長標題：美國病毒學家Bloom新冠溯源研究恢復、依據的基礎數據，是武漢大學“納米孔靶向測序檢測”技術研發、測試過程中測序、輸出的新冠病毒基因序列片斷，這些基因序列片斷準確度欠佳，存在大量的核苷酸測序缺失。

Long title: the basic data on which American virologist Bloom's origination research of Sars-Cov-2 based, is the Sars-Cov-2 sequence fragments which sequenced and output by the "nanopore targeted sequencing detection" technology of Wuhan University, these sequence fragments is produced during the developing and testing process, their accuracy is not good enough for gene and Sars-Cov-2’s origination research。There are lots of nucleotide miss in the Sars-Cov-2  sequence fragments Bloom recovered.

本文是 "病毒學家Bloom溯源論文的基礎數據問題"的一個中英對照版本，寫作中藉助了谷歌翻譯。原中文版本地址：病毒學家Bloom溯源論文的基礎數據問題

This article is the Chinese-English version of the article "病毒學家Bloom溯源論文的基礎數據問題"，Google Translate was used in my writing. This is the address of original Chinese version:


對美國病毒學家Jesse Bloom的新冠溯源論文作了初步研究，發現了一些疑點、缺陷和錯誤。本文整理的是與論文的基礎研究數據相關的一組問題。成文倉促，請各位網友批評、指正。

Preliminary research has been done on the Sars-Cov-2 origination paper of American virologist Jesse Bloom, and some doubts, defects and errors have been found. This article sorts out a set of questions related to the basic research data of the thesis. Written hastily, looking forward to your criticisms and corrections。

2021年6月22日，美國西雅圖賀勤森癌症研究中心(Fred Hutchinson Cancer Research Center，福瑞德·哈金森癌症研究中心)的病毒學家傑西·布魯姆（Jesse Bloom）在生物學預印本平台biorxiv發布了如下論文：Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic（恢復刪除的深度測序數據為新冠病毒在武漢的早期流行提供了更多信息）
https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1
https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1.full

On June 22, 2021, virologist Jesse Bloom released the following paper on the preprint platform biorxiv : Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

Jesse Bloom is a virologist of the Fred Hutchinson Cancer Research Center in Seattle, USA.

本文將說明以下6點：

This article will explain the following 6 points:

1、Bloom恢復的基因序列，是武漢大學“納米孔靶向測序檢測”技術研發過程中產生的測試數據；

1. The Sars-Cov-2 sequences restored by Bloom is the testing data generated during the research and development of the "Nanopore Targeted Sequencing Detection" technology of Wuhan University;

2、關於數據是如何刪除的，還存在疑點，還不能下定論。一種可能是：武漢大學在完成相關項目後，向NIH請求撤回（刪除或移走）了他們在研發、測試階段輸出的，提交到SRA保存的新冠病毒基因序列片斷；

2. Regarding how the data was deleted, there are still doubts and no conclusion can be drawn. One possibility is that after completing the relevant project, Wuhan University requested NIH to withdraw the Sars-Cov-2 sequence fragments that they exported during the R&D and testing stages and submitted to the SRA for preservation;

3、“納米孔靶向測序檢測”技術是qPCR病毒檢測技術的替代技術，其核心功能是病毒檢測，而非病毒測序。檢測樣本中是否存在目標病毒是這一技術的首要功能，對病毒進行部分測序並輸出測序結果是其輔助功能。而且，這一技術測序、輸出的不是新冠病毒的全基因組序列，只是與檢測功能相關的全基因組序列的若乾片斷；

3. "Nanopore targeted sequencing detection" technology is an alternative to qPCR virus detection technology, and its core function is virus detection, not virus sequencing. Detecting the presence of the target virus in a sample is the primary function of this technology, and partially sequencing the virus and outputting the sequencing result is its auxiliary function. Moreover, the sequencing and output of this technology is not the whole genome sequence of Sars-Cov-2, but only several fragments of the whole genome sequence related to the detection function;

4、“納米孔靶向測序檢測”技術輸出的基因序列，允許更大誤差和更高錯誤率，不應將它們等同於專門測序得到的，可向國際生物數據庫正式提交的，可用於嚴謹基因科學研究的，權威性的基因序列。即使這些基因序列片斷仍存在科學研究價值，在將它們用於對準確性要求極高的基因科學研究，特別是新冠溯源研究時，也應當非常審慎，也應當對其中的測序錯誤可能產生的影響、誤導進行充分的分析、評估。

4. The gene sequences output by the "Nanopore Targeted Sequencing Detection" technology allow larger errors and higher error rates. They should not be equated with the authoritative gene sequence obtained by special sequencing，the latter can be formally submitted to the international biological database，taken as base data of rigorous gene research. Even if these sequence fragments still have scientific research value, they should be used very cautiously when they are used in genetic scientific research that requires extremely high accuracy, especially the origination research of Sars-Cov-2, careful and adequate analysis and evaluation should be made to avoid being misled by the sequencing errors.

5、Bloom恢復的序列片斷證明，武漢大學“納米孔靶向測序檢測”技術的測序結果中存在大量的核苷酸測序缺失。

5. The sequence fragments recovered by Bloom prove that there are a large number of nucleotide sequencing deletions in the sequencing results of the "Nanopore Targeted Sequencing Detection" technology of Wuhan University.

6、武漢大學“納米孔靶向測序檢測”技術輸出的欠精確、可靠的研發、測試數據，被Bloom拿來充當了其溯源論文的基礎數據。是否採取措施規避了基礎數據中的測序錯誤？測序錯誤可能對研究過程及論文結論造成什麼樣的影響或誤導？Bloom在論文中沒有進行討論、評估。

6. The inaccurate and reliable R&D and test data output by Wuhan University's "Nanopore Targeted Sequencing Detection" technology was used by Bloom as the basic data in its paper about origination of Sars-Cov-2. Have measures been taken to avoid the effects of sequencing errors in the basic data? What kind of influence or misleading might the sequencing error have on the research process and the conclusion of the paper? Bloom did not discuss or evaluate in the paper.

下面對上述6點予以展開。

The above 6 points will be expanded below.

Bloom在論文中說，他通過谷歌雲恢復了去年6月被刪除的一些測序數據，他通過這些數據重建了13個新冠病毒的基因序列。論文提供了這13個基因序列的下載地址：
https://github.com/jbloom/SARS-CoV-2_PRJNA612766/raw/main/results/consensus/consensus_seqs.csv

Bloom said in the paper, he recovered some sequencing data deleted in June last year, and he reconstructed 13 Sars-Cov-2 sequences through the data. The paper provides the download address of these 13 sequences:

需要指出的是，Bloom重建的13個序列都不是完整的新冠病毒全基因組序列，每個序列都是新冠全基因組序列一大一小的兩個片斷。Bloom未得到全基因組序列，不是因為他恢復得不完全，而是因為他恢復的數據本來就是基因組片斷。這些新冠基因組片斷來自武漢大學“納米孔靶向測序檢測”（Nanopore Targeted Sequencing，簡稱NTS）項目，是這一項目研發、測試過程中產生、輸出的。NTS技術不需要檢測新冠病毒的全基因組，只需要比對、測序全基因組中的約12個區段。

It should be noted that 13 sequences reconstructed by Bloom are not complete Sars-Cov-2 genome sequences, each sequence contains two fragments, one long，another very short. Bloom did not get the whole genome sequences, not because he recovered incomplete, but because the data he recovered were originally genome pieces. These Sars-Cov-2 genomic pieces come from Wuhan University Nanopore Targeting Sequencing（referred to as NTS) project, produced and output during the developing、testing process of this project. NTS technology does not need to detect the whole genome of Sars-Cov-2, only about 12 sections need to be compared and sequencing.


後續內容將涉及一個生物信息數據庫SRA。SRA，即Sequence Read Archive（序列讀取檔案）是NIH（National Institutes of Health，美國國立衛生研究院）管理、維護的兩個生物學數據庫之一，另一個是GenBank。

Subsequent content will involve a biological information database SRA. SRA, the Sequence Read Archive is one of the two biological databases of NIH (National Institutes Of Health), the other is GenBank.

NTS項目使用SRA為研發的數據存儲平台，它在SRA上的項目代號為Bio-Project PRJNA612766。Bloom論文中說，截止2020年3月30日，PRJNA612766項目共向SRA提交了282 份數據，其中241份數據的相關信息被一位名叫Carlos Farkas的科學家（等人）整理在一個Excel表格中，Bloom就是依據表格中的信息恢復了部分數據並重建了13個序列片斷。Bloom恢復的數據只是PRJNA612766即武漢大學NTS項目提交數據的很小一部分。我粗略地瀏覽了該表格，NTS項目最早的數據提交時間應該是2020年1月15日。順便附上Bloom論文提供的Farkas表格的下載地址。
https://web.archive.org/web/20210502130356/https://dfzljdn9uc3pi.cloudfront.net/2020/9255/1/Supplementary_Table_1.xlsx.

The NTS project uses SRA as their data storage platform, its SRA project code is Bio-Project PRJNA612766.In the bloom paper, as of March 30, 2020, PRJNA612766 projects submitted 282 data to SRA, 241 of them were organized by scientists called Carlos Farkas (et al.) In an Excel form. In accordance with the information in the table, Bloom recovered and reconstructed 13 sequence pieces. The data Bloom recovered are only a small part of PRJNA612766，the NTS project of Wuhan University. I roughly browsed the form, the earliest data submission time of the NTS project should be January 15, 2020. By the way, the download address of the FARKAS table provided by the bloom paper.

Bloom重建的13個序列片斷的對象時間戳都是2020年2月15日。Bloom推測，對象時間戳可能是指數據上傳到SRA的時間。也就是說，Bloom恢復的數據應該是同一批數據，它們都是2020年2月15日這天上傳到SRA的。

The target timestamps of the 13 sequence fragments Bloom reconstructed are all  February 15, 2020. Bloom speculates that an object timestamp may refer to the time of data submitted to SRA. That is, the data recovered by Bloom should be the same batch of data, which are all uploaded to SRA on February 15, 2020.


Bloom自已通過谷歌雲恢復、重建了13個序列片斷。其實，他可以通過NIH，利用SRA的數據庫備份系統恢復所有相關數據。論文沒有提及這一數據恢復途徑，沒有解釋Bloom為什麼不通過這一途徑完整地、更可靠地恢復數據。

Bloom restored 13 sequence fragments through Google Cloud by himself. In fact, he can restore all relevant data by NIH, using SRA's database backup system. The papers did not mention this data recovery approach, and did not explain why Bloom did not restore data completely and  more reliably by this way.

Bloom論文引用的武漢大學NTS（納米孔靶向測序檢測）研究的相關論文為：Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses（納米孔靶向測序可準確、全面檢測 SARS-CoV-2 和其他呼吸道病毒）
https://www.medrxiv.org/content/10.1101/2020.03.04.20029538v1.full-text

The related papers of NTS (nanopore target sequencing detection) studies quoted by bloom papers is as:Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses

這一論文投稿到預印版平台medRxiv的時間是2020年2月29日，正式發布時間是2020年3月6日。

The time of this paper submitted to the pre-printed platform Medrxiv was February 29, 2020, and it officially released on March 6, 2020.

2020年3月4日，中國人民日報和新華網報道了這一新技術： 武漢大學研發納米孔靶向測序檢測方法
http://www.xinhuanet.com/science/2020-03/04/c_138841605.htm

On March 4, 2020, the People's Daily and Xinhuanet reported this new technology: Wuhan University R & D nanopore target sequencing detection method

概要地介紹一下武漢大學“納米孔靶向測序檢測”技術（NTS）的功能特點，這將有助於我們作出進一步的正確判斷：

The below is the summary introduction to the functional characteristics of Wuhan University "Nanohole Targeting Detection" Technology (NTS), which will help us make further correct judgment:

1、相比傳統的qPCR（quantitative polymerase chain reaction，實時熒光定量PCR，或實時定量聚合酶鏈反應）檢測30%~50%的陽性檢出率，NTS將陽性檢出率提升了43.8%，達到約75%~94%；

1, compared to positive detection rate of 30% to 50%  of the traditional QPCR (Quantitative Polymerase Chain Reaction,or real-time fluorescent PCR, or real-time quantitative polymerase chain), NTS increased the positive detection rate by 43.8% and achieve about 75% to 94%;

2、對於高濃度病毒樣本，NTS僅需測序10分鐘即可檢測陽性，即使極低濃度病毒樣本，也僅需測序4小時完成檢測，從收到樣本到出具結果，全程控制在6-10小時；

2. For high concentration virus samples, NTS only needs to sequencing for 10 minutes to detect positive, even if the virus sample is very low concentration, only 4 hours is needed to complete the detection, from receiving the sample to returning the results, only 6-10 hours is need for the full steps;

3、NTS可在測序後4小時內高敏感性、高準確性地同時檢測SARS-CoV-2和其他10大類、40餘種呼吸道病毒；

3, NTS can detect SARS-COV-2 and other 10 categories, more than 40 kinds of respiratory viruses with high sensitivity and high accuracy within 4 hours after sequencing.

4、NTS最低檢測敏感度是廣泛使用的傳統qPCR的100倍；

4, The minimum detection sensitivity of NTS is 100 times that of traditional QPCR extensively used;

5、NTS還可輸出檢測樣本中病原體（如新冠病毒）的基因組序列片斷，可用於考察新冠病毒基因組的變異情況，監控病毒變異引起的毒性與傳播能力改變。這是qPCR所沒有的功能，qPCR病毒檢測只作基因比對，不作基因測序，不記錄、輸出任何基因組序列。

5. NTS also outputs gene sequence fragments for the detecting pathogens (such as Sars-Cov-2) in the sample, which can be used to investigate the mutation of Sars-Cov-2, and monitor the variation of the toxicity and communication capacity caused by viral mutation. This is the function that QPCR does not have.QPCR only performs gene comparison between sample virus and target virus, does not make gene sequencing, does not record, and output any genomic sequence.

6、NTS所需的納米孔測序平台對實驗室要求不高，其中最小測序儀MinION是便攜式的，因此NTS也適合不同級別的醫院使用。

6. The Nanohole-sequencing platform has no very high requirement on laboratory conditions，specially, its minimum sequencer named as MinION is portable, so NTS is also suitable for different levels of hospitals.

由上述功能細節可知，NTS技術是面向、服務於醫院和普通實驗室的；NTS技術對實驗室條件要求不高，這應該暗示着它並不能勝任有着極高精度的專業測序；第5組功能是錦上添花性質的，該組部分功能很可能有誇大其詞的噱頭成份。一個倉促研發的產品，如果號稱擁有眾多強大功能，那很可能意味着，至少，它的相當一部分功能是不盡善盡美的。

According to the above functional details, NTS technology is facing, serving hospitals and ordinary laboratories; NTS technology has no high requirement on laboratory conditions, which should imply that it does not compete with extremely high precision professional sequencing; The fifth group functions is very likely to be exaggerated. A rush-developed product, If it claims to have a lot of powerful features, it likely means that, at least，its considerable parts of the functionality is not perfect.

下面討論數據撤回、刪除的有關情況。

The following discussion is about the relevant situation of data withdrawal and deletion.

Bloom在論文中說，當他按照Carlos Farkas論文和表格的指引去查閱武漢大學提交到SRA的數據時，在 NCBI-SRA系統中已經搜索不到相關項目PRJNA612766了，用Farkas提供的Accession ID直接搜索該項目下的相關序列數據，搜索結果提示：序列數據已被刪除。

Bloom said in the paper that, when he check the data submitted by Wuhan University  following the guidance of Carlos Farkas paper and form, the relevant project PRJNA612766 could not be searched in the NCBI-SRA system, and when he search this project relevant data directly by the Accession ID provided by Farkas, the search result prompts: the sequence data has been deleted.

Bloom說，SRA 被設計為深度測序數據的永久存檔，上傳數據到SRA後，只能通過向 SRA 工作人員發送電子郵件來刪除數據。為說明可以通過發送郵件來請求刪除數據，Bloom舉了一個例子，他提供了一個Xiao姓科學家向SRA工作人員發送email，請求刪除數據的電子郵件截圖。

Bloom said that SRA is designed as a permanent archive of deep sequencing data. After uploading the data to the SRA, the data can only be deleted by sending an email to the SRA staff. To illustrate that one can request deletion of data by sending an email, Bloom gave an example. He provided a screenshot of an email, the email is from a scientist surnamed Xiao, who sent this email to an SRA staff member requesting deletion of data.

Bloom說，這位xiao姓科學家是一篇穿山甲冠狀病毒論文的lead author。Bloom論文的“Literature Cited”（引用的文獻）中指示了xiao姓科學家的論文：
https://www.nature.com/articles/s41586-020-2313-x

Bloom said that the scientist Xiao is the lead author of a pangolin coronavirus paper. The "Literature Cited" of the Bloom paper indicated the papers of the scientist Xiao:

由論文作者列表可知，這個xiao姓的lead author或者是論文的通訊作者之一，華南農業大學特聘教授肖立華，或者是論文的第一作者Kangpeng Xiao。

According to the authors list of the pangolin related paper, the lead author with the surname Xiao is either one of the corresponding authors of the paper, Lihua Xiao, a distinguished professor of South China Agricultural University, or Kangpeng Xiao, the first author of the paper.

Bloom提供Xiao姓科學家的email截圖是為了例證：SRA數據可通過email請求撤回、刪除。由截圖可見，Xiao姓科學家刪除的項目與武漢大學的NTS項目二者的BioProject ID不同，它們是兩個不同的項目。

The purpose that Bloom provided the email screenshot of the scientist Xiao is to illustrate: SRA data can be withdrawn or deleted via email request. It can be seen from the screenshot that the BioProject ID of the project deleted by the scientist Xiao is different from the NTS project of Wuhan University. They are two different projects.

Bloom是怎麼得到Xiao姓科學家郵件截圖的？Bloom也未作說明。郵件截圖是NIH提供的嗎？如果是的話，NIH為什麼不直接提供武漢大學PRJNA612766項目（即“納米孔靶向測序檢測”項目）相關的郵件，而要提供一個無關項目的郵件呢？如果郵件不是NIH提供的，那麼，如此私密的信息，Bloom又是怎麼得到的呢？Bloom和xiao姓科學家有什麼直接或間接的關係嗎？

How did Bloom get the email screenshot of scientist Xiao? Bloom also didn't say anything. Are the email screenshots provided by NIH? If so, why doesn't NIH directly provide email related to Wuhan University's PRJNA612766 project, but give email of unrelated project? If the email was not provided by NIH, how did Bloom get such private information? Is there any direct or indirect relationship between Bloom and the scientist Xiao?

這些疑點暫時無法得到澄清。至少有以下兩種可能性：
1、xiao姓科學家的郵件是NIH提供的，但NIH未提供或未能提供武漢大學PRJNA612766項目組人員請求刪除數據的郵件；
2、xiao姓科學家的郵件是Bloom通過私人渠道獲得的。在2018回國工作，被華南農業大學特聘前，肖立華在美國學習、工作了至少18年，在美國CDC工作了14年。

These doubts cannot be clarified temporarily. There are at least two possibilities:
1. The email of the scientist Xiao was provided by NIH, but NIH did not provide or failed to provide the email by which the team member of PRJNA612766 project of Wuhan University requesting to delete the data;
2. The email of the scientist surnamed Xiao was obtained by Bloom through private channels. Before returning to work in China in 2018, and being specially hired by South China Agricultural University, Lihua Xiao studied and worked in the United States for at least 18 years, and worked for CDC of the United States for 14 years.


小結一下上述幾段內容。Bloom稱數據被刪除了，稱SRA數據只能通過發送email請求刪除，他還舉了一個其它項目通過這一途徑請求刪除數據的例子，但他未提供武漢大學項目組人員要求刪除數據的直接證據。Bloom論文提供的信息，讓我無法肯定，相關數據確實是武漢大學項目組人員要求刪除的，我不能排除數據刪除的其它可能性。

Summarize the above paragraphs. Bloom claimed that the data was deleted, saying that SRA data can only be deleted by sending an email request. He also cited an example of another project requesting data deletion through this approach, but he did not provide direct evidence that the Wuhan University project team requested the deletion of the data. The information provided in the Bloom paper makes me not sure that the relevant data was indeed deleted by the project team of Wuhan University, and I cannot rule out other possibilities of data deletion.

華爾街日報（The Wall Street Journal）6月28日的一篇文章含糊其辭、語焉不詳地聲稱：NIH證實，應一名中國研究人員的申請刪除了這些序列。這篇新聞的標題為：美國應中方要求刪除新冠基因序列，病毒溯源難度加大
https://cn.wsj.com/articles/%E7%BE%8E%E5%9B%BD%E5%BA%94%E4%B8%AD%E6%96%B9%E8%A6%81%E6%B1%82%E5%88%A0%E9%99%A4%E6%96%B0%E5%86%A0%E5%9F%BA%E5%9B%A0%E5%BA%8F%E5%88%97%EF%BC%8C%E7%97%85%E6%AF%92%E6%BA%AF%E6%BA%90%E9%9A%BE%E5%BA%A6%E5%8A%A0%E5%A4%A7-11624509310

A June 28 article in The Wall Street Journal vaguely and unclearly claimed: NIH confirmed that these sequences were deleted under the request of a Chinese researcher. The headline of this news article is: The United States deletes the Sars-Cov-2 gene sequence under the request of China, making it more difficult to trace the virus to the source

令人不解的是，對如此重要的事情，華爾街日報的文章竟不說明，NIH何時證實了相關信息，證實相關信息的是NIH的哪一位工作人員，其title是什麼，證實信息的有關聲明發表於何處。無法判定華爾街日報的做法是有意，抑或僅僅是大意疏忽。

What is puzzling is that the article does not explain when NIH confirmed the relevant information, which NIH staff member confirmed the relevant information, what its title is, and where the relevant statement confirming the information was published. It is impossible to determine whether the Wall Street Journal’s actions were intentional or merely negligent.

儘管至今仍疑點重重，但我不想過多糾纏數據到底是怎麼刪除的，這不是第一位的問題。以下，我將假定相關數據確實被刪除了，而且確實是武漢大學項目組人員請求刪除的。

Although there are still many doubts, I don't want to always dwell on how the data is deleted. This is not the first problem. In the following, I will assume that the relevant data has indeed been deleted, and the deletion or withdrawal is indeed requested by the Wuhan University project team.

Bloom提到了一個叫Aisu Fu的人，論文說，武漢大學PRJNA612766項目的病毒樣本是Aisu Fu和武漢大學人民醫院搜集的。論文沒有提供此人的更多信息，事實上，Aisu Fu在論文中只出現了一次。

Bloom mentioned a person named Aisu Fu. The paper stated that the virus samples of Wuhan University's PRJNA612766 project were collected by Aisu Fu and Wuhan University People's Hospital. The paper did not provide more information about this person. In fact, Aisu Fu only appeared once in the paper.

Aisu Fu是誰呢？

Who is Aisu Fu?

Aisi Fu，中文名付愛思，是武漢臻熙醫學檢驗實驗室有限公司的總負責人，他與武漢大學藥學院劉天罡教授，武漢大學人民醫院李艷教授、余鋰鐳教授是NTS技術的共同研發者，這些信息可由以下新聞獲得：武漢大學新聞網- 重磅！武漢大學聯合團隊開發納米孔靶向測序 大幅提升新冠病毒陽性檢出率
https://news.whu.edu.cn/info/1002/57753.htm

Aisi Fu, whose Chinese name is 付愛思, is the general manager of Wuhan Zhenxi Medical Laboratory Co., Ltd. He and Professor Liu Tiangang from the School of Pharmacy of Wuhan University, Professor Li Yan and Professor Yu Lilei from the People’s Hospital of Wuhan University are Co-developers of NTS technology. This information can be obtained from the following news: Wuhan University News Network-Heavy! Wuhan University joint team develops nanopore targeted sequencing to greatly increase the positive detection rate of new coronavirus

在前面提到過的武漢大學medRxiv預印本論文中，付愛思是第二作者，不過，在那篇論文中，他的署名不是Aisu Fu，而是Aisi Fu。
https://www.medrxiv.org/content/10.1101/2020.03.04.20029538v1.full

In the aforementioned medRxiv preprint paper of Wuhan University, Fu Aisi is the second author. However, in that paper, his signature is not Aisu Fu, but Aisi Fu.

假定Bloom恢復的SRA數據確實是武漢大學請求刪除的，那麼，我認為，情況應該是：NTS（納米孔靶向測序檢測）項目研發完成後，武漢大學項目組人員向NIH-SRA發出申請，撤回、刪除了他們提交到SRA的數據。這些數據本來就是項目研發、測試過程中產生的非正式數據。

Assuming that the SRA data recovered by Bloom was indeed deleted under the request of Wuhan University, then I think the situation should be: After the development of the NTS (Nanopore Targeted Sequencing Detection) project is completed, the Wuhan University project team sent an application to NIH-SRA and withdrew, deleted the data they submitted to SRA. These data are originally informal data generated in the process of project development and testing.

這一撤回、刪除非正式的研發、測試數據的做法有什麼不正常嗎？隱藏着什麼不良動機嗎？我看不出來。

Is there anything unusual about this withdrawal and deletion of informal R&D and test data? Are there any bad motives hidden? I can't tell.

學術論文應當專注於學術本身，基於事實，有一說一，有二說二，力求客觀中立，避免被利用為政治工具，更不主動充當政治工具。妄加揣測，輕率貿然地陷人以罪，是有違科學精神，不道德，不負責任的行為。Bloom是怎麼做的呢？在論文的Discussion部分，Bloom對中國科學家提出了如下指控：顯然，對樣本進行完全測序比偷偷刪除部分序列更能提供科學信息。。。這些序列似乎很可能被刪除以掩蓋它們的存在。原文為：and it clearly would have been more scientifically informative to fully sequence the samples rather than surreptitiously delete the partial sequences。。。It therefore seems likely the sequences were deleted to obscure their existence.

Academic papers should focus on the academic itself, based on facts, one says one, the other says two, strive to be objective and neutral, avoid being used as a political tool, let alone actively serving as a political tool. It is against the spirit of science, immorality, and irresponsible behavior to speculate and rashly accuse crimes. How does Bloom do it? In the Discussion section of the paper, Bloom made the following accusations against Chinese scientists:  and it clearly would have been more scientifically informative to fully sequence the samples rather than surreptitiously delete the partial sequences。。。It therefore seems likely the sequences were deleted to obscure their existence.

Bloom的這些言辭，是強詞奪理、自相矛盾、邏輯錯亂、無恥下作的造謠中傷。

Bloom's words are rumors and slander of strong words, self-contradictions, logical confusion, shamelessness and despicableness.

首先，Bloom恢復的基因序列片斷並非來自專門測序過程，它們是NTS（納米孔靶向測序檢測）技術研發、測試過程中產生的非正式數據，NTS主要用於醫學檢測、臨床診斷，其輸出的基因序列不是為嚴肅基因研究準備的。

First of all, the gene sequence fragments recovered by Bloom do not come from a special sequencing process. They are informal data generated during the development and testing of NTS (Nanopore Targeted Sequencing Detection) technology. NTS is mainly used for medical testing and clinical diagnosis. The genetic sequence is not prepared for serious genetic research.

第二，武漢大學在NTS研究中沒有進行完全測序，不是他們故意不進行完全測序，而是因為NTS不需要進行全基因組測序，對基因組的某些重要片斷進行測序就很充分了。事實上，NTS的序列檢測範圍，已經大大超過傳統qPCR的序列比對範圍，“相當於撒下了十幾張大網”，同時捕捉病毒樣本中的可疑基因片斷。 這是NTS陽性檢出率大大提高的根本原因。

Second, Wuhan University did not perform complete sequencing in the NTS research, not because they deliberately did not perform complete sequencing, but because NTS does not need to perform whole-genome sequencing. It is sufficient to sequence some important fragments of the genome. In fact, the scope of NTS sequence detection has greatly exceeded the scope of traditional qPCR sequence comparison, "equivalent to a dozen large nets," while capturing suspicious gene fragments in virus samples. This is the fundamental reason why the positive detection rate of NTS has greatly increased.

NTS多區段比對、檢測與qPCR有限位置比對對照圖

comparison chart between NTS multi-segment comparison, detection and qPCR limited position comparison

第三，Bloom的溯源研究論文基於一個最基本的假設：新冠病毒是自然演化產生的。如果這一假設不成立，Bloom的論文就崩潰了。Bloom一方面以武漢大學的數據作為自己自然演化理論的基礎數據，基本依據，一方面又指控武漢大學的科學家偷偷摸摸刪除這些可支持其自然演化理論的數據。這是一種非常錯亂的邏輯。武漢大學的科學家為什麼要刪除“新冠自然演化”的證據？刪除這些證據對中國科學家，對中國政府有什麼好處？刪除“新冠自然演化”的證據，掩蓋“新冠自然演化”的“真相”對中國科學家，對中國政府有什麼好處？

Third, Bloom's traceability research paper is based on one most basic assumption: Sars-Cov-2 is a product of natural evolution. If this assumption is not true, Bloom's paper will collapse. On the one hand, Bloom uses the data of Wuhan University as the basic data for its natural evolution theory, and on the other hand, it accuses scientists of Wuhan University of secretly deleting these data that can support its natural evolution theory. This is a very confusing logic. Why did scientists at Wuhan University delete the evidence of "natural evolution of Sars-Cov-2"? What are the benefits to Chinese scientists and the Chinese government by deleting these evidences? Deleting the evidence of the "natural evolution of Sars_Cov-2" and covering up the "truth" of the "natural evolution of Sars-Cov-2" will benefit Chinese scientists and the Chinese government?

第四，2017年12月19日，Trump政府解除了奧巴馬政府3年前頒布的“功能增益研究”(Gain-of-Function, G-o-F)禁令，允許美國科學家重新申請聯邦經費，開展功能增益研究，在實驗室中研發、製造更具致病能力或更具傳播能力的病毒或其它病原體。奧巴馬禁令頒布於2014年10月22日。美國的功能增益研究與新冠病毒的出現沒有關係嗎？奧巴馬功能增益研究禁令解除兩年後，新冠病毒就出現了，這只是一種巧合嗎？從2017年12月解除功能增益研究禁令，到2019年11月前後出現新冠病毒，在這近兩年的時間裡，美國的病毒學家們沒有功能增益-改造出任何一種可怕的病毒嗎？ 對於Trump政府解禁功能增益研究，打開了潘多拉災難之盒，對於美國科學家可以在聯邦經費支持下，合法地在實驗室功能增益-改造病毒，Bloom不置一詞，裝作沒有這回事。事實上，對解除奧巴馬禁令，重啟功能增益研究，美國科學界諱莫如深，全體失聲；Bllom不僅不做深刻的自我反思、自我檢討，反而扮出清白無辜的模樣對中國科學家造謠中傷，栽贓嫁禍，其言行非常無恥下作。

Fourth, on December 19, 2017, the Trump administration lifted the Gain-of-Function research ban promulgated by the Obama administration three years ago, allowing American scientists to reapply for federal funding to carry out G-o-F research, developing and manufacturing viruses or other Pathogens that are more pathogenic or more transmissible in the laboratory. The Obama ban was issued on October 22, 2014. Is there no relationship between the Gain-of-Function research in the United States and the emergence of Sars-Cov-2? Two years after Obama’s G-o-F ban was lifted, Sars-Cov-2 appeared. Is this just a coincidence? From the lifting of the G-o-F ban in December 2017 to the emergence of Sars-Cov-2 around November 2019, in the past two years, American virologists have not G-o-F-transformed any terrible virus? Regarding the Trump government’s lifting of the G-o-F ban, opening Pandora's disaster box, regarding American scientists, with federal funding, they can legally perform virus G-o-F and transforming, in laboratories, Bloom does not say a word, pretending that there is no such thing. In fact, the American scientific community is very secretive about lifting the Obama ban and restarting G-o-F research; instead of deep self-reflection and self-examination, Bloom instead pretends to be innocent, spreads rumors, slander, and frames Chinese scientists. His words and deeds are very shameless and despicableness.

下面討論Bloom所恢復數據的精確性、可靠性問題。

The following discussion is about the accuracy and reliability of the data recovered by Bloom.

由研發目的、用途及功能特點可判斷，NTS檢測技術是傳統qPCR檢測的替代技術，它的首要目的是病毒檢測，而非病毒測序。即，確定樣本中是否存在目標病毒是它的首要功能，測序並輸出基因序列片斷只是它的輔助功能。NTS技術與專門的測序明顯不同，它的測序精度難以與專門測序相提並論，它的測序結果無法直接提交到國際基因數據庫作為權威數據供嚴謹的基因研究使用。將NTS輸出的基因序列片斷等同於專門測序得出的權威基因組序列，並將之用於對精確度、可靠度要求極高的新冠溯源研究，我認為是不恰當的。即使這些數據確有溯源研究的價值，如線索價值，在使用時也應當非常審慎、小心，避免被數據中的錯誤誤導。

Judging by the purpose, use, and functional characteristics, NTS detection technology is an alternative to traditional qPCR detection. Its primary purpose is virus detection, not virus sequencing. That is, determining whether the target virus is present in the sample is its primary function, and sequencing and outputting gene sequence fragments is only its auxiliary function. NTS technology is obviously different from specialized sequencing. Its sequencing accuracy is difficult to compare with that of specialized sequencing. Its sequencing results cannot be directly submitted to the international gene database as authoritative data for rigorous genetic research. I think it is inappropriate to equate the gene sequence fragments output by NTS with the authoritative genome sequence obtained by special sequencing and use it for Sars-Cov-2 traceability research that requires extremely high accuracy and reliability. Even if these data do have research value on origination of Sars-Cov-2, such as clue value, they should be used with great care and caution to avoid being misled by errors within the data.

相比qPCR，NTS技術的陽性檢出率雖大大提高，達到了約75%~94%，但仍遠遠稱不上高度精準，可以想見，它的測序功能的精準程度也是有限的；同時，NTS是疫情發生後短期內開發出來的，數據上傳的2月15日，項目剛剛啟動了約一個月，NTS技術尚在研發階段，其輸出的基因序列更可能存在誤差、偏差甚至錯誤。

Compared with qPCR, the positive detection rate of NTS technology is greatly improved, reaching about 75% to 94%, but it is still far from being highly accurate. It is conceivable that the accuracy of its sequencing function is also limited; at the same time, NTS was developed within a short period of time after the outbreak of the epidemic. The data was uploaded on February 15th, at that time, and the project was just launched for about a month, NTS technology is still in the development stage, its output gene sequence is more likely to contain errors, deviations or even errors.


NTS測序功能精確度欠佳。這不是一個推測，而是一個事實。Bloom恢復、重建的基因序列片斷就是這一事實的確鑿證明。

The accuracy of the NTS sequencing function is relatively poor. This is not a speculation, but a fact. The gene sequence fragments recovered and reconstructed by Bloom are conclusive proof of this fact.

Bloom在論文中說：I aligned the recovered deep sequencing data to the SARS-CoV-2 genome using minimap2。。。
即：我使用minimap2比對了恢復的深度測序數據與新冠病毒基因組的一致性。minimap2是一種基因組序列比對工具。

Bloom said in the paper：I aligned the recovered deep sequencing data to the SARS-CoV-2 genome using minimap2。。。
minimap2 is a genome sequence alignment tool

稍作間隔後，Bloom提供了如下表格：
After a short interval, Bloom provides the following table:

表格第一列的新冠病毒sample一共有14個，其中13個對應Bloom從SRA恢復、重建的基因序列片斷，另外一個來自某個2月住院的患者。

There are a total of 14 Sars-Cov-2 samples in the first column of the table, 13 of which correspond to the gene sequence fragments recovered and reconstructed by Bloom from SRA, and the other is from a patient who was hospitalized in February.

表格中的第二列應該是14個sample與proCov2的基因序列一致性比對結果。proCov2是天普大學（Temple University）科學家Sudhir Kumar提出的一個虛擬的新冠病毒的祖病毒。proCov2與最早發現的新冠病毒樣本之一WuHan-hu-1隻相差三個核苷酸，將WuHan-hu-1進行以下三個單核苷酸的更改：C8782T、C18060T和 T28144C，就得到了proCov2。

The second column in the table should be the result of the genetic sequence consistency comparison between the 14 samples and proCov2. proCov2 is a virtual progenitor virus of Sars-Cov-2 proposed by Temple University scientist Sudhir Kumar. proCov2 is only three nucleotides apart from WuHan-hu-1, one of the first samples of Sars-Cov-2, make the following three single nucleotides modification to WuHan-hu-1: C8782T, C18060T, and T28144C, then you get ProCov2.

注1：C8782T代表：將基因序列中8782位點的胞嘧啶C對應的核苷酸（鹼基對）改為胸腺嘧啶T對應的核苷酸。

Note 1: C8782T stands for: Change the nucleotide (base pair) corresponding to cytosine C at position 8782 in the gene sequence to the nucleotide corresponding to thymine T.

注2：WuHan-hu-1的基因序列是上海復旦大學張永振團隊2020年1月5日上傳的，是第一個上傳到國際生物信息數據庫的新冠病毒全基因組序列。WuHan-hu-1的病毒樣本由武漢市中心醫院採集提供，採集時間是2019年12月30日或26日，採集自一名41歲的陳姓新冠早期患者，該患者是華南海鮮市場的一名個體經營者。

Note 2: The gene sequence of WuHan-hu-1 was uploaded by Zhang Yongzhen's team at Fudan University in Shanghai on January 5, 2020. It is the first new coronavirus complete genome sequence uploaded to the International Bioinformatics Database. The virus sample of WuHan-hu-1 was collected and provided by Wuhan Central Hospital. The collection time was December 30 or 26, 2019. It was collected from a 41-year-old Chen surnamed early-stage patient who was Self-employed person of the South China Seafood Market.

proCov2與Wuhan-hu-1隻相差3個核苷酸，而二者基因組序列（核苷酸序列）長度均為29903（含近3萬個核苷酸）。易知，二者基因組序列的差異度約為0.01%（萬分之一），即一致性約為99.99%。所以，Table-1中各病毒sample與proCov2的基因序列一致性比對結果，可視為這些sample與Wuhan-hu-1的一致性比對結果。

The difference between proCov2 and Wuhan-hu-1 is only 3 nucleotides, and the length of their genome sequence (nucleotide sequence) is 29903 (containing nearly 30,000 nucleotides). It is easy to know that the difference between the two genome sequences is about 0.01% (one in 10,000), that is, the identity is about 99.99%. Therefore, the genetic sequence consistency comparison result of each virus sample and proCov2 in Table-1 can be regarded as the consistency comparison result of these samples and Wuhan-hu-1.

要注意的是，由於Bloom恢復的基因序列，也就是武漢大學NTS技術輸出的基因序列不是全基因組序列，而只是全基因組序列的片斷，因些，Table-1顯示的不是病毒間全基因組序列的一致性，而是對應的基因組片斷的一致性。Table-1標題欄已標明，比對的序列區間是21570~29550，這一區間含近8000個核苷酸。

It should be noted that the gene sequence restored by Bloom, that is, the gene sequence output by the NTS technology of Wuhan University is not the whole genome sequence, but only fragments of the whole genome sequence. Therefore, Table-1 shows not the consistency of the whole genome sequence between viruses. but the consistency of corresponding genome fragments. The title bar of Table-1 has indicated that the sequence interval for comparison is 21570~29550, which contains nearly 8000 nucleotides.

觀察各個病毒sample與Wuhan-hu-1或proCov2的一致性，可知：Table-1所列14個病毒sample中，8個與Wuhan-hu-1的一致性差別超過1%，6個超過2%，4個超過3%，3個超過4%。

Observing the consistency of each virus sample with Wuhan-hu-1 or proCov2, it can be seen that among the 14 virus samples listed in Table-1, 8 are more than 1% different from Wuhan-hu-1, 6 are more than 2%, and 4 are more than 3%, 3 more than 4%.

由於比對的基因片斷含近8000個核苷酸，因此，如果序列一致性差別超過1%，那就意味着該病毒Sampe與Wuhan-hu-1至少有80個核苷酸不同；
如果一致性差別超過2%，就至少有160個核苷酸不同；
如果一致性差別超過3%，就至少有240個核苷酸不同；
如果一致性差別超過4%，就至少有320個核苷酸不同。

Since the aligned gene fragments contain nearly 8000 nucleotides, if the sequence identity differs by more than 1%, it means that at least 80 nucleotides are different between the virus sampe and Wuhan-hu-1;
If it differs by more than 2%, at least 160 nucleotides are different;
If it differs by more than 3%, at least 240 nucleotides are different;
If it differs by more than 4%, at least 320 nucleotides are different.

比對區間外還有2萬多個核苷酸位點，如果考慮這些位點，那麼這些病毒sample與Wuhan-hu-1的核苷酸差異可能會更多。

There are more than 20,000 nucleotide sites outside the comparison interval. If these sites are considered, the nucleotide differences between these virus samples and Wuhan-hu-1 may be more.

新冠病毒的變異速度是：一個病毒平均一年產生約25個核苷酸突變。產生上述規模的突變，正常情況下需要幾年、十幾年的時間。在疫情早期的2月15日前，武漢大學人民醫院的13位患者，其體內的新冠病毒同時發生了如此顯著的突變，這可能嗎？

The mutation rate of Sars-Cov-2 is: a virus produces about 25 nucleotide mutations a year on average. Under normal circumstances, it will take several to ten years to produce mutations scale above-mentioned. Before February 15 in the early stage of the epidemic, Sars-Cov-2 viruses from the bodies of 13 patients in the People's Hospital of Wuhan University had such a significant mutation at the same time, Is this possible?

對比一下迄今為止，新冠病毒的實際變異情況：
英國Alpha變種B.1.1.7的核苷酸變異位點約為28~32個；
南非Beta變種B.1.351的變異位點約為23個；
巴西Gamma變種P.1的變異位點約為17個；
印度Delta變種B.1.617.2的變異位點約為13~17個。

Compare the actual mutation of the new coronavirus so far:
There are about 28-32 nucleotide variation sites in the British Alpha variant B.1.1.7;
There are about 23 mutation sites in South Africa Beta variety B.1.351;
There are about 17 mutation sites in the Brazilian Gamma variety P.1;
There are about 13-17 mutation sites in the Indian Delta variety B.1.617.2.

可見，疫情發展至今，四個最重要的新冠病毒變種，其變異位點數都小於40個核苷酸；相比之下，Bloom恢復的數據有8個呈現出了超過80個核苷酸位點的不同，有3個呈現出了超過320個核苷酸位點的不同。而且，這麼大幅度的核苷酸差異發生在去年2月15日前發現的病毒樣本中。

It can be seen that the four most important Sars-Cov-2 variants so far have less than 40 nucleotide sites; in contrast, 8 of the data recovered by Bloom show more than 80 nucleotide sites. Three of them showed a difference of more than 320 nucleotide positions. Moreover, such a large nucleotide difference occurred in virus samples discovered before February 15 last year.


這些核苷酸位點的差異都是突變造成的嗎？如果是的話，如此超常的突變，Bloom怎麼會視而不見呢？這個困惑昨天未能解決。今天，我返回Bloom的論文，下載了幾個Bloom恢復、重建的基因序列，將它們的基因序列與Wuhan-Hu-1的基因序列加以比對（使用NCBI Blast工具），而後發現：原來，絕大多數核苷酸差異對應着核苷酸缺失，與變異無關。Bloom重建序列中存在着大量的字母N，每一個字母N都代表着其所在位點的核苷酸缺失。

Are these differences in nucleotide positions all caused by mutations? If so, how could Bloom turn a blind eye to such an extraordinary mutation? This confusion could not be resolved yesterday. Today, I returned to Bloom’s paper, downloaded several Bloom’s restored and reconstructed gene sequences, and compared their gene sequences with the Wuhan-Hu-1 gene sequence (using NCBI Blast tool), and then found that: it turns out, Overwhelming majority nucleotide differences correspond to nucleotide deletions and have nothing to do with variation. There are a large number of letters N in the Bloom reconstruction sequence, and each letter N represents a nucleotide deletion at its location.

Bloom重建序列中的大量核苷酸缺失，要麼是Bloom重建序列時產生的，要麼是武漢大學NTS測序錯誤造成的。

A large number of nucleotide deletions in Bloom's reconstructed sequence are either caused by Bloom's reconstruction of the sequence, or due to sequencing errors of NTS technology of  Wuhan University.

對所採用的基礎數據的準確性、可靠性問題，以及它們對研究過程、論文結論可能造成的影響，Bloom在論文中沒有進行討論和評估。

Bloom did not discuss and evaluate the accuracy and reliability of the basic data used, and their possible impact on the research process and the conclusion of the paper.

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附錄：Bloom重建的基因序列片斷示例（見原中文版文尾部分）。

Appendix: Examples of gene sequence fragments reconstructed by Bloom（See the end of the original Chinese version）

該示例對應Table-1中的C9，即第四個病毒Sample，序列中的N代表核苷酸缺失的位點。該示例是C9基因序列片斷的一部分，未展示全部近8000個核苷酸（鹼基對）。

This example corresponds to C9 in Table-1 of the main post, which is the fourth virus Sample. The N in the sequence represents the site of nucleotide deletion. This example is part of a fragment of the C9 gene sequence and does not show all of the nearly 8000 nucleotides (base pairs).

Bloom論文提供了13個重建新冠基因序列片斷的下載地址：
https://github.com/jbloom/SARS-CoV-2_PRJNA612766/raw/main/results/consensus/consensus_seqs.csv

The Blooms‘ paper provides the download address of 13 reconstructed sequence fragments of Sars-Cov-2.:



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