名字以便于政府和民众沟通,尤其是现在诸如口罩之类的公卫措施正在减少的时候。他们同时指出,媒体还很少提及关于免疫逃逸的问题。与Delta的亚型不同,BA.4和BA.2.12.1可以突破其它早期Omicron亚型感染带来的免疫屏障。南非CERI的生物信息学家Houriiyah Tegally说:“这令人非常意外。每个人都认为只有新变异株会造成新流行。但现在我们看到Omicron的亚型就可以做到。也许需要改变命名系统了。”
But the WHO is so far resisting this idea. WHO virologist Lorenzo Subissi says that the capacity for immune evasion isn’t wildly different between Omicron subvariants. He adds that the agency’s assessment could change if future studies prove that an Omicron subvariant causes more severe disease than other Omicron varieties. The technical lead of the WHO’s COVID-19 response, Maria Van Kerkhove, adds that the agency also doesn’t recommend swapping a technical label for a Greek name in the hope of spurring leaders to take the ongoing pandemic more seriously. “This is already a scary virus, it is still killing huge numbers of people unnecessarily,” she says, suggesting that world leaders should already be paying attention. 但世卫组织目前还没有这样的计划。世卫的病毒学家Lorenzo Subissi说Omicron的亚型间免疫逃逸能力的差别不大,无需单独命名。他补充说如果未来的研究证明Omicron的某个亚型会导致更严重的症状,世卫的评估可能会改变。世卫新冠反应小组的技术负责人Maria Van Kerkhove补充,世卫组织并不推荐通过用希腊字母命名的方式来提起领导人的重视。她表示:“新冠已经是一个可怕的病毒,造成了大量人口的非必要死亡。”她认为这足以让领导人提起重视。
翻译完这篇新闻,我不由想起了魔法部…… |