New outbreak of a mysterious SARS-like virus in China

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The true scale of the outbreak of a mysterious SARS-like virus in China is likely far bigger than officially reported, scientists have warned, as countries ramp up measures to prevent the disease from spreading.

Fears that the virus will spread are growing ahead of the Lunar New Year holiday, when hundreds of millions of Chinese move around the country and many others host or visit extended family members living overseas.

Authorities in China say two people have died and at least 45 have been infected, with the outbreak centred around a seafood market in the central city of Wuhan, a city of 11 million inhabitants that serves as a major transport hub.

But a paper published Friday by scientists with the MRC Centre for Global Infectious Disease Analysis at Imperial College in London said the number of cases in the city was likely closer to 1,700.

The researchers said their estimate was largely based on the fact that cases had been reported overseas – two in Thailand and one in Japan.

The virus – a new strain of coronavirus that humans can contract—has caused alarm because of its connection to SARS (Severe Acute Respiratory Syndrome), which killed nearly 650 people across mainland China and Hong Kong in 2002-2003.

China has not announced any travel restrictions, but authorities in Hong Kong have already stepped up detection measures, including rigorous temperature checkpoints for inbound travellers from the Chinese mainland.

The US said from Friday it would begin screening flights arriving from Wuhan at San Francisco airport and New York’s JFK—which both receive direct flights—as well as Los Angeles, where many flights connect.

And Thailand said it was already screening passengers arriving in Bangkok, Chiang Mai and Phuket and would soon introduce similar controls in the beach resort of Krabi.

Two deaths

No human-to-human transmission has been confirmed so far, but Wuhan’s health commission has said the possibility “cannot be excluded”.

A World Health Organization doctor said it would not be surprising if there was “some limited human-to-human transmission, especially among families who have close contact with one another”.

Scientists with the MRC Centre for Global Infectious Disease Analysis—which advises bodies including the World Health Organization—said they estimated a “total of 1,723” people in Wuhan would have been infected as of January 12.

“For Wuhan to have exported three cases to other countries would imply there would have to be many more cases than have been reported,” Professor Neil Ferguson, one of the authors of the report, told the BBC.

“I am substantially more concerned than I was a week ago,” he said, while adding that it was “too early to be alarmist”.

“People should be considering the possibility of substantial human-to-human transmission more seriously than they have so far,” he continued, saying it was “unlikely” that animal exposure was the sole source of infection.

Local authorities in Wuhan said a 69-year-old man died on Wednesday, becoming the second fatal case, with the disease causing pulmonary tuberculosis and damage to multiple organ functions.

After the death was reported, online discussion spread in China over the severity of the Wuhan coronavirus—and how much information the government may be hiding from the public.

Several complained about censorship of online posts, while others made comparisons to 2003, when Beijing drew criticism from the WHO for underreporting the number of SARS cases.

“It’s so strange,” wrote a web user on the social media platform Weibo, citing the overseas cases in Japan and Thailand.

“They all have Wuhan pneumonia cases but (in China) we don’t have any infections outside of Wuhan—is that scientific?”


Fifteen years after the first highly pathogenic human coronavirus caused the severe acute respiratory syndrome coronavirus (SARS-CoV) outbreak, another severe acute diarrhea syndrome coronavirus (SADS-CoV) devastated livestock production by causing fatal diseases in pigs. Both outbreaks began in China and were caused by coronaviruses of bat origin [1,2]. This increased the urgency to study bat coronaviruses in China to understand their potential of causing another virus outbreak.

In this review, we collected information from past epidemiology studies on bat coronaviruses in China, including the virus species identified, their host species, and their geographical distributions. We also discuss the future prospects of bat coronaviruses cross-species transmission and spread in China.

Why Study Bat Coronaviruses in China?

Coronavirus Taxonomy

Coronaviruses (CoVs) belong to the subfamily Orthocoronavirinae in the family Coronaviridae and the order Nidovirales. CoVs have an enveloped, crown-like viral particle from which they were named after. The CoV genome is a positive-sense, single-strand RNA (+ssRNA), 27–32 kb in size, which is the second largest of all RNA virus genomes. Typically, two thirds of the genomic RNA encodes for two large overlapping polyproteins, ORF1a and ORF1b, that are processed into the viral polymerase (RdRp) and other nonstructural proteins involved in RNA synthesis or host response modulation.

The other third of the genome encodes for four structural proteins (spike (S), envelope (E), membrane (M), and nucleocapsid (N)) and other accessory proteins. While the ORF1a/ORF1b and the four structural proteins are relatively consistent, the length of the CoV genome is largely dependent on the number and size of accessory proteins [3].

Compared with other RNA viruses, the expanded genome size of CoVs is believed to be associated with increased replication fidelity, after acquiring genes encoding RNA-processing enzymes [4]. Genome expansion further facilitates the acquisition of genes encoding accessory proteins that are beneficial for CoVs to adapt to a specific host [5].

As a result, genome changes caused by recombination, gene interchange, and gene insertion or deletion are common among CoVs. The CoV subfamily is expanding rapidly, due to the application of next generation sequencing which has increased the detection and identification of new CoV species. As a result, CoV taxonomy is constantly changing.

According to the latest International Committee of Taxonomy of Viruses (ICTV) classification, there are four genera (α-, β-, δ-, and γ-) consisting of thirty-eight unique species in the subfamily [6]. The number of species will continue to increase, as there are still many unclassified CoVs [7,8].

CoVs cause disease in a variety of domestic and wild animals as well as in humans, where α- and β-CoVs mainly infect mammals and γ- and δ-CoVs mainly infect birds (Table 1). Two highly pathogenic β-CoVs, SARS-CoV, and MERS-CoV have caused pandemics in humans since 2002 [1,9].

Originating in China and then spreading to other parts of the world, SARS-CoV infected around 8000 individuals with an overall mortality of 10% during the 2002–2003 pandemic [1]. Since its emergence in 2012 in the Middle East, MERS-CoV spread to 27 countries, resulting in 2249 laboratory-confirmed cases of infection with an average mortality of 35.5% (until September 2018) [9].

Besides these two viruses, α-CoVs 229E and NL63 and β-CoVs OC43 and HKU1 can also cause respiratory diseases in humans [10]. Moreover, CoVs cause pandemic disease in domestic and wild animals (Table 1). SADS-CoV was recently identified as the etiological agent responsible for a large-scale outbreak of fatal disease in pigs in China that caused the death of more than 20,000 piglets [2].

Porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) that belong to α-CoV and porcine δ-CoV (PDCoV) are also important emerging and re-emerging viruses in pigs that pose significant economic threat to the swine industry [11].

In addition, avian infectious bronchitis virus (IBV, γ-CoV) causes a highly contagious disease that affects poultry production worldwide [12]. Coronaviruses have also been associated with catarrhal gastroenteritis in mink (MCoV) and whale deaths (BWCoV-SW1) [13,14].

Table 1

International Committee of Taxonomy of Viruses (ICTV) classification of coronaviruses species, reservoir hosts, and presence reported in China.

Coronavirus SpeciesAbbreviationsHumanBatsOther AnimalsReported in China
Bat coronavirus HKU10BtCoV-HKU10YesYes [7,8,26,27]α-CoV
Bat coronavirus CDPHE15BtCoV-CDPHE15YesNo
Rhinolophus ferrumequinum alphacoronavirus HuB-2013BtRfCoV-HuB13YesYes [8]
* Human coronavirus 229EHCoV-229EYesYes [28,29]
Lucheng Rn rat coronavirusLRNVYes (rat)Yes [30]
Ferret coronavirusFRCoVYes (ferret)No [31]
* Mink coronavirus 1MCoVYes (mink)No [14]
Miniopterus bat coronavirus 1BtMiCoV-1YesYes [7,8,32,33,34,35,36,37]
Miniopterus bat coronavirus HKU8BtMiCoV-HKU8YesYes [7,8,33,34,35,37,38,39,40,41]
Myotis ricketti alphacoronavirus Sax-2011BtMy-Sax11YesYes [8,37]
Nyctalus velutinus alphacoronavirus SC-2013BtNy-Sc13YesYes [8]
* Porcine epidemic diarrhea virusPEDVYes (pig)Yes [42]
Scotophilus bat coronavirus 512BtScCoV-512YesYes [37]
Rhinolophus bat coronavirus HKU2 (SADS)BtRhCoV-HKU2YesYesYes [2,7,8,38,43,44,45]
* Human coronavirus NL63HCoV-NL63YesYes [28,29]
NL63-related bat coronavirus strain BtKYNL63-9bBtKYNL63YesNo [24]
* Alphacoronavirus 1 (Transmissible gastroenteritis virus)TGEVYes (pig)Yes [42]
China Rattus coronavirus HKU24RtCoV-HKU24Yes (rat)Yes [46]β-CoV
* Human coronavirus HKU1HCoV-HKU1YesYes [28,29]
* Murine coronavirus (Murine hepatitis coronavirus)MHVYes (mouse)No [47]
Bat Hp-betacoronavirus Zhejiang2013BtHpCoV-ZJ13YesYes [8]
Hedgehog coronavirus 1EriCoV-1Yes (hedgehog)No [48]
* Middle East respiratory syndrome-related coronavirusMERSr-CoVYesYesYes [49,50]
Pipistrellus bat coronavirus HKU5BtPiCoV-HKU5YesYes [38,39,49,51,52]
Tylonycteris bat coronavirus HKU4BtTyCoV-HKU4YesYes [36,38,39,49,50,51]
Rousettus bat coronavirus GCCDC1# BtEoCoV-GCCDC1YesYes [53,54,55]
Rousettus bat coronavirus HKU9BtRoCoV-HKU9YesYes [39,55,56,57]
* Severe acute respiratory syndrome-related coronavirusSARSr-CoVYesYesYes [7,8,20,21,22,27,37,40,45,58,59,60,61,62,63,64]
* Betacoronavirus 1 (Human coronavirus OC43)HCoV-OC43YesYes [28,29]
Wigeon coronavirus HKU20WiCoV-HKU20Yes (bird)Yes [65]δ-CoV
Bulbul coronavirus HKU11BuCoV-HKU11Yes (bird)Yes [65]
Coronavirus HKU15PoCoV-HKU15Yes (pig)Yes [66]
Munia coronavirus HKU13MuCoV-HKU13Yes (bird)Yes [65]
White-eye coronavirus HKU16WECoV-HKU13Yes (bird)Yes [65]
Night heron coronavirus HKU19NHCoV-HKU19Yes (bird)Yes [65]
Common moorhen coronavirus HKU21CMCoV-HKU21Yes (bird)Yes [65]
*? Beluga whale coronavirus SW1BWCoV-SW1Yes (whale)No [13]γ-CoV
* Avian infectious bronchitis virusIBVYes (bird)Yes [12]

* The disease-causing CoVs are indicated and the three zoonotic CoVs are in bold. *? BWCoV-SW1 was found in a sick whale, but whether it was the etiological agent of the infection was not proven. # Carrier of this virus was confirmed as Eonycteris spelaea, but not Rousettus bats. The virus was renamed accordingly.

 Linking Bats to Coronaviruses

Bat are the only mammals with the capability of powered flight, which enables them to have a longer range of migration compared to land mammals. Bats are also the second largest order of mammals, accounting for about a fifth of all mammalian species, and are distributed worldwide. Phylogenetic analysis classified bats into two large suborders—the Yinpterochiroptera, consisting of one Pteropodidae (megabat) and five Rhinolophoidea (microbat) families, and the Yangochiroptera comprising a total of thirteen microbat families [15].

It is hypothesized that flight provided the selection pressure for coexistence with viruses, while the migratory ability of bats has particular relevance in the context of disease transmission [16]. Indeed, bats were linked to a few highly pathogenic human diseases, supporting this hypothesis. Some of these well characterized bat viruses, including bat lyssaviruses (Rabies virus), henipaviruses (Nipah virus and Hendra virus), CoVs (SARS-CoV, MERS-CoV, and SADS-CoV), and filoviruses (Marburg virus, Ebola virus, and Mengla virus), pose a great threat to human health [16,17].

A comprehensive analysis of mammalian host–virus relationships demonstrated that bats harbor a significantly higher proportion of zoonotic viruses than other mammalian orders [18]. Viruses from most of the viral families can be found in bats [16].

Bats are now recognized as important reservoir hosts of CoVs (Table 1). Although civet cats were initially identified as the animal origin of SARS-CoV, bats were soon found to be the most likely natural reservoir hosts of this virus [19,20,21]. Long-term surveillance revealed an average 10% SARS-related CoV nucleotide positivity in bats, including some viruses that can use same human entry receptor ACE2 as SARS-CoV [7,22]. Similarly, bats have been proposed to harbor the progenitor viruses of MERS-CoV, although dromedary camels can transmit this virus to humans directly [9].

The most recent SADS-CoV spillover was traced back to bats [2]. In addition, bats also carry α-CoVs that are related to pathogenic human 229E- and NL63-CoVs, as well as pandemic swine coronavirus PEDV [23,24]. In summary, bats carry major α- (10 out of 17) and β- (7 out of 12) CoV species that may spillover to humans and cause disease (Table 1). Attributed to the wide distribution of bats, CoVs can be found worldwide, including China [25].

Why China?

Two bat CoVs caused outbreaks in China; it is thus urgent to study the reasons to avoid future outbreaks. China is the third largest territory and is also the most populous nation in the world. A vast homeland plus diverse climates bring about great biodiversity including that of bats and bat-borne viruses – most of the ICTV coronavirus species (22/38) were named by Chinese scientists studying local bats or other mammals.

The majority of the CoVs can be found in China (Table 1). Moreover, most of the bat hosts of these CoVs live near humans, potentially transmitting viruses to humans and livestock. Chinese food culture maintains that live slaughtered animals are more nutritious, and this belief may enhance viral transmission.

It is generally believed that bat-borne CoVs will re-emerge to cause the next disease outbreak. In this regard, China is a likely hotspot. The challenge is to predict when and where, so that we can try our best to prevent such outbreaks.

Bat Coronaviruses That Are Associated with Diseases

SARS-Related Coronaviruses

In November 2012, the first case of SARS was recorded in Foshan city, Guangdong Province, China (Figure 1). In 2005, two independent Chinese groups reported the first bat SARS-related CoV (SARSr-CoV) that was closely related to human SARS-CoV, implying a bat origin of the latter [20,21]. Since then, more bat SARSr-CoV isolates were identified in China (Table 1).

Genome identities of these bat SARSr-CoVs are as high as 92% to human SARS-CoV, but their major receptor binding spike proteins cannot use the human virus entry receptor ACE2 [67]. Whether they are the progenitor viruses of SARS-CoV is debatable. In 2013, the isolation of a bat SARSr-CoV that uses the ACE2 receptor provided the strongest evidence of the bat origin of SARS-CoV [22]. Furthermore, the building blocks for SARS-CoV were identified from eleven different SARSr-CoV viral strains in a five-year surveillance program in a cave inhabited by multiple species of horseshoe bats in Yunnan Province, China [62].

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Object name is viruses-11-00210-g001.jpg
Geographical distribution of bat coronaviruses (CoVs) and their corresponding bat hosts in China. Each red box represents one CoV positive sample found in that particular bat species. One dot matrix was drawn for each province where a CoV positive sample had been reported. Guangdong Province, where SARS and SADS began, is circled in red. Abbreviations of bat species and virus species are indicated.

SARSr-CoVs found in China show great genomic diversity (Figure 2). Sequence identities of the conserved 440 bp RdRp region ranges from 80 to 100% with human SARS-CoV. CoV diversity in bats is thought to be shaped by both species richness and geographical distribution, and CoVs exhibit clustering at the bat genera level, with these genus-specific clusters largely associated with distinct CoV species [25]. Our analysis supports this theory. SARSr-CoVs are present in different bat species but all belong to the family of Rhinolophidae and Hipposideridae (Figure 1). 

Chaerephon plicata bats were also reported as carriers in one study, but this cannot be conclusively supported without molecular identification of the bat species [8]. In China, horseshoe bat species (Rhinolophus spp.) are widely distributed, including R. sinicusR. ferrumequinumR. macrotisR. pearsoni, and R. pusillus, and are also the most frequent SARSr-CoV carriers throughout the nation [7,8,20,21,22,27,40,43,45,58,59,61,62,63,68] (Figure 1). The most variable regions among bat SARSr-CoVs are the S and ORF8 genes [62]. The S protein in certain strains is capable of using human ACE2 as a receptor and thus poses a direct threat to humans [69].

Interestingly, all the SARSr-CoVs that are capable of using human ACE2 were found in R. sinicus in Yunnan Province [7,22,27,62]. Other SARSr-CoVs that cannot use human ACE2 were distributed in multiple provinces, from north Jilin, Shaanxi, Shanxi to south Hubei, Zhejiang, Yunnan, Guizhou, and Guangdong (Figure 1).

Another protein, ORF8, was suggested to be important for interspecies transmission, as most human SARS-CoV epidemic strains contain a signature 29-nucleotide deletion in ORF8 compared to civet SARSr-CoVs, which results in the formation of two separate open reading frames, ORF 8a and 8b [40]. Only two R. ferrumequinum and one R. sinicus from Yunnan Province carried viruses that possess ORF8 proteins with exceptionally high amino acid identities to that of human/civet SARSr-CoVs [40,62]. It was strongly suggested that SARS-CoV most likely originated from Yunnan Rhinolophus bats via recombination events among existing SARSr-CoVs.

These studies revealed that various SARSr-CoVs capable of using human ACE2 are still circulating among bats in China, highlighting the possibly of another SARS-like disease outbreak. Certain areas in Yunnan Province are hotspots for spillover. To support this hypothesis, we provide serological evidence of bat SARSr-CoV infection in humans in Yunnan Province where no prior exposure to SARS-CoV was recorded [70].

The majority of the SARSr-CoVs appear not able to use ACE2, but their infectivity or pathogenesis to humans are still unknown. Frequent interspecies recombination may result in another human infectious coronavirus from these SARSr-CoVs.

Furthermore, there are still unanswered questions about SARS, e.g., ‘Why did the first SARS case occur in Guangdong Province, but all the human-ACE2-using SARSr-CoVs were found in Yunnan Province?’ and ’Why does R. sinicus in certain areas carry human-ACE2-using SARSr-CoVs but no other Rhinolophus species carry the same viruses?’ Above all, further extensive surveillance of SARSr-CoVs in China is warranted.

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