Evolution of the SARS virus: An open Science research seminar

12/04/2022

SARS. What’s in a name?

WHO press conferences 2020

Questions

Viral species and viral sequences

Number of viral “species”

Definitions

Monophyletic evolution

Species, strains and variants

Coronaviridae Study Group of the International Committee on Taxonomy of Viruses

Overlaps between SARS-CoV-1 and SARS-CoV-2 cluster of sequences

Non-identical base pairs

Next strain SARS-CoV-2

Questions

Implications

Time line of the first recorded SARS outbreak

First reports in China.

Questions

CDC April 2003

Beijing outbreaks Pang et al. (2003)

Toronto outbreaks

Toronto outbreaks

Low (2006)

Toronto outbreaks

"Provincial emergency on March 26, 2003. All hospitals in the Greater Toronto Area (GTA) suspended nonessential services, limited visitors and created isolation units for potential SARS patients with PPR for exposed staff (i.e., gowns, masks, and goggles). Four days later, provincial officials extended access restrictions to all Ontario hospitals.

Toronto outbreaks

Reactions

The CDC were quite relaxed in an April 22 2003 press conference

“CDC and the State Department routinely issue various kinds of advice to outbound travelers. One kind of advice is called a health alert, that’s just simply a heads-up. We have issued a health alert to travelers to Toronto, Canada. And that health alert basically says, no reason to stay home, but if you’re going there, be aware that SARS is present in some settings in the community and you may wish to avoid the hospital environment or the health care environment. A different level of advice to outbound passengers is a travel advisory, and we also have travel advisories for SARS. These are now in effect for China, including mainland China as well as the Hong Kong Special Administrative Region, Hanoi, and Singapore. These outbound advisories right now are saying, please avoid non-essential travel to these areas because there is ongoing transmission in the community that is not linked back to the initial cases.”

Official end of the epidemic (July 2003)

Toronto July 2003

Postscript. China 2004

Questions

The PCR test

Hamburg 1 (Muth et al. 2018)

Could deletions actually increase fitness?

(Muth et al. 2018) “As pointed out in Marzi et al. for Ebola virus Makona, a prolonged survival time as seen with late epidemic strains could have increased the duration of infectious virus shedding in humans and may thus have increased the long-term fitness of those viruses. We cannot, at present, exclude whether similar effects may have provided a fitness advantage to SARS-CoV on host population level, such as by keeping infected individuals socially interactive for prolonged times while infected with a slightly attenuated virus.”

Endemic coronavirus prevalence often drops to unoticeable levels (Killerby et al. 2018)

Could a mild version of SARS have become endemic in humans?

Severe pneumonia in normal times is not easily attributable

Zoonotic origins. Civets?

Guan et al. (2003)

Questions

Were do bats come in to the story?

Bat viral diversity

Spillovers

Spillovers

(Cui, Li, and Shi 2019)

Studies of bat coronavirus diversity

Illustrative studies in bats

Example from Luxembourg

(Pauly et al. 2017)

Drexler et al. (2010)

Muth et al. (2018)

V. Corman et al. (2020)

Rhinolophus distribution

Cats as intermediate hosts?

Carnivore hosts

Cats in China

Cats and SARS-Cov-2

(Zhang et al. 2020)

Bat to human direct transmission?

N. Wang et al. (2018) claimed to have found recent (pre covid19) antibodies to SARS in rural China.

“During questioning, none of the 6 seropositive subjects could recall any clinical symptoms in the past 12 months, suggesting that their bat SARSr-CoV infection either occurred before the time of sampling, or that infections were subclinical or caused only mild symptoms. Our previous work based on cellular and humanized mouse infection studies suggest that these viruses are less virulent than SARS-CoV (Ge et al. 2013; Menachery et al. 2016; Yang et al. 2016). Masked palm civets appeared to play a role as intermediate hosts of SARS-CoV in the 2002–2003 outbreak (Guan et al. 2003). However, considering that these individuals have a high chance of direct exposure to bat secretion in their villages, this study further supports the notion that some bat SARSr-CoVs are able to directly infect humans without intermediate hosts, as suggested by receptor entry and animal infection studies (Menachery et al. 2016).”

Italy 2019

Lecis et al. (2019)

“The detected virus (SarBatCoV1) belonged to clade 2b, including most of the SARS-like CoVs found in bats, as well as human SARS Coronavirus”

Questions

Suggestions for future research

Postscript

Age adjusted all cause mortality

(Office for National Statistics 2022)

Deaths from pneumonia England and Wales

Statista web site (2021)

References

Alimpiev, Egor. 2019. Rethinking the Virus Species Concept 25.
Anthony, Simon J., Jonathan H. Epstein, Kris A. Murray, Isamara Navarrete-Macias, Carlos M. Zambrana-Torrelio, Alexander Solovyov, Rafael Ojeda-Flores, et al. 2013. A strategy to estimate unknown viral diversity in mammals.” mBio 4 (5): 1–15. https://doi.org/10.1128/mBio.00598-13.
———, et al. 2013. A strategy to estimate unknown viral diversity in mammals.” mBio 4 (5): 1–15. https://doi.org/10.1128/mBio.00598-13.
Balboni, A., A. Palladini, G. Bogliani, and M. Battilani. 2011. Detection of a virus related to betacoronaviruses in Italian greater horseshoe bats.” Epidemiology and Infection 139 (2): 216–19. https://doi.org/10.1017/S0950268810001147.
CDC archive. 2020. “SARS | 2004 Media News and Alerts Archive | CDC.” 2020. https://www.cdc.gov/sars/media/index.html.
Corman, Victor Max, Heather J. Baldwin, Adriana Fumie Tateno, Rodrigo Melim Zerbinati, Augustina Annan, Michael Owusu, Evans Ewald Nkrumah, et al. 2015. Evidence for an Ancestral Association of Human Coronavirus 229E with Bats.” Journal of Virology 89 (23): 11858–70. https://doi.org/10.1128/jvi.01755-15.
Corman, Victor, Tobias Bleicker, Sebastian Brünink, Christian Drosten, Olfert Landt, Marion Koopmans, and Maria Zambon Public Health England. 2020. Diagnostic detection of 2019-nCoV by real-time RT-RCR incl. workflow protocoll on the last 3 pages.” Carité Berlin.
Cui, Jie, Fang Li, and Zheng Li Shi. 2019. Origin and evolution of pathogenic coronaviruses.” Nature Reviews Microbiology 17 (3): 181–92. https://doi.org/10.1038/s41579-018-0118-9.
De Sabato, Luca, Davide Lelli, Francesca Faccin, Sabrina Canziani, Ilaria Di Bartolo, Gabriele Vaccari, and Ana Moreno. 2019. Full genome characterization of two novel Alpha-coronavirus species from Italian bats.” Virus Research 260 (January): 60–66. https://doi.org/10.1016/j.virusres.2018.11.007.
Drexler, Jan Felix, Victor Max Corman, and Christian Drosten. 2014a. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS.” Antiviral Research 101 (1): 45–56. https://doi.org/10.1016/j.antiviral.2013.10.013.
———. 2014b. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS.” Antiviral Research 101 (1): 45–56. https://doi.org/10.1016/j.antiviral.2013.10.013.
———. 2014a. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS.” Antiviral Research 101 (1): 45–56. https://doi.org/10.1016/j.antiviral.2013.10.013.
Drexler, Jan Felix, Victor Max Corman, Tom Wegner, Adriana Fumie Tateno, Rodrigo Melim Zerbinati, Florian Gloza-Rausch, Antje Seebens, Marcel A. Müller, and Christian Drosten. 2011. Amplification of emerging viruses in a bat colony.” Emerging Infectious Diseases 17 (3): 449–56. https://doi.org/10.3201/eid1703.100526.
Drexler, Jan Felix, Florian Gloza-Rausch, Jörg Glende, Victor Max Corman, Doreen Muth, Matthias Goettsche, Antje Seebens, et al. 2010. Genomic Characterization of Severe Acute Respiratory Syndrome-Related Coronavirus in European Bats and Classification of Coronaviruses Based on Partial RNA-Dependent RNA Polymerase Gene Sequences.” Journal of Virology 84 (21): 11336–49. https://doi.org/10.1128/jvi.00650-10.
Drosten, Christian, Stephan Günther, Wolfgang Preiser, Sylvie van der Werf, Hans-Reinhard Brodt, Stephan Becker, Holger Rabenau, et al. 2003. Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome.” New England Journal of Medicine 348 (20): 1967–76. https://doi.org/10.1056/nejmoa030747.
Dukes, Billy. 2015. “When AC/DC, the Rolling Stones and Rush Rocked SARSstock.” 2015. https://ultimateclassicrock.com/rolling-stones-acdc-and-rush-benefit-concert/.
Gorbalenya, Alexander E., Susan C. Baker, Ralph S. Baric, Raoul J. de Groot, Christian Drosten, Anastasia A. Gulyaeva, Bart L. Haagmans, et al. 2020. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.” Nature Microbiology 5 (4): 536–44. https://doi.org/10.1038/s41564-020-0695-z.
———, et al. 2020. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.” Nature Microbiology 5 (4): 536–44. https://doi.org/10.1038/s41564-020-0695-z.
Guan, Y., B. J. Zheng, Y. Q. He, X. L. Liu, Z. X. Zhuang, C. L. Cheung, S. W. Luo, et al. 2003. Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China.” Science 302 (5643): 276–78. https://doi.org/10.1126/science.1087139.
Guo, Hongyan, Aizhen Guo, Chong Wang, Bangfen Yan, Haisong Lu, and Huanchun Chen. 2008. Expression of feline angiotensin converting enzyme 2 and its interaction with SARS-CoV S1 protein.” Research in Veterinary Science 84 (3): 494–96. https://doi.org/10.1016/j.rvsc.2007.05.011.
Hayman, D. T. S., R. A. Bowen, P. M. Cryan, G. F. Mccracken, T. J. O’Shea, A. J. Peel, A. Gilbert, C. T. Webb, and J. L. N. Wood. 2013. Ecology of Zoonotic Infectious Diseases in Bats: Current Knowledge and Future Directions.” Zoonoses and Public Health 60 (1): 2–21. https://doi.org/10.1111/zph.12000.
Hu, Ben, Lei Ping Zeng, Xing Lou Yang, Xing Yi Ge, Wei Zhang, Bei Li, Jia Zheng Xie, et al. 2017. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus.” PLoS Pathogens 13 (11): 1–27. https://doi.org/10.1371/journal.ppat.1006698.
Jain, Seema, Wesley H. Self, Richard G. Wunderink, Sherene Fakhran, Robert Balk, Anna M. Bramley, Carrie Reed, et al. 2015. Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults.” New England Journal of Medicine 373 (5): 415–27. https://doi.org/10.1056/nejmoa1500245.
Jo, Wendy K., Edmilson Ferreira de Oliveira-Filho, Andrea Rasche, Alex D. Greenwood, Klaus Osterrieder, and Jan Felix Drexler. 2020. Potential zoonotic sources of SARS-CoV-2 infections.” Transboundary and Emerging Diseases, no. July: 1–11. https://doi.org/10.1111/tbed.13872.
Killerby, Marie E., Holly M. Biggs, Amber Haynes, Rebecca M. Dahl, Desiree Mustaquim, Susan I. Gerber, and John T. Watson. 2018. Human coronavirus circulation in the United States 2014–2017.” Journal of Clinical Virology 101 (August): 52–56. https://doi.org/10.1016/j.jcv.2018.01.019.
———. 2018. Human coronavirus circulation in the United States 2014–2017.” Journal of Clinical Virology 101 (August): 52–56. https://doi.org/10.1016/j.jcv.2018.01.019.
Kivistö, Ilkka, Eeva Maria Tidenberg, Thomas Lilley, Kati Suominen, Kristian M. Forbes, Olli Vapalahti, Anita Huovilainen, and Tarja Sironen. 2020. First Report of Coronaviruses in Northern European Bats.” Vector-Borne and Zoonotic Diseases 20 (2): 155–58. https://doi.org/10.1089/vbz.2018.2367.
Lacroix, Audrey, Nicole Vidal, Alpha K. Keita, Guillaume Thaurignac, Amandine Esteban, Hélène de Nys, Ramadan Diallo, et al. 2020. Wide diversity of coronaviruses in frugivorous and insectivorous bat species: A pilot study in Guinea, West Africa.” Viruses 12 (8). https://doi.org/10.3390/v12080855.
Lau, Susanna K. P., Yun Feng, Honglin Chen, Hayes K. H. Luk, Wei-Hong Yang, Kenneth S. M. Li, Yu-Zhen Zhang, et al. 2015. Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.” Journal of Virology 89 (20): 10532–47. https://doi.org/10.1128/jvi.01048-15.
Lecis, Roberta, Mauro Mucedda, Ermanno Pidinchedda, Marco Pittau, and Alberto Alberti. 2019. Molecular identification of Betacoronavirus in bats from Sardinia (Italy): first detection and phylogeny.” Virus Genes 55 (1): 60–67. https://doi.org/10.1007/s11262-018-1614-8.
Low, Donald E. 2006. “FIGURE 1-1, SARS Toronto: Phases i and II.” 2006. https://www.ncbi.nlm.nih.gov/books/NBK92467/figure/ch1.f1/?report=objectonly.
Mendenhall, Ian H, Aslan A Kerimbayev, Vitaliy M Strochkov, Gavin J D Smith, and Mukhit B Orynbayev. 2019. Discovery and Characterization of Novel Bat.” Viruses, 1–8.
Monchatre-Leroy, Elodie, Franck Boué, Jean Marc Boucher, Camille Renault, François Moutou, Meriadeg Ar Gouilh, and Gérald Umhang. 2017. Identification of alpha and beta coronavirus in wildlife species in france: bats, rodents, rabbits, and hedgehogs.” Viruses 9 (12). https://doi.org/10.3390/v9120364.
Musso, Nicolò, Angelita Costantino, Sebastiano La Spina, Alessandra Finocchiaro, Francesca Andronico, Stefano Stracquadanio, Luigi Liotta, Rosanna Visalli, and Giovanni Emmanuele. 2020. New SARS-CoV-2 infection detected in an Italian pet cat by RT-qPCR from deep pharyngeal swab.” Pathogens 9 (9): 1–9. https://doi.org/10.3390/pathogens9090746.
Muth, Doreen, Victor Max Corman, Hanna Roth, Tabea Binger, Ronald Dijkman, Lina Theresa Gottula, Florian Gloza-Rausch, et al. 2018. Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission.” Scientific Reports 8 (1): 1–11. https://doi.org/10.1038/s41598-018-33487-8.
Office for National Statistics. 2022. “Annual Deaths and Mortality Rates, 1838 to 2020 (Provisional).” 2022. https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/adhocs/12735annualdeathsandmortalityrates1938to2020provisional.
Pang, Xinghuo, Zonghan Zhu, Fujie Xu, Jiyong Guo, Xiaohong Gong, Donglei Liu, Zejun Liu, Daniel P. Chin, and Daniel R. Feikin. 2003. Evaluation of Control Measures Implemented in the Severe Acute Respiratory Syndrome Outbreak in Beijing, 2003.” Journal of the American Medical Association 290 (24): 3215–21. https://doi.org/10.1001/jama.290.24.3215.
Pauly, Maude, Jacques B. Pir, Catherine Loesch, Aurélie Sausy, Chantal J. Snoeck, Judith M. Hübschen, and Claude P. Muller. 2017. Novel alphacoronaviruses and paramyxoviruses cocirculate with type 1 and severe acute respiratory system (SARS)-related betacoronaviruses in synanthropic bats of luxembourg.” Applied and Environmental Microbiology 83 (18): 1–14. https://doi.org/10.1128/AEM.01326-17.
Plowright, Raina K., Peggy Eby, Peter J. Hudson, Ina L. Smith, David Westcott, Wayne L. Bryden, Deborah Middleton, et al. 2014. Ecological dynamics of emerging bat virus spillover.” Proceedings of the Royal Society B: Biological Sciences 282 (1798). https://doi.org/10.1098/rspb.2014.2124.
Rizzo, Francesca, Kathryn M. Edenborough, Roberto Toffoli, Paola Culasso, Simona Zoppi, Alessandro Dondo, Serena Robetto, et al. 2017. Coronavirus and paramyxovirus in bats from Northwest Italy.” BMC Veterinary Research 13 (1): 1–11. https://doi.org/10.1186/s12917-017-1307-x.
Smith, C. S., C. E. De Jong, J. Meers, J. Henning, L. F. Wang, and H. E. Field. 2016. Coronavirus infection and diversity in bats in the Australasian region.” EcoHealth 13 (1): 72–82. https://doi.org/10.1007/s10393-016-1116-x.
Statista web site. 2021. “Mortality Rate from Pneumonia England and Wales.” 2021. https://www.statista.com/statistics/1051438/mortality-rate-from-pneumonia-england-and-wales/.
Tao, Ying, and Suxiang Tong. 2019. Complete Genome Sequence of a Severe Acute Respiratory Syndrome-Related Coronavirus from Kenyan Bats.” Edited by Kenneth M. Stedman. Microbiology Resource Announcements 8 (28): 1–5. https://doi.org/10.1128/MRA.00548-19.
Van Regenmortel, M. H. V. 2003. Viruses are real, virus species are man-made, taxonomic constructions.” Archives of Virology 148 (12): 2481–88. https://doi.org/10.1007/s00705-003-0246-y.
Wang, L. F., and B. T. Eaton. 2007. Bats, civets and the emergence of SARS.” Current Topics in Microbiology and Immunology 315: 325–44. https://doi.org/10.1007/978-3-540-70962-6_13.
Wang, Ning, Shi Yue Li, Xing Lou Yang, Hui Min Huang, Yu Ji Zhang, Hua Guo, Chu Ming Luo, et al. 2018. Serological Evidence of Bat SARS-Related Coronavirus Infection in Humans, China.” Virologica Sinica 33 (1): 104–7. https://doi.org/10.1007/s12250-018-0012-7.
Wong, Antonio C. P., Xin Li, Susanna K. P. Lau, and Patrick C. Y. Woo. 2019. Global epidemiology of bat coronaviruses.” Viruses 11 (2): 1–17. https://doi.org/10.3390/v11020174.
Woo, P. C. Y., S. K. P. Lau, C. S. F. Lam, C. C. Y. Lau, A. K. L. Tsang, J. H. N. Lau, R. Bai, et al. 2012. Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavi.” Journal of Virology 86 (7): 3995–4008. https://doi.org/10.1128/jvi.06540-11.
Woo, Patrick C. Y., Susanna K. P. Lau, Kenneth S. M. Li, Rosana W. S. Poon, Beatrice H. L. Wong, Hoi wah Tsoi, Bethanie C. K. Yip, Yi Huang, Kwok hung Chan, and Kwok yung Yuen. 2006. Molecular diversity of coronaviruses in bats.” Virology 351 (1): 180–87. https://doi.org/10.1016/j.virol.2006.02.041.
Wu, Zhiqiang, Li Yang, Xianwen Ren, Guimei He, Junpeng Zhang, Jian Yang, Zhaohui Qian, et al. 2016. Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases.” ISME Journal 10 (3): 609–20. https://doi.org/10.1038/ismej.2015.138.
Yip, Chi Wai, Chung Chau Hon, Mang Shi, Tommy Tsan Yuk Lam, Ken Yan Ching Chow, Fanya Zeng, and Frederick Chi Ching Leung. 2009. Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses.” Infection, Genetics and Evolution 9 (6): 1185–96. https://doi.org/10.1016/j.meegid.2009.09.015.
Zhang, Qiang, Huajun Zhang, Jindong Gao, Kun Huang, Yong Yang, Xianfeng Hui, Xinglin He, et al. 2020. A serological survey of SARS-CoV-2 in cat in Wuhan.” Emerging Microbes and Infections 9 (1): 2013–19. https://doi.org/10.1080/22221751.2020.1817796.