科学家恢复被删除的早期新冠病毒基因序列_OK阅读网
双语新闻
Bilingual News


双语对照阅读
分级系列阅读
智能辅助阅读
在线英语学习
首页 |  双语新闻 |  双语读物 |  双语名著 | 
[英文] [中文] [双语对照] [双语交替]    []        


科学家恢复被删除的早期新冠病毒基因序列
Scientist Finds Early Virus Sequences That Had Been Mysteriously Deleted

来源:纽约时报    2021-06-28 07:50



        About a year ago, genetic sequences from more than 200 virus samples from early cases of Covid-19 in Wuhan disappeared from an online scientific database.        大约一年前,来自武汉新冠早期病例的200多个病毒样本的基因序列从一个在线科学数据库中消失了。
        Now, by rooting through files stored on Google Cloud, a researcher in Seattle reports that he has recovered 13 of those original sequences — intriguing new information for discerning when and how the virus may have spilled over from a bat or another animal into humans.        现在,西雅图的一位研究人员报告说,通过对存储在谷歌云上的文件进行分析,他已经恢复了其中的13个原始序列——这是一个有趣的新信息,可以用来识别病毒可能是何时,以及如何从蝙蝠或其他动物传播到人类的。
        The new analysis, released on Tuesday, bolsters earlier suggestions that a variety of coronaviruses may have been circulating in Wuhan before the initial outbreaks linked to animal and seafood markets in December 2019.        周二发布的新分析支持了早些时候的说法,即在2019年12月与生鲜市场有关的最初疫情暴发之前,多种冠状病毒可能已经在武汉传播开来。
        As the Biden administration investigates the contested origins of the virus, known as SARS-CoV-2, the study neither strengthens nor discounts the hypothesis that the pathogen leaked out of a famous Wuhan lab. But it does raise questions about why original sequences were deleted, and suggests that there may be more revelations to recover from the far corners of the internet.        目前拜登政府正在调查这种名为SARS-CoV-2的病毒的有争议来源。这项研究既没有加强,也没有否定病原体是从武汉一家著名实验室泄露出来的假设。但它确实提出了一个问题,那就是原始序列为何被删除,并表明可能有更多信息可以从互联网的偏远角落恢复。
        “This is a great piece of sleuth work for sure, and it significantly advances efforts to understand the origin of SARS-CoV-2,” said Michael Worobey, an evolutionary biologist at the University of Arizona who was not involved in the study.        没有参与这项研究的亚利桑那大学(University of Arizona)进化生物学家迈克尔·伍罗贝(Michael Worobey)说:“这无疑是一项伟大的侦查工作,它大大推进了了解SARS-CoV-2起源的努力。”
        Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center who wrote the new report, called the deletion of these sequences suspicious. It “seems likely that the sequences were deleted to obscure their existence,” he wrote in the paper, which has not yet been peer-reviewed or published in a scientific journal.        撰写这份新报告的弗雷德·哈钦森癌症研究中心(Fred Hutchinson Cancer Research Center)的病毒学家杰斯·布鲁姆(Jesse Bloom)称,这些序列被删除是可疑的。他在文中写道,“删除这些序列似乎是为了掩盖它们的存在,”该论文尚未经过同行评审或发表在科学期刊上。
        Dr. Bloom and Dr. Worobey belong to an outspoken group of scientists who have called for more research into how the pandemic began. In a letter published in May, they complained that there wasn’t enough information to determine whether it was more likely that a lab leak spread the coronavirus, or that it leapt to humans from contact with an infected animal outside of a lab.        布鲁姆和伍罗贝属于一个直言不讳的科学家团体,他们呼吁对大流行如何开始进行更多研究。在5月发表的一封信中,他们抱怨说,没有足够的信息来确定新冠病毒的传播是由于实验室泄漏,还是由于与实验室外的受感染动物接触,从而传到人类身上。
        The genetic sequences of viral samples hold crucial clues about how SARS-CoV-2 shifted to our species from another animal, most likely a bat. Most precious of all are sequences from early in the pandemic, because they take scientists closer to the original spillover event.        病毒样本的基因序列提供了关于SARS-CoV-2如何从另一种动物(很可能是蝙蝠)转移到我们这个物种的关键线索。最宝贵的是大流行早期的序列,因为它们让科学家更接近最初的溢出事件。
        As Dr. Bloom was reviewing what genetic data had been published by various research groups, he came across a March 2020 study with a spreadsheet that included information on 241 genetic sequences collected by scientists at Wuhan University. The spreadsheet indicated that the scientists had uploaded the sequences to an online database called the Sequence Read Archive, managed by the U.S. government’s National Library of Medicine.        布鲁姆在审查各个研究小组公布的基因数据时,看到了2020年3月的一项研究,其中包含武汉大学科学家收集的241个基因序列的信息。电子表格显示,科学家们已经将这些序列上传到一个名为“序列读取档案”(Sequence Read Archive)的在线数据库中,该数据库由美国政府的国家医学图书馆(National Library of Medicine)管理。
        But when Dr. Bloom looked for the Wuhan sequences in the database earlier this month, his only result was “no item found.”        但当布鲁姆本月早些时候在数据库中查找武汉的基因序列时,他得到的唯一结果是“项目未找到”。
        Puzzled, he went back to the spreadsheet for any further clues. It indicated that the 241 sequences had been collected by a scientist named Aisi Fu at Renmin Hospital in Wuhan. Searching medical literature, Dr. Bloom eventually found another study posted online in March 2020 by Dr. Fu and colleagues, describing a new experimental test for SARS-CoV-2. The Chinese scientists published it in a scientific journal three months later.        他很困惑,回到电子表格中寻找更多的线索。它显示,这241个序列是由武汉人民医院一位名叫付爱思的科学家收集的。通过搜索医学文献,布鲁姆最终发现了付爱思及其同事于2020年3月在网上发布的另一项研究,该研究描述了一种针对SARS-CoV-2的新实验测试。三个月后,中国科学家在一份科学杂志上发表了这篇文章。
        In that study, the scientists wrote that they had looked at 45 samples from nasal swabs taken “from outpatients with suspected Covid-19 early in the epidemic.” They then searched for a portion of SARS-CoV-2’s genetic material in the swabs. The researchers did not publish the actual sequences of the genes they fished out of the samples. Instead, they only published some mutations in the viruses.        在这项研究中,科学家们写道,他们观察了45份鼻拭子样本,这些样本取自“疑似Covid-19流行初期的门诊患者”。然后他们在棉签中寻找部分SARS-CoV-2的遗传物质。研究人员没有公布他们从样本中找到的基因的实际序列,只公布了一些病毒的突变。
        But a number of clues indicated to Dr. Bloom that the samples were the source of the 241 missing sequences. The papers included no explanation as to why the sequences had been uploaded to the Sequence Read Archive, only to disappear later.        但是一些线索向布鲁姆表明,这些样本是241个丢失序列的来源。这些论文没有解释为什么这些序列被上传到序列读取档案后又消失了。
        Perusing the archive, Dr. Bloom figured out that many of the sequences were stored as files on Google Cloud. Each sequence was contained in a file in the cloud, and the names of the files all shared the same basic format, he reported.        通过仔细研究档案,布鲁姆发现很多序列都以文件的形式存储在谷歌云上。他报告说,每个序列都包含在云中的一个文件内,文件的名称都有相同的基本格式。
        Dr. Bloom swapped in the code for a missing sequence from Wuhan. Suddenly, he had the sequence. All told, he managed to recover 13 sequences from the cloud this way.        布鲁姆将武汉的一个遗失序列的编码换了进去。突然,他得到了序列。他总共用这种方法从云中恢复了13个序列。
        With this new data, Dr. Bloom looked back once more at the early stages of the pandemic. He combined the 13 sequences with other published sequences of early coronaviruses, hoping to make progress on building the family tree of SARS-CoV-2.        有了这些新数据,布鲁姆再次回顾了大流行的早期阶段。他将这13个序列与其他已发表的早期冠状病毒序列结合,希望在构建SARS-CoV-2病毒族谱方面取得进展。
        Working out all the steps by which SARS-CoV-2 evolved from a bat virus has been a challenge because scientists still have a limited number of samples to study. Some of the earliest samples come from the Huanan Seafood Wholesale Market in Wuhan, where an outbreak occurred in December 2019.        弄清SARS-CoV-2从蝙蝠病毒演化而来的所有步骤一直是一个挑战,因为科学家需要研究的样本数量仍然有限。一些最早的样本来自2019年12月暴发疫情的武汉华南海鲜批发市场。
        But those market viruses actually have three extra mutations that are missing from SARS-CoV-2 samples collected weeks later. In other words, those later viruses look more like coronaviruses found in bats, supporting the idea that there was some early lineage of the virus that did not pass through the seafood market.        但这些市场上的病毒实际上有三种额外的突变,而这些突变在几周后收集的SARS-CoV-2样本中是缺失的。换句话说,这些后来的病毒看起来更像在蝙蝠身上发现的冠状病毒,这支持了这种病毒的一些早期谱系没有经过海鲜市场的观点。
        Dr. Bloom found that the deleted sequences he recovered from the cloud also lack those extra mutations. “They’re three steps more similar to the bat coronaviruses than the viruses from the Huanan fish market,” Dr. Bloom said.        布鲁姆发现,他从云中恢复的被删除序列也没有这些额外的突变。“它们与蝙蝠冠状病毒的相似度比华南海鲜市场的病毒高三倍,”布鲁姆说。
        This suggests, he said, that by the time SARS-CoV-2 reached the market, it had been circulating for awhile in Wuhan or beyond. The market viruses, he argued, aren’t representative of full diversity of coronaviruses already loose in late 2019.        他说,这表明当SARS-CoV-2进入市场时,它已经在武汉或其他地方传播了一段时间。他认为,市场的病毒并不代表2019年底已经传播开来的冠状病毒的全部多样性。
        “Maybe our picture of what was present early in Wuhan from what has been sequenced might be somewhat biased,” he said.        他说:“也许我们根据测序得出的情况和武汉早期存在的情况可能有些偏差。”
        In his report, Dr. Bloom acknowledged that this conclusion would have to be confirmed with a deeper analysis of the virus sequences. Dr. Worobey said that he and his colleagues are working on a large-scale study of SARS-CoV-2 genes to better understand its origin and that they’ll now add Dr. Bloom’s 13 recovered sequences.        布鲁姆在他的报告中承认,必须通过对病毒序列的更深入分析来证实这一结论。沃罗比说,他和他的同事正在对SARS-CoV-2基因进行大规模研究,以更好地了解其起源,他们现在将添加布鲁姆恢复的13个病毒序列。
        “These additional data will play a big role in that effort,” Dr. Worobey said.        “这些额外的数据将在这项工作中发挥重要作用,”沃罗比说。
        It’s not clear why this valuable information went missing in the first place. Scientists can request that files be deleted by sending an email to the managers of the Sequence Read Archive. The National Library of Medicine, which manages the archive, said that the 13 sequences were removed last summer.        目前尚不清楚一开始为什么这些宝贵的信息丢失了。科学家可以通过向序列读取档案的管理员发送电子邮件来请求删除文件。管理该档案的国家医学图书馆表示,这13个序列是在去年夏天删除的。
        “These SARS-CoV-2 sequences were submitted for posting in SRA in March 2020 and subsequently requested to be withdrawn by the submitting investigator in June 2020,” said Renate Myles, a spokeswoman for the National Institutes of Health.        “这些SARS-CoV-2序列于2020年3月提交给SRA发表,随后在2020年6月被提交它的调查人员要求撤回,”美国国立卫生研究院发言人雷纳特·迈尔斯(Renate Myles)说。
        She said that the investigator, whom she did not name, told the archive managers that the sequences were being updated and would be added to a different database. But Dr. Bloom has searched every database he knows of, and has yet to find them. “Obviously I can’t rule out that the sequences are on some other database or web page somewhere, but I have not been able to find them any of the obvious places I’ve looked,” he said.        她说,调查员——她未透露其姓名——告诉档案管理员,序列正在更新,并将被添加到另一个数据库中。但是布鲁姆已经搜索了他知道的每一个数据库,都没有找到。“显然,我不能排除这些序列在某个其他数据库或网页上的某个地方,但我无法在我该找的地方找到它们,”他说。
        Three of the co-authors of the 2020 testing study that produced the 13 sequences did not immediately respond to emails inquiring about Dr. Bloom’s finding. That study did not give contact information for another co-author, Dr. Fu, who was also named on the spreadsheet from the other study.        得出13个序列的该2020年实验研究的合著者中,有三人没有立即回复就布鲁姆的发现发出的询问电邮。该研究没有提供另一位合著者付爱思的联系信息,他的名字也出现在另一项研究的电子表格中。
        Some scientists are skeptical that there is anything sinister behind the removal of the sequences. “I don’t really understand how this points to a cover-up,” said Stephen Goldstein, a virologist at the University of Utah.        一些科学家觉得,删除这些序列不见得就等于背后有什么不可告人的事。犹他大学(University of Utah)病毒学家斯蒂芬·戈德斯坦(Stephen Goldstein)说:“我不太明白这怎么就意味着掩盖了。”
        Dr. Goldstein noted that the testing paper listed the individual mutations the Wuhan researchers found in their tests. Although the full sequences are no longer in the archive, the key information has been public for over a year, he said. It was just tucked away in a format that is hard for researchers to find.        戈德斯坦指出,实验研究列出了武汉研究人员在其中发现的个体突变。他说,虽然完整的序列不再在档案中,但关键信息已经公开了一年多。它只是被塞在一种研究人员难以找到的格式中。
        “We all missed this relatively obscure paper,” Dr. Goldstein said.        “我们都错过了这篇相对不为人知的论文,”戈德斯坦说。
        “You can’t really say why they were removed,” Dr. Bloom acknowledged in an interview. “You can say that the practical consequence of removing them was that people didn’t notice they existed.” He also noted that the Chinese government ordered the destruction of a number of early samples of the virus and barred the publication of papers on the coronavirus without its approval.        “你真的说不好为什么它们会被删除,”布鲁姆在接受采访时承认。“你可以说移除它们的实际后果是人们没有注意到它们的存在。”他还指出,中国政府下令销毁一些早期病毒样本,并禁止未经批准发表有关冠状病毒的论文。
        For his part, Dr. Worobey still wants answers. “I hope we hear from the authors who generated, but then deleted, these crucial sequences so we can understand more about their motivation for doing so,” he said. “It certainly is strange at face value and really demands an explanation.”        而对沃罗比来说,他仍然想要答案。“我希望我们听到那些生成但随后删除这些关键序列的作者的意见,以便我们能够更多地了解他们这样做的动机,”他说。“从表面上看,这确实很奇怪,确实需要一个解释。”
        Regardless of what happened to these 13 sequences, Dr. Bloom now wonders what other clues might be discovered online. In order to reconstruct the origin of Covid-19, all those clues potentially matter.        不管这13个序列下落如何,布鲁姆现在想知道在网上还能发现什么样的线索。为了重建Covid-19的起源,所有这些线索可能都很重要。
        “Ideally, we need to try to find as many other early sequences as possible,” he said. “And I think this study suggests that we should look everywhere.”        “理想情况下,我们需要尝试找到尽可能多的其他早期序列,”他说。“而且我认为这项研究表明我们应该所有地方都看看。”
                
   返回首页                  

OK阅读网 版权所有(C)2017 | 联系我们