PDF(Pubmed)
Abstract：
In March 2023, the Chinese CDC publicly released raw metagenomic sequencing data for environmental samples collected in early 2020 from the Huanan Seafood Market. Prior to that data release, some scientists had suggested that these samples could be informative for establishing if animals such as raccoon dogs had been infected with severe acute respiratory syndrome virus 2 (SARS-CoV-2). However, no one had analyzed how much SARS-CoV-2 was actually present in the metagenomic sequencing data. After the raw data became available, I fully analyzed the abundance of both viral and animal genetic material in the samples. That analysis, which was published in Virus Evolution, found that the SARS-CoV-2 content of most samples was very low and that the abundance of SARS-CoV-2 was most strongly associated with animals such as largemouth bass that are not plausible candidates for having been infected. Based on these results, I concluded that the metagenomic content of the samples was not informative for determining if any non-human animals in the market had been infected with SARS-CoV-2. One of the authors of an earlier study of these samples, Florence Débarre, recently submitted a response to my paper. Here, I reply in turn to explain why it is important to quantify the abundance of viral material before drawing conclusions from metagenomic sequencing. I also report new analyses of other animal coronaviruses in the samples and show that material from some other animal coronaviruses is much more abundant than SARS-CoV-2 in samples collected on the date when most wildlife stall sampling was performed. I further show that material from some of these animal coronaviruses is associated with the animals they probably infect but that no such association exists for SARS-CoV-2. Overall, these new analyses further emphasize the importance of quantifying the actual amount of viral material in metagenomic samples and underscore why the environmental samples from the Huanan Seafood Market are not informative for determining if any non-human animals were infected with SARS-CoV-2.
摘要：
2023年3月，中国疾病预防控制中心公开发布了2020年初从华南海鲜市场收集的环境样本的原始宏基因组测序数据。在数据发布之前，一些科学家建议，这些样本可以提供信息，以确定动物如浣熊犬是否感染了严重急性呼吸道综合症病毒2（SARS-CoV-2）。然而,没有人分析过宏基因组测序数据中实际存在多少SARS-CoV-2.原始数据可用后，我充分分析了样本中病毒和动物遗传物质的丰度。这种分析,发表在《病毒进化》上，发现大多数样本的SARS-CoV-2含量非常低，并且SARS-CoV-2的丰度与诸如大嘴鲈鱼之类的动物密切相关，这些动物不是被感染的似是而非。基于这些结果,我得出的结论是，样品的宏基因组含量对于确定市场上是否有任何非人类动物感染了SARS-CoV-2没有意义。这些样本的早期研究的作者之一，FlorenceDébarre,最近对我的论文做出了回应。这里,我反过来回答解释为什么在从宏基因组测序得出结论之前量化病毒材料的丰度很重要。我还报告了对样本中其他动物冠状病毒的新分析，并表明在进行大多数野生动物摊位采样的日期收集的样本中，来自其他动物冠状病毒的物质比SARS-CoV-2丰富得多。我进一步表明，来自这些动物冠状病毒中的一些的物质与它们可能感染的动物有关，但是对于SARS-CoV-2不存在这种关联。总的来说,这些新的分析进一步强调了量化宏基因组样本中病毒物质实际数量的重要性，并强调了为什么华南海鲜市场的环境样本对于确定是否有任何非人类动物感染SARS-CoV-2没有提供信息。
