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It's disingenuous of the Telegraph journalist not to provide links to, or attributed quotes from, the Hungarian scientists. After doing some in-depth research

by iam-TJ 5y ago

It's disingenuous of the Telegraph journalist not to provide links to, or attributed quotes from, the Hungarian scientists. After doing some in-depth research to find the original research or reports I've found nothing published by the Hungarian institutions nor Dr Jesse Bloom - the only person quoted in the article. Having dug further I don't take his statements at face value either, for the reasons described below, since there's more than a hint of preconceived bias in his general thrust and previous publications. I REALLY wish journalists would clearly share published sources to original research and data for such important events rather than stir up controversy without demonstrating a strong foundation. Especially when claiming this is a "finding". For clarity, I've no opinion on SARS-Cov-2 origin but I do want to see claims well-supported by evidence. I went looking on both the mentioned Hungarian web-sites [0][1], searched biorxiv, and checked the Bloom Lab [2] publications since the only person quoted is Jesse Bloom [3] who claims to have reproduced (Hungarian) results. In my research I also found a prior report by Bloom in June 2021 [4] reporting 'recovery of deleted files containing partial sequences' [4] that were soon criticised by multiple other scientists; e.g: "...The language of the paper is unusual, its contains a significant degree of supposition and conjecture, cites blog posts..." [5]. [0] https://univet.hu/en/research/topics/ https://univet.hu/en/research/topics/ [1] https://www.elte.hu/en/facts https://www.elte.hu/en/facts [2] https://research.fredhutch.org/bloom/en/publications.html https://research.fredhutch.org/bloom/en/publications.html [3] https://research.fredhutch.org/bloom/en/members.html https://research.fredhutch.org/bloom/en/members.html [4] https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1.abstract https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1.... [5] https://edition.cnn.com/2021/06/23/health/coronavirus-sequences-database-scientist/index.html https://edition.cnn.com/2021/06/23/health/coronavirus-sequen... Updated: just discovered there's a recent github repo [6] created by Bloom with much more detail. Telegraph should really have pointed to this. [6] https://github.com/jbloom/PRJNA692319_public https://github.com/jbloom/PRJNA692319_public Update 2: Pre-print [7] of the Hungarian report (see [6] for details as to why it was rejected by Biorxiv several times). [7] https://www.researchsquare.com/article/rs-1330800/v1 https://www.researchsquare.com/article/rs-1330800/v1

iam-TJ 5y ago
The pre-print's introduction suggests the most likely cause of contamination is machine misalignment. Date of sequencing has not been determined other than to say late December 2019 to early January 2020 (when results were sent to the sample submitters). "We think that the most likely scenario is that the SARS-CoV-2 sequence fragments are not from the Antarctic soil samples,but are mistakenly assigned reads from another sample(s) sequenced on the same flow cell at the Sangon Biotech sequencing facility in Shanghai. The equipment, Illumina HiSeq 4000 that was used for sequencing according to the project’s metadata, is known to be prone to barcode misassignment errors6,7.In a nutshell, as detailed in Illumina’s whitepaper6, this artifact is related to the exponentially increasing density of next-generation sequencing (NGS) chips. Nowadays a single flow cell has such a large capacity that it is rarely filled up by a single sample. For example the 12 antarctic soil samples in PRJNA692319 altogether contain around 320 million paired end reads, while Illumina HiSeq 4000’s capacity is up to 10 billion paired end reads. The increased capacity is utilized through multiplexing, which adds unique sequences, called indexes or barcodes, to each DNA fragment during library preparation.Before final data analysis, sequencing reads from pooled libraries need to be identified and sorted computationally in a process called demultiplexing. This allows large numbers of libraries to be pooled and sequenced simultaneously during a single sequencing run. After adapters are ligated to nucleic acid fragments, the products are cleaned up to remove any free, unligated adapters. Libraries can be cleaned up by a bead-based or gel purification step to remove free adapters or primers. Failure to remove free adapters or primers can lead to contamination of prepared libraries and may result in index hopping and misassignment. As a results, sequencing reads from other, not related samples that are sequenced on the same flow cell can get into our samples."

by iam-TJ 5y ago

iam-TJ 5y ago

The pre-print's introduction suggests the most likely cause of contamination is machine misalignment. Date of sequencing has not been determined other than to say late December 2019 to early January 2020 (when results were sent to the sample submitters). "We think that the most likely scenario is that the SARS-CoV-2 sequence fragments are not from the Antarctic soil samples,but are mistakenly assigned reads from another sample(s) sequenced on the same flow cell at the Sangon Biotech sequencing facility in Shanghai. The equipment, Illumina HiSeq 4000 that was used for sequencing according to the project’s metadata, is known to be prone to barcode misassignment errors6,7.In a nutshell, as detailed in Illumina’s whitepaper6, this artifact is related to the exponentially increasing density of next-generation sequencing (NGS) chips. Nowadays a single flow cell has such a large capacity that it is rarely filled up by a single sample. For example the 12 antarctic soil samples in PRJNA692319 altogether contain around 320 million paired end reads, while Illumina HiSeq 4000’s capacity is up to 10 billion paired end reads. The increased capacity is utilized through multiplexing, which adds unique sequences, called indexes or barcodes, to each DNA fragment during library preparation.Before final data analysis, sequencing reads from pooled libraries need to be identified and sorted computationally in a process called demultiplexing. This allows large numbers of libraries to be pooled and sequenced simultaneously during a single sequencing run. After adapters are ligated to nucleic acid fragments, the products are cleaned up to remove any free, unligated adapters. Libraries can be cleaned up by a bead-based or gel purification step to remove free adapters or primers. Failure to remove free adapters or primers can lead to contamination of prepared libraries and may result in index hopping and misassignment. As a results, sequencing reads from other, not related samples that are sequenced on the same flow cell can get into our samples."