references.bib

@misc{USRTK2020,
  title = {Altered datasets raise more questions about reliability of key studies on coronavirus origins},
  author = {{USRTK}},
  year = {2020},
  note = {\url{https://usrtk.org/tag/pangolin-papers/}, which links to the actual SRA e-mails at \url{https://usrtk.org/wp-content/uploads/2020/12/NCBI-Emails.pdf}},
}

@misc{wang2021why,
  title = {{Why did Wuhan University researchers delete COVID-19 data at NIH?}},
  author = {Wang, Zicheng},
  year = {2021},
  note = {\url{https://pekingnology.substack.com/p/why-did-wuhan-university-researchers}},
}

@misc{wang2021exclusive,
  title = {{Exclusive: Chinese researcher, at the center of COVID data withdrawal controversy, speaks up}},
  author = {Wang, Zicheng},
  year = {2021},
  note = {\url{https://beijingchannel.substack.com/p/exclusive-chinese-researcher-at-the}},
}

@article{farkas2020insights,
  title={Insights on early mutational events in {SARS-CoV-2} virus reveal founder effects across geographical regions},
  author={Farkas, Carlos and Fuentes-Villalobos, Francisco and Garrido, Jose Luis and Haigh, Jody and Barr{\'\i}a, Mar{\'\i}a In{\'e}s},
  journal={PeerJ},
  volume={8},
  pages={e9255},
  year={2020},
  publisher={PeerJ Inc.}
}

@misc{SRA_deletion,
  title={{SRA} data updates},
  author={SRA},
  year={2021},
  howpublished={\url{https://www.ncbi.nlm.nih.gov/sra/docs/submitupdate/#how-do-i-withdraw-sra-data}},
  note={Last accessed June 2, 2021; a copy of the page is digitally archived on the Wayback Machine at \url{https://web.archive.org/web/20210505002105/https://www.ncbi.nlm.nih.gov/sra/docs/submitupdate/}},
}

@article{xiao2020isolation,
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  year={2020},
  publisher={Nature Publishing Group}
}

@article{chan2020single,
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  journal={bioRxiv},
  year={2020},
  volume={10.1101/2020.07.07.184374},
  publisher={Cold Spring Harbor Laboratory}
}

@article{wang2020medRxiv,
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	title = {Nanopore target sequencing for accurate and comprehensive detection of {SARS-CoV-2} and other respiratory viruses},
	elocation-id = {2020.03.04.20029538},
	year = {2020},
	volume = {10.1101/2020.03.04.20029538},
	publisher = {Cold Spring Harbor Laboratory Press},
	URL = {https://www.medrxiv.org/content/early/2020/03/06/2020.03.04.20029538},
	eprint = {https://www.medrxiv.org/content/early/2020/03/06/2020.03.04.20029538.full.pdf},
	journal = {medRxiv}
}

@article{wang2020small,
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title = {Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of {SARS-CoV-2} and Other Respiratory Viruses},
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}

@misc{Kang2020,
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}

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  publisher={Oxford University Press}
}

@article{kumar2021evolutionary,
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    title = {An evolutionary portrait of the progenitor {SARS-CoV-2} and its dominant offshoots in {COVID-19} pandemic},
    journal = {Molecular Biology and Evolution},
    year = {2021},
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}

@article{shu2017gisaid,
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  publisher={European Centre for Disease Prevention and Control}
}

@misc{garry2021early,
  title={Early appearance of two distinct genomic lineages of {SARS-CoV-2} in different Wuhan wildlife markets suggests {SARS-CoV-2} has a natural origin},
  author={Garry, Robert F},
  journal={virological.org},
  year={2021},
  note={\url{https://virological.org/t/early-appearance-of-two-distinct-genomic-lineages-of-sars-cov-2-in-different-wuhan-wildlife-markets-suggests-sars-cov-2-has-a-natural-origin/691}},
}

@misc{twiv2021,
  title = {{TWiV 762: SARS-CoV-2 origins with Robert Garry}},
  author = {Racaniello, Vincent and Despommier, Dickson and Dove, Alan and Condit, Rich and Barker, Brianne},
  year={2021},
  note={\url{https://www.microbe.tv/twiv/twiv-762/}},
}

@misc{WHO2021origins,
  title = {{WHO-convened global study of origins of SARS-CoV-2: China Part}},
  year = {2021},
  author =  {{WHO}},
  note = {\url{https://www.who.int/publications/i/item/who-convened-global-study-of-origins-of-sars-cov-2-china-part}},
}

@article{rambaut2020dynamic,
  title={A dynamic nomenclature proposal for {SARS-CoV-2} lineages to assist genomic epidemiology},
  author={Rambaut, Andrew and Holmes, Edward C and O’Toole, {\'A}ine and Hill, Verity and McCrone, John T and Ruis, Christopher and du Plessis, Louis and Pybus, Oliver G},
  journal={Nature Microbiology},
  volume={5},
  number={11},
  pages={1403--1407},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{forster2020phylogenetic,
  title={Phylogenetic network analysis of {SARS-CoV-2} genomes},
  author={Forster, Peter and Forster, Lucy and Renfrew, Colin and Forster, Michael},
  journal={Proceedings of the National Academy of Sciences},
  volume={117},
  number={17},
  pages={9241--9243},
  year={2020},
  publisher={National Acad Sciences}
}

@article{pipes2021assessing,
  title={Assessing uncertainty in the rooting of the {SARS-CoV-2} phylogeny},
  author={Pipes, Lenore and Wang, Hongru and Huelsenbeck, John P and Nielsen, Rasmus},
  journal={Molecular Biology and Evolution},
  volume={38},
  number={4},
  pages={1537--1543},
  year={2021},
  publisher={Oxford University Press}
}

@article{pekar2021timing,
  title={Timing the {SARS-CoV-2} index case in Hubei province},
  author={Pekar, Jonathan and Worobey, Michael and Moshiri, Niema and Scheffler, Konrad and Wertheim, Joel O},
  journal={Science},
  volume={372},
  number={6540},
  pages={412--417},
  year={2021},
  publisher={American Association for the Advancement of Science}
}

@article{tang2020origin,
  title={On the origin and continuing evolution of {SARS-CoV-2}},
  author={Tang, Xiaolu and Wu, Changcheng and Li, Xiang and Song, Yuhe and Yao, Xinmin and Wu, Xinkai and Duan, Yuange and Zhang, Hong and Wang, Yirong and Qian, Zhaohui and others},
  journal={National Science Review},
  volume={7},
  number={6},
  pages={1012--1023},
  year={2020},
  publisher={Oxford University Press}
}

@article{lytras2021exploring,
    author = {Lytras, Spyros and Hughes, Joseph and Martin, Darren and de Klerk, Arn{\'e} and Lourens, Rentia and Kosakovsky Pond, Sergei L and Xia, Wei and Jiang, Xiaowei and Robertson, David L},
    title = {{Exploring the natural origins of SARS-CoV-2 in the light of recombination}},
    elocation-id = {2021.01.22.427830},
    year = {2021},
    doi = {10.1101/2021.01.22.427830},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2021/05/27/2021.01.22.427830},
    eprint = {https://www.biorxiv.org/content/early/2021/05/27/2021.01.22.427830.full.pdf},
    journal = {bioRxiv}
}

@article{zhou2020pneumonia,
  title={A pneumonia outbreak associated with a new coronavirus of probable bat origin},
  author={Zhou, Peng and Yang, Xing-Lou and Wang, Xian-Guang and Hu, Ben and Zhang, Lei and Zhang, Wei and Si, Hao-Rui and Zhu, Yan and Li, Bei and Huang, Chao-Lin and others},
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  number={7798},
  pages={270--273},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{zhou2021identification,
  title={Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses},
  author={Zhou, Hong and Ji, Jingkai and Chen, Xing and Bi, Yuhai and Li, Juan and Wang, Qihui and Hu, Tao and Song, Hao and Zhao, Runchu and Chen, Yanhua and others},
  journal={Cell},
  year={2021},
  publisher={Elsevier},
}

@article{zhou2020novel,
  title={A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein},
  author={Zhou, Hong and Chen, Xing and Hu, Tao and Li, Juan and Song, Hao and Liu, Yanran and Wang, Peihan and Liu, Di and Yang, Jing and Holmes, Edward C and others},
  journal={Current Biology},
  volume={30},
  number={11},
  pages={2196--2203},
  year={2020},
  publisher={Elsevier}
}

@article{rahalkar2020anomalous,
  title={The Anomalous Nature of the Fecal Swab Data, Receptor Binding Domain and Other Questions in {RaTG13} Genome},
  author={Rahalkar, Monali and Bahulikar, Rahul},
  year={2020},
  journal={Preprints},
  pages={2020080205},
}

@article{singla2020novo,
  title={De-novo Assembly of {RaTG13} Genome Reveals Inconsistencies Further Obscuring {SARS-CoV-2} Origins},
  author={Singla, Mohit and Ahmad, Saad and Gupta, Chandan and Sethi, Tavpritesh},
  year={2020},
  journal={Preprints},
  pages={2020080595},
}

@article{chan2020familial,
  title={A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster},
  author={Chan, Jasper Fuk-Woo and Yuan, Shuofeng and Kok, Kin-Hang and To, Kelvin Kai-Wang and Chu, Hin and Yang, Jin and Xing, Fanfan and Liu, Jieling and Yip, Cyril Chik-Yan and Poon, Rosana Wing-Shan and others},
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  volume={395},
  number={10223},
  pages={514--523},
  year={2020},
  publisher={Elsevier}
}

@article{kang2020evidence,
    author = {Kang, Min and Wu, Jie and Ma, Wenjun and He, Jianfeng and Lu, Jing and Liu, Tao and Li, Baisheng and Mei, Shujiang and Ruan, Feng and Lin, Lifeng and Zou, Lirong and Ke, Changwen and Zhong, Haojie and Zhang, Yingtao and Chen, Xuguang and Liu, Zhe and Zhu, Qi and Xiao, Jianpeng and Yu, Jianxiang and Hu, Jianxiong and Zeng, Weilin and Li, Xing and Liao, Yuhuang and Tang, Xiujuan and Xiao, Songjian and Wang, Ying and Song, Yingchao and Zhuang, Xue and Liang, Lijun and Zeng, Siqing and He, Guanhao and Lin, Peng and Deng, Huihong and Song, Tie},
    title = {Evidence and characteristics of human-to-human transmission of SARS-CoV-2},
    year = {2020},
    doi = {10.1101/2020.02.03.20019141},
    publisher = {Cold Spring Harbor Laboratory Press},
    eprint = {https://www.medrxiv.org/content/early/2020/02/17/2020.02.03.20019141.full.pdf},
    journal = {medRxiv}
}

@article{worobey2020emergence,
  title={{The emergence of SARS-CoV-2 in Europe and North America}},
  author={Worobey, Michael and Pekar, Jonathan and Larsen, Brendan B and Nelson, Martha I and Hill, Verity and Joy, Jeffrey B and Rambaut, Andrew and Suchard, Marc A and Wertheim, Joel O and Lemey, Philippe},
  journal={Science},
  volume={370},
  number={6516},
  pages={564--570},
  year={2020},
  publisher={American Association for the Advancement of Science}
}

@misc{ProMED2109,
  title = {Undiagnosed pneumonia---{China (Hubei)}: Request for information},
  author = {ProMED},
  year = {2019},
  note = {\url{https://promedmail.org/promed-post/?id=6864153}},
}

@misc{GlobalTimes2020,
  title = {Wuhan's Huanan seafood market a victim of {COVID-19}: {CDC} director},
  author = {{Global Times}},
  year = {2020},
  note = {\url{https://www.globaltimes.cn/content/1189506.shtml}, archived at \url{https://web.archive.org/web/20200528062530/https://www.globaltimes.cn/content/1189506.shtml}},
}

@article{huang2020clinical,
  title={Clinical features of patients infected with 2019 novel coronavirus in {Wuhan, China}},
  author={Huang, Chaolin and Wang, Yeming and Li, Xingwang and Ren, Lili and Zhao, Jianping and Hu, Yi and Zhang, Li and Fan, Guohui and Xu, Jiuyang and Gu, Xiaoying and others},
  journal={Lancet},
  volume={395},
  number={10223},
  pages={497--506},
  year={2020},
  publisher={Elsevier}
}

@article{chen2020epidemiological,
  title={Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in {Wuhan, China}: a descriptive study},
  author={Chen, Nanshan and Zhou, Min and Dong, Xuan and Qu, Jieming and Gong, Fengyun and Han, Yang and Qiu, Yang and Wang, Jingli and Liu, Ying and Wei, Yuan and others},
  journal={Lancet},
  volume={395},
  number={10223},
  pages={507--513},
  year={2020},
  publisher={Elsevier}
}

@misc{ma2020SCMP,
  author = {Ma, Josephine},
  year = {2020},
  title = {{Coronavirus: China’s first confirmed Covid-19 case traced back to November 17}},
  howpublished = {South China Morning Post},
  note = {\url{https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back}, archived at \url{https://web.archive.org/web/20200315011702/https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back}},
}

@misc{pinghui2020SCMP,
  author = {Pingui, Zhuang},
  year = {2020},
  title = {China confirms unauthorised labs were told to destroy early coronavirus samples},
  howpublished = {South China Morning Post},
  note = {\url{https://www.scmp.com/news/china/society/article/3084635/china-confirms-unauthorised-labs-were-told-destroy-early}, archived at \url{https://web.archive.org/web/20210103124552/https://www.scmp.com/news/china/society/article/3084635/china-confirms-unauthorised-labs-were-told-destroy-early}},
}
      

@misc{healthtimes2020,
  title = {Experts judge the source of the new coronavirus: {December} 8 last year may not be the earliest time of onset},
  author = {{Health Times}},
  year = {2020},
  note = {\url{https://www.guancha.cn/politics/2020_02_27_538822.shtml}, archived and detailed at \url{https://docs.google.com/document/d/e/2PACX-1vTQxG822DtqP7IZSjLj751Mrm8Ev7leksXfjBLsA9KJ0_tbGV6YJAAjuijPnwz_YmUQGY1PZUl5LcCI/pub}},
}

@misc{chinacdc2020,
  title = {{Memo to the Offices of the Chinese Center for Disease Control and Prevention}},
  author = {{China CDC}},
  year = {2020},
  note = {\url{https://www.documentcloud.org/documents/7340336-China-CDC-Sup-Regs.html}},
}

@article{bedford2020cryptic,
  title={Cryptic transmission of {SARS-CoV-2} in Washington state},
  author={Bedford, Trevor and Greninger, Alexander L and Roychoudhury, Pavitra and Starita, Lea M and Famulare, Michael and Huang, Meei-Li and Nalla, Arun and Pepper, Gregory and Reinhardt, Adam and Xie, Hong and others},
  journal={Science},
  volume={370},
  number={6516},
  pages={571--575},
  year={2020},
  publisher={American Association for the Advancement of Science}
}

@article{deng2020genomic,
  title={Genomic surveillance reveals multiple introductions of {SARS-CoV-2 into Northern California}},
  author={Deng, Xianding and Gu, Wei and Federman, Scot and Du Plessis, Louis and Pybus, Oliver G and Faria, Nuno R and Wang, Candace and Yu, Guixia and Bushnell, Brian and Pan, Chao-Yang and others},
  journal={Science},
  volume={369},
  number={6503},
  pages={582--587},
  year={2020},
  publisher={American Association for the Advancement of Science}
}

@article{fauver2020coast,
  title={{Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States}},
  author={Fauver, Joseph R and Petrone, Mary E and Hodcroft, Emma B and Shioda, Kayoko and Ehrlich, Hanna Y and Watts, Alexander G and Vogels, Chantal BF and Brito, Anderson F and Alpert, Tara and Muyombwe, Anthony and others},
  journal={Cell},
  volume={181},
  number={5},
  pages={990--996},
  year={2020},
  publisher={Elsevier}
}

@article{morel2021phylogenetic,
  title={Phylogenetic analysis of {SARS-CoV-2} data is difficult},
  author={Morel, Benoit and Barbera, Pierre and Czech, Lucas and Bettisworth, Ben and H{\"u}bner, Lukas and Lutteropp, Sarah and Serdari, Dora and Kostaki, Evangelia-Georgia and Mamais, Ioannis and Kozlov, Alexey M and others},
  journal={Molecular Biology and Evolution},
  volume={38},
  number={5},
  pages={1777--1791},
  year={2021},
  publisher={Oxford University Press}
}

@article{turakhia2020stability,
  title={Stability of {SARS-CoV-2} phylogenies},
  author={Turakhia, Yatish and De Maio, Nicola and Thornlow, Bryan and Gozashti, Landen and Lanfear, Robert and Walker, Conor R and Hinrichs, Angie S and Fernandes, Jason D and Borges, Rui and Slodkowicz, Greg and others},
  journal={PLoS Genetics},
  volume={16},
  number={11},
  pages={e1009175},
  year={2020},
  publisher={Public Library of Science}
}

@article{boni2020evolutionary,
  title={{Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic}},
  author={Boni, Maciej F and Lemey, Philippe and Jiang, Xiaowei and Lam, Tommy Tsan-Yuk and Perry, Blair W and Castoe, Todd A and Rambaut, Andrew and Robertson, David L},
  journal={Nature Microbiology},
  volume={5},
  number={11},
  pages={1408--1417},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{cohen2020wuhan,
  title={Wuhan seafood market may not be source of novel virus spreading globally},
  author={Cohen, Jon},
  journal={Science},
  volume={10},
  pages = {10.1126/science.abb0611},
  year={2020}
}

@article{molder2021sustainable,
  title={Sustainable data analysis with Snakemake},
  author={M{\"o}lder, Felix and Jablonski, Kim Philipp and Letcher, Brice and Hall, Michael B and Tomkins-Tinch, Christopher H and Sochat, Vanessa and Forster, Jan and Lee, Soohyun and Twardziok, Sven O and Kanitz, Alexander and others},
  journal={F1000Research},
  volume={10},
  pages = {33},
  year={2021},
  publisher={Faculty of 1000 Ltd}
}

@article{chen2018fastp,
  title={fastp: an ultra-fast all-in-one FASTQ preprocessor},
  author={Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
  journal={Bioinformatics},
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  pages={i884--i890},
  year={2018},
  publisher={Oxford University Press}
}

@article{katoh2013mafft,
  title={MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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  publisher={Society for Molecular Biology and Evolution}
}

@article{li2021novel,
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  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@article{zhu2020brief,
  title={Brief Report: A Novel Coronavirus from Patients with Pneumonia in China, 2019},
  author={Zhu, Na and Zhang, Dingyu and Wang, Wenling and Li, Xingwang and Yang, Bo and Song, Jingdong and Zhao, Xiang and Huang, Baoying and Shi, Weifeng and Lu, Roujian and others},
  journal={The New England Journal of Medicine},
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  year={2020},
  publisher={Various}
}

@article{vanderplas2018altair,
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@article{minh2020iq,
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@article{huerta2016ete,
  title={ETE 3: reconstruction, analysis, and visualization of phylogenomic data},
  author={Huerta-Cepas, Jaime and Serra, Fran{\c{c}}ois and Bork, Peer},
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@article{yang2020epidemiological,
	author = {Yang, Yang and Lu, Qing-Bin and Liu, Ming-Jin and Wang, Yi-Xing and Zhang, An-Ran and Jalali, Neda and Dean, Natalie E. and Longini, Ira and Halloran, M. Elizabeth and Xu, Bo and Zhang, Xiao-Ai and Wang, Li-Ping and Liu, Wei and Fang, Li-Qun},
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    volume = {10.1101/2020.02.10.20021675},
	eprint = {https://www.medrxiv.org/content/early/2020/02/21/2020.02.10.20021675.full.pdf},
	journal = {medRxiv},
	publisher = {Cold Spring Harbor Laboratory Press},
	title = {Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China},
	url = {https://www.medrxiv.org/content/early/2020/02/21/2020.02.10.20021675},
	year = {2020},
	Bdsk-Url-1 = {https://www.medrxiv.org/content/early/2020/02/21/2020.02.10.20021675},
	Bdsk-Url-2 = {https://doi.org/10.1101/2020.02.10.20021675},
    }