In the Chinese zodiac, 2020 was the Year of the Rat. But it was remembered more as a “Year of the Bat” due to the great attention in the general public and scientific community on the role of bats as the reservoir of emerging zoonotic viruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) (1) and the coronavirus disease 2019 (COVID-19) virus, also known as SARS-CoV-2 (2). Here we provide a summary of our current knowledge on the relationship between bats and viruses, particularly coronaviruses, and discuss the various hypotheses for the origin of the COVID-19 virus.
In the last 2–3 decades, the world has experienced 6 major viral disease outbreaks caused by emerging zoonotic viruses of bat origin. These include Hendra virus in Australia in 1994, Nipah virus in Malaysia/Singapore 1998/1999, SARS-CoV in China 2002/2003, Marburg in Africa in 2005, MERS-CoV in the Middle East in 2012, Ebola virus in West Africa in 2013, and COVID-19 virus in 2019 in China (Table 1). In addition, there have been many other “less impactful” emerging viruses of bat origin from Australia (Menangle virus) to Malaysia (Tioman virus and Melaka virus) and Africa (Sosuga virus). For more information on this rapid growing area of research, please refer to reviews and books published recently on this topic (3–4).
Viral Disease Year Country (initial) Infected Deaths Cumulative infected (deaths) Origin Intermediate host Hendra 1994 Australia 2 (+19 horses) 1 7 (5) Bat Horse Nipah 1998–1999 Malaysia 265 105 704 (412) Bat Bat*/Pig SARS 2003–2004 China 8,098 774 8,098 (774) Bat Civet Marburg 2005 Angola 252 227 474 (380) Bat Monkey/Bat† Ebola 2013 Guinea/West Africa 28,646 11,323 34,975 (15,253) Bat Bat/Monkey MERS 2014 Saudi Arabia 255 93 2,494 (858) Bat§ Camel COVID-19 2019 China 99,931 4,810 98,280,844(2,115,759)¶ Bat* X** * Direct bat to human transmission via urine in palm sap as well as bat to pig, pig to human transmission.
† Either macaques (intermediate) or bats (direct) believed to be hosts.
§ Ancestral origin believed to be bat based on close genetic relatedness to bat-borne viruses and evolutionary trajectory.
¶ Data current on 27 January 2021. https://www.who.int/publications/m/item/weekly-epidemiological-update---27-january-2021.
** Currently unknown.
Table 1. Emerging zoonotic virus outbreaks related to bats. Cumulative infected humans is the sum from all outbreaks.
One year after the first detection of COVID-19 infection and more than 100,000 scientific publications on the COVID-19 pandemic, there are still many key questions remaining unanswered. One major question involves the origin of the causative agent of COVID-19. To address this question, it is important to differentiate the following viral terms. 1) Outbreak virus: the virus which was directly responsible for causing the outbreak, such as the first isolate (Wuhan-Hu-1) of COVID-19 virus. 2) Progenitor virus: this refers to a very closely related virus which is not identical to the outbreak virus, but could have evolved into an outbreak virus with minimal mutation(s). 3) Ancestral virus: this is the ancestor of both the progenitor virus and the outbreak virus residing in its natural reservoir host for a long time.
COVID-19 virus is a member of the species SARS-related coronavirus (SARSr-CoV) which includes SARS-CoV and many other CoVs of bat origin. The species is currently composed of two lineages or clades, one related to SARS-CoV and the other more related to virus causing COVID-19 (2). More than 10 COVID-19-virus related coronavirus genome sequences have been reported and over 80% of them originated from bats (9), including the RaTG13 sequence which has a genome that identifies 96% with COVID-19 virus. It is therefore most likely that the ancestral virus is from bats (10). The origin and geographic distribution of the progenitor virus remains elusive. In Table 2, alternative hypotheses of key events related to the origin of COVID-19 virus are summarized.
Event Hypothesis-1 Hypothesis-2 First human infection time December 2019 Months earlier First human infection location Wuhan Other site in China or outside China Introduction of virus to Wuhan By infected animal By infected human Type of virus introduced to Wuhan The progenitor virus The outbreak virus The role of the Huanan Seafood Wholesale Market The site of spillover (i.e., animal to human transmission) The site of spillback-then-spillover (i.e. human to animal transmission, which led to amplification/adaptation in animal and followed up by animal to human transmission) Host of the progenitor virus Animal Human
Table 2. Uncertainties surrounding key events relating to the origin and early transmission of COVID-19 virus.