Review
Feature Review
Interspecies transmission and
emergence of novel viruses:
lessons from bats and birds
1,2,3,4* 1,2,3,4* 1,2,3,4
Jasper Fuk-Woo Chan , Kelvin Kai-Wang To , Herman Tse ,
5 1,2,3,4
Dong-Yan Jin , and Kwok-Yung Yuen
1
State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong Special Administrative Region, China
2
Carol Yu Centre for Infection, University of Hong Kong, Hong Kong Special Administrative Region, China
3
Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong Special Administrative Region, China
4
Department of Microbiology, University of Hong Kong, Hong Kong Special Administrative Region, China
5
Department of Biochemistry, University of Hong Kong, Hong Kong Special Administrative Region, China
As exemplified by coronaviruses and influenza viruses, human travel and trading directly led to the spread of
bats and birds are natural reservoirs for providing viral viruses to distant and isolated places. The migration of early
genes during evolution of new virus species and viruses humans over long distances was very limited and effec-
for interspecies transmission. These warm-blooded ver- tively a unidirectional ‘rare’ event. Eventually, improve-
tebrates display high species biodiversity, roosting and ments in transportation technology enabled distant trade
migratory behavior, and a unique adaptive immune sys- missions in early Mesopotamia around 5000 years ago and
tem, which are favorable characteristics for asymptom- possibly earlier in other regions [1]. These periodic yet
atic shedding, dissemination, and mixing of different infrequent visits might have enabled transmission of var-
viruses for the generation of novel mutant, recombinant, ious disease agents to previously segregated non-immune
or reassortant RNA viruses. The increased intrusion of populations, leading to a serial founder effect associated
humans into wildlife habitats and overcrowding of dif- with a boom and bust cycle. However, further technologi-
ferent wildlife species in wet markets and farms have cal improvements, especially the development of aviation
also facilitated the interspecies transmission between and the flight industry in the last century, have allowed
different animal species. this type of travel to occur at such high frequencies that
multiple segregated host populations effectively have be-
Emergence of new viruses come a single large population. These changes coincided
Both mammalian and avian coronaviruses (CoV) have di- with increased breeding between different host popula-
verse host ranges. Phylogenetic dating of RNA-dependent tions (for both humans and domestic animals), which can
RNA polymerase (RdRp) sequence divergence suggested significantly impact the genetic and immunological make-
that the most recent common ancestor (MRCA) of mamma- up of the host populations. When these occurrences are
lian CoVs appeared around 7000–8000 years ago, whereas considered in the context of the high mutation rate of RNA
the MRCA of avian CoVs dates back to 10 000 years ago viruses, they become a driving force for speciation and
(Figure 1). These results are likely underestimations be- subsequent evolution of new viruses. Although phyloge-
cause they could not account for additional sequence diver- netic analysis and dating of individual influenza genes and
sity from undiscovered viruses. Nonetheless, the present lineages have been reported previously, large sequence
estimates roughly coincide with the dispersal of the human divergence and frequent reassortment led to difficulties in
population around the world about 50 000–100 000 years precisely dating and phylogenetic positioning the common
ago and greatly increased in the last 10 000 years during the ancestor of modern influenza viruses [2].
first historic transition. During this transition, humans About 70% of the emerging pathogens infecting humans
began various farming activities, such as forest clearing originate from animals. Most of these major outbreaks
for agriculture and animal herding, leading to a significant were due to RNA viruses as a result of their higher muta-
shift in the ecology and population dynamics of viruses tion rates compared with other types of microbes and their
owing to the intrusion of wildlife habitats and intensive capability for unique genetic change, either by genetic
mixing of different animal hosts. Finally, the expansion of recombination in positive-sense RNA viruses or genetic
reassortment in RNA viruses with segmented genomes.
Corresponding author: Yuen, K.-Y. ([email protected]). Those with greatest impact on humans include the severe
*
These authors contributed equally to the manuscript.
acute respiratory syndrome coronavirus (SARS-CoV), in-
Keywords: coronavirus; influenza; RNA virus; virus evolution;
fluenza virus, and HIV. Little was known about CoVs until
emerging infectious disease.
the 2003 SARS epidemic, which caused 774 deaths among
0966-842X/$ – see front matter
ß 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tim.2013.05.005 8098 cases in over 30 countries [3]. The natural reservoir of
544 Trends in Microbiology, October 2013, Vol. 21, No. 10
Review Trends in Microbiology October 2013, Vol. 21, No. 10
FIPV/1979 TGEV/1952 PRCV/1990 CCoV/2008 4381 RhBatCoV-HKU2/2006 HCoV-NL63/1988 HCoV-229E/1966 Alphacoronavirus Sc-BatCoV-512/2005 PEDV/1977 Mi-BatCoV 1B/2006 Mi-BatCoV 1A/2005 7163 Mi-BatCoV HKU8/2008 SARS CoV/2003 SARSr-CiCoV/2003 SARSr CoV CFB/2003 SARSr-Rh-BatCoV HKU3/2005 Ro-BatCoV-HKU9/2006 PHEV/1972 HCoV OC43/1967 5301 GiCoV/2003 Betacoronavirus 7890 AntelopeCoV/2003 BCoV/1972 ECoV/1999 HCoV-HKU1/2004 MHV/1961 Ty-BatCoV-HKU4/2006 Pi-BatCoV-HKU5/2006 MERS-CoV 10141 IBV-partridge/2003 TCoV/2007 4838 IBV/1935 Gammacoronavirus IBV-peafowl/2003 BWCoV-SW1/2006 NHCoV HKU19/2007 4973 WiCoV HKU20/2008 CMCoV HKU21/2007 PorCoV HKU15-44/2009 523 PorCoV HKU15-155/2010 Deltacoronavirus SpCoV HKU17/2007 MunCoV HKU13/2007 MRCoV HKU18/2007 ThCoV HKU12/2007 BuCoV HKU11/2007
WECoV HKU16/2007
10 8 6 4 2 0 Thousand years ago
First historical transi on: agriculture and animal herding (5000–10000 years ago)
TRENDS in Microbiology
Figure 1. The divergence of coronaviruses into Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus is estimated to have occurred approximately
5000 years ago. This tree was generated by analyzing RNA-dependent RNA polymerase (RdRp) genes under the relaxed-clock model with an uncorrelated log-normal
distribution in Bayesian evolutionary analysis sampling trees (BEAST) software. Values at branch points represent the estimated timing of divergence events in numbers of
years before the present. Adapted from [45].
the more ancestral bat SARS-CoV is the Chinese horseshoe natural reservoirs of emerging influenza viruses is under-
bat (Rhinolophus sinicus), which may have transmitted the scored by the persistent threat of avian influenza H5N1
virus to other game mammals including Himalayan palm since 1997 and the emergence of H7N9 in 2013 [9–12]. The
civets (Paguma larvata), raccoon dogs (Nyctereutes procyo- role of bats in the emergence of novel influenza viruses is
noides), and Chinese ferret badgers (Melogale moschata) in less clear although influenza A H17 and H3N2 viruses
wildlife markets in South China [4]. This finding sparked have been discovered in Sturnira lilium recently and in
intense hunting for novel CoVs in humans and different Nyctalus noctula bats in Kazakhstan in 1970, respectively.
animal species, especially in bats. The latest emerging We review the importance of bats and birds in the genesis
novel human CoV, originally named human coronavirus of new virus mutants and interspecies jumping using CoVs
EMC/2012 and later renamed Middle East respiratory and influenza viruses as examples.
syndrome coronavirus (MERS-CoV), which has caused
30 deaths among 54 cases in the Middle East, Europe, Bats as natural reservoirs for emerging viruses
and Africa, is also phylogenetically closely related to the A number of unique ecological, biological, immunological,
Tylonycteris bat CoV HKU4 (Ty-BatCoV-HKU4) and Pipis- and genetic features make bats a favorable animal reser-
trellus bat CoV HKU5 (Pi-BatCoV-HKU5) discovered in voir for the emergence of novel viruses. Bats have remark-
bats in Hong Kong [5–8] (http://www.who.int/csr/don/ able species diversity, with over 1240 species (20% of the
2013_06_05/en/index.html). The importance of birds as nearly 5000 known species within Mammalia and only
545
Review Trends in Microbiology October 2013, Vol. 21, No. 10
second to rodents) [9]. Because viruses are obligatory observed. In the humoral response, bats have an antibody
intracellular microbes, it is assumed that viruses have repertoire as diverse as those of humans and mice. At least
multiple independent evolutionary origins not separable 23 genes for immunoglobulin (Ig) VH and the l and k loci of
from co-evolution of their hosts. This high biodiversity of Ig VL have been identified in P. alecto, and diverse Ig DH
bats makes them an important source of new viruses for and Ig JH elements and the l locus of Ig VL have been found
interspecies jumping. in M. lucifugus and other microbats (Table 1). However, the
Bats are widely distributed in all continents except the amino acid sequence composition of the antigen-binding
polar regions and a few oceanic islands. Their roosting or site (CDR3 region) of the expressed VH region in bats is
hibernation environment ranges from natural habitats such different from those of humans and mice with a higher
as caves, rock crevices, bird nests, and tree cavities, to man- proportion of arginine and alanine residues, and lower
made structures like mines, tombs, buildings, and bridges, proportion of tyrosine residues, and thus possibly a lower
which bring them closer to humans and companion animals poly-reactivity [20]. Such antibodies have lower avidity
or livestock. Their unique ability among mammals to fly long and form a weaker association with antigens. Further-
distances (up to 2000 km) to locate suitable habitats also more, the primary antibody response may be delayed from
allows them to acquire or disseminate viruses [9]. Their reaching a peak and the secondary antibody response may
habit of roosting in large colonies ranging from 10–200 000 also be slow or delayed in bats. In adverse environmental
bats and relative longevity of up to 35 years also provide situations such as prolonged exposure to low temperature
abundant mating opportunities and thus exchange of viral at 88C simulating the state of hibernation, bats may tem-
genetic material and further viral spread to other species. porarily fail to mount an antibody response but resume
Exposures to infected urine and aerosols generated during this ability 1 week after transferring to 248C. Importantly,
defecation have been suggested as possible routes of intra- bats may clear viral infection even in the absence of
species and interspecies transmission of viruses from bats neutralizing antibody by other unknown mechanisms
[9]. Bats may also transmit viruses to human and other [14]. Bats appeared asymptomatic during bat–SARS-
animals via bites and scratches as in the case of rabies. CoV infection despite a high viral load in their anal swabs
Consumption and handling of undercooked bat meat is still with absent or low serum neutralizing antibody although
practiced in China, Guam, and some parts of Asia. their body weights were generally lower than the uninfect-
Besides ecological and biological traits, bats also possess ed bats [4,21]. As for a cell-mediated immune response,
special immunological attributes that enhance their ability those of bats are generally slower to peak after stimulation
to serve as gene pools for emerging viruses (Table 1). by T-cell mitogens. Environmental changes such as roost
Asymptomatic or persistent viral shedding with little evi- ecology and physiological alterations such as pregnancy
dence of pathology in bats is well reported [13]. One possible also affect cell-mediated immunity of bats [14]. Further
mechanism is the very early control of viral replication by studies should be performed to ascertain if these quanti-
their innate immune response involving the early recogni- tative and qualitative differences in the adaptive immune
tion by pattern recognition receptors (PRRs) and interferons response of bats may account for their unique interaction
(IFNs) followed by partial control by the adaptive immune with viruses leading to asymptomatic infection and viral
response [14]. Similar to other mammalian species, some persistence.
bats possess the two major families of virus-sensing PRRs, The discovery of influenza virus in bats challenges the
namely the Toll-like receptors (TLRs), which are mem- notion that aquatic birds are the only source of all influenza
brane-bound PRRs that detect single-stranded RNA A gene segments [9,10]. The recently discovered H17 influ-
(ssRNA) or double-stranded RNA (dsRNA), and retinoic enza virus from Guatemala bats is unique in that all eight
acid inducible gene I (RIG-I)-like helicases (RLHs), which gene segments appear to be distinct from any known
are cytosolic PRRs that detect dsRNA. Bat TLRs have been influenza A gene segments [10]. The hemagglutinin (HA)
described in many fruit bat species and are highly similar to of this virus has unique structural features and exhibits
other mammalian TLRs [15,16]. In addition, cytoplasmic receptor binding and fusogenic activities that are distinct
RLHs including RIG-I, melanoma differentiation-associat- from its counterparts in other influenza viruses [22]. Like-
ed protein 5 (MDA5), and laboratory of genetics and physi- wise, the neuraminidase (NA) of this virus, called N10, is
ology 2 (LGP2) have been found in Pteropus alecto and their phylogenetically distinct from the NAs of all influenza A
homologs in Myotis davidii [16]. These PRRs allow bats to and B viruses. The N10 is also structurally distinct with no
recognize a similar range of pathogens as other mammalian enzymatic activity [23]. Additional surveillance is neces-
species and in turn these pathogens are controlled by IFNs. sary to understand the ecology of influenza viruses in bats.
Type I IFNs have been described in numerous fruit bat
species [17], and type III IFNs have been found in Myotis Waterfowl and shorebirds as a source of influenza virus
lucifugus, P. alecto, and Pteropus vampyrus [18]. Notably, genes
the type I IFNv family of genes are expanded in some bat The high biodiversity of birds (over 10 000 species) allows
species with up to a dozen members, and the type III IFN avian influenza viruses to evolve in different host environ-
receptors are more widely distributed in tissues of P. alecto ments. Birds living near wetlands or aquatic environ-
than in humans and mice [19]. Bats may also demonstrate a ments, especially in the orders Anseriformes (aquatic
delayed or differential IFN response during in vitro infection waterfowls) and Charadriiformes (shorebirds), are consid-
by different kinds of viruses [17,18]. ered to be the sources or gene pool for all influenza viruses
However, important differences between the adaptive [24,25]. Waterfowl feed on submerged water plants in
immune response of bats and other mammals have been marsh water that are readily contaminated by virus from
546
Review Trends in Microbiology October 2013, Vol. 21, No. 10
Table 1. Innate and adaptive immune systems in bats and birds
Protein Function Bats Birds
Innate RIG-I Cytosolic PRR; detects dsRNA Present and functional in the black flying Present and functional in mallard duck
immunity fox (Pteropus alecto; AEW46678); (ACA61272) and present in goose
homolog also present in David’s Myotis (ADV58759), but absent in chicken [33]
(Myotis davidii; ELK34300) [16]
MDA5 Cytosolic PRR; detects dsRNA Present and functional in black flying fox Present in mallard duck (GU936632),
(P. alecto; AEW46679); homolog also goose (AGC51036), and chicken
present in David’s Myotis (M. davidii; (ADD83027) [33,86]
ELK28159)
LGP2 Cytosolic PRR; detects dsRNA Present and functional in black flying Present in chicken [34]
fox (P. alecto); homolog also present in
David’s Myotis (M. davidii)
TLR7 Membrane-bound PRR; detects ssRNA Present in black flying fox (P. alecto; Present in chicken (ACR26250) and
ADO01609), Leschenault’s rousette mallard duck (ABK51522) [35,87,88]
(Rousettus leschenaultia; BAH02556),
and David’s Myotis (M. davidii;
ELK30184) [15,85]
TLR3 Membrane-bound PRR; detects dsRNA Present in black flying fox (P. alecto; Present in chicken (ABG79022) and
ADO01605), Leschenault’s rousette muscovy duck (AFK29094) [89]
(R. leschenaultia; BAH02555), and
David’s Myotis (M. davidii; ELK23529)
[15,85]
TLR8 Membrane-bound PRR; detects ssRNA Present in black flying fox (P. alecto; Disrupted in chicken and duck genome
ELK17709) and David’s Myotis [90]
(M. davidii; ELK30183) [85]
IFN-a Type I IFN; inducible cytokine that Variable number of members present At least 13 putative IFN-a genes
regulates the antiviral response in multiple bat species, including black identified in the chicken genome [91];
flying fox (P. alecto; a1: ELK15818, a5: also identified in the mallard duck
ELK06973) and David’s Myotis (ADU60335) and Gerylag goose
(M. davidii; a3: ELK29335); may be (AFU54612), but exact number of
absent in other Myotis sp. [17] members is not known
IFN-b Type I IFN; inducible cytokine that Present in multiple bat species, Present in chicken (NP_001020007) and
regulates the antiviral response including black flying fox (P. alecto; mallard duck
ELK06976) and David’s Myotis
(M. davidii; ELK29334)
IFN-v Type I IFN; inducible cytokine that Multiple members present in bats, Absent
regulates the antiviral response including black flying fox (P. alecto;
ELK06971, ELK06975, ELK08131,
ELK15817, and ELK15819) and David’s
Myotis (M. davidii; ELK26494,
ELK26493, and ELK26495)
IFN-l Type III IFN; inducible cytokine that Two members identified in black flying At least one member present in chicken
regulates the antiviral response fox (P. alecto; l1: AEF33950, l2: (ABU82742) [92]
AEF33949); also present in the closely
related Malaysian flying fox (Pteropus
vampyrus) [18]
Adaptive Ig VH Variable region of immunoglobulin At least 23 genes classified into five Single functional VH gene in chicken; 58
immunity heavy chain; contributes to diversity of families were identified in the black cVH pseudogenes located upstream in
antibody repertoire flying fox (P. alecto; IgH locus also contribute to repertoire
GQ427153:GQ427172) [18]; diverse diversity through gene conversion;
genes in the VH3 family repertoire also similar organization in ducks and other
reported for other bat species [93] birds [37]
Ig DH Diversity region of Ig heavy chain; Diverse DH elements in the little brown Approximately 15 DH elements in
contributes to diversity of antibody bat (Myotis lucifugus) [93] chicken
repertoire
Ig JH Joining region of Ig heavy chain At least 13 elements identified in the Single JH element in chicken
little brown bat (M. lucifugus) [93]
Ig VL Variable region of immunoglobulin l and k loci present in black flying fox Single functional VL gene in single (l)
light chain; contributes to diversity of (P. alecto) [94], representative of IgL locus in chicken; approximately 25
antibody repertoire megabats; l locus present in cVL pseudogenes contribute through
microbats, but k locus is absent [94] gene conversion [95]
Ig JL Joining region of Ig light chain (Not studied) Single JL element in chicken
Ig Cd Constant region of IgD Absent in black flying fox (P. alecto) Absent
and probably other megabats; present
in microbats, such as the little brown
bat (Myotis lucifugus; ADI96045,
ADI96044) [96]
547
Review Trends in Microbiology October 2013, Vol. 21, No. 10
(A)
Alphacoronavirus Betacoronavirus Gammacoronavirus Deltacoronavirus Bats Human Bats Human Birds Other animals Birds Other animals Sc-BatCoV 512 HCoV-229E [APN] B: SARSr-Rh-BatCoV A: HCoV-OC43 [ASA] IBV (Chickens) BWCoV-SW1 BuCoV HKU11 PorCoV HKU15 Rh-BatCoV HKU2 HCoV-NL63 HKU3 A: HCoV-HKU1 DCoV (Ducks) (Beluga whales) ThCoV HKU12 (Pigs) My-BatCoV HKU6 [ACE2] C: Ty-BatCoV HKU4 B: SARS-CoV [ACE2] GCoV (Geese) MunCoV HKU13 C: Pi-BatCoV HKU5 C: MERS-CoV [DPP4] PCoV (Pigeons) WECoV HKU16 Mi-BatCoV HKU7 Other animals D: Ro-BatCoV HKU9 PhCoV SpCoV HKU17 Mi-BatCoV HKU8 Other animals (Pheasant) MRCoV HKU18 Mi-BatCoV 1A TGEV (Pigs) PRCV (Pigs) A: MHV (Mice) TCoV (Turkeys) NHCoV HKU19 Mi-BatCoV 1B PEDV (Pigs) A: BCoV (Cows) WiCoV HKU20 Hi-BatCoV HKU10 FIPV (Cats) A: AntelopeCoV (Sables) CMCoV HKU21 Ro-BatCoV HKU10 CCoV (Dogs) A: GiCoV (Giraffes) A: RCoV (Rats) A: RbCoV HKU14 (Rabbits) A: ECoV (Horses) A: PHEV (Pigs) B: SARSr-CiCoV (Civets) B: SARSr-CoV-CFB (Chinese ferret badgers)
(B)
Bats: H17* Birds: H1-H16 H1-H13 ? H1N1, H3N2, H3N3 H2N2, H5N1, H7N2, H7N3, H4N1, H4N6, H4N8, H7N7, H7N9, H9N2, H10N7 H5N1, H5N2, H9N2, H3N3 H4N6 H5N1 H1N3 Domes c poultry H10N5, H11N6 H3N8 H10N4 H13N2 Pig H4N5 H13N9 H4N6 H3N8 H2N2 H7N2 H7N7 H5N1 H5N1 H7N3 H7N7 H9N2 H7N7 H10N7 H7N9 H1N1 H3N2
Mink H7N7 Human Seal
H1N1 Muskrat Whale H5N1 Horse H3N8 H1N1 H3N2 H5N1 H1N1 Bornean Tiger Skunk binturong H1N1† H3N2, H5N1 Dog Leopard H3N2 Giant anteater American Black-footed H1N1 Viverrid Cat badger ferret
TRENDS in Microbiology
Figure 2. Bats and birds as probable gene sources for the evolution of (A) coronaviruses and (B) influenza viruses, based on epidemiological, virological, and phylogenetic
evidence. ‘A’, ‘B’, ‘C’, and ‘D’ represent groups A, B, C, and D in Betacoronavirus. * denotes the undetermined role of bats as reservoirs for emerging influenza viruses. y
denotes the undetermined source of A(H1N1)pdm09 virus found in American badger, black-footed ferret, Bornean binturong, and skunk.? with dotted line denotes the
unproven direct wild bird-to-human transmission of influenza viruses. Figure 2A is adapted from [45]. Abbreviations: [], host receptor utilized by coronavirus; (), animal
host; ACE2, angiotensin converting enzyme 2; AntlopeCoV, sable antelope coronavirus; APN, aminopeptidase N; ASA, 9-O-acetylated sialic acid; BCoV, bovine coronavirus;
BuCoV HKU11, bulbul coronavirus HKU11; BWCoV-SW1, beluga whale coronavirus SW1; CCoV, canine coronavirus; CMCoV HKU21, common moorhen coronavirus
HKU21; DCoV, duck coronavirus; ECoV, equine coronavirus; FIPV, feline infectious peritonitis virus; GCoV, goose coronavirus; GiCoV, giraffe coronavirus; HCoV-229E,
human coronavirus 229E; MERS-CoV, Middle East respiratory syndrome coronavirus; HCoV-HKU1, human coronavirus HKU1; HCoV-NL63, human coronavirus NL63; HCoV-
OC43, human coronavirus OC43; Hi-BatCoV HKU10, Hipposideros bat coronavirus HKU10; IBV, infectious bronchitis virus; MHV, murine hepatitis virus; Mi-BatCoV 1A,
(Figure legend continued on the bottom of the next page.)
548
Review Trends in Microbiology October 2013, Vol. 21, No. 10
excreta of infected waterfowls or other small animals. inhibition, complement fixation, opsonization, and anti-
Birds are frequently infected by influenza A viruses. Re- body-dependent cellular cytotoxicity. IgA is not produced
infection during the same season with the same virus and until ducks are 2 weeks old and is expressed late after an
coinfection with different viruses can occur [26]. Despite infection [37]. T lymphocytes, although present, are not fully
frequent infections, waterfowl usually remain asymptom- functional in young birds [38]. Although ducks have five
atic even when infected by avian influenza viruses highly MHC-I genes for antigen presentation, only two are
pathogenic in chicken [27]. Asymptomatic infections in expressed [39], which limits the repertoire of presentable
ducks and geese often preceded devastating outbreaks in peptides. These immunological features may allow water-
chickens. Influenza viruses persisting in asymptomatic fowl to shed large amount of viruses for a prolonged period
waterfowls allow accumulation of mutations that may [40]. In ducks infected by low pathogenic avian influenza
facilitate interspecies transmission [28]. Moreover, wild virus, RIG-I, CCL19, and CCL21 are only slightly upregu-
waterfowls often aggregate with domestic ducks and geese lated in intestinal tissues [29,33]. These unique features in
during feeding and roosting and therefore allow efficient the immune system of birds, especially in ducks, allow them
mixing of different influenza viruses to form new subtypes. to be the reservoir for influenza viruses.
In the backyard farm setting, domestic ducks and geese are
often mixed with chickens and other domestic poultries Interspecies transmission of CoVs
allowing interspecies transmission, which may eventually Before the discovery of SARS-CoV, CoVs were considered as
transmit into humans. Finally, migratory waterfowls can causative agents of respiratory tract infections, gastroen-
disseminate novel influenza viruses to very distant loca- teritis, hepatitis, and encephalomyelitis in birds and mam-
tions [9]. mals. The first two human CoVs, HCoV-229E and HCoV-
Similar to bats, birds have a unique immune system OC43, primarily caused self-limiting upper respiratory tract
that is best studied in ducks (Table 1). Genes related to infections such as the common cold [41]. The emergence of
antiviral immunity, including major histocompatibility SARS-CoV represented a new era in the history of CoV
complex type I (MHC-I), interferon-induced protein with research. The significant global medical, economical, and
tetratricopeptide repeats 5 (IFIT5), oligoadenylate synthe- social impact of the 2003 outbreak regenerated research
tase-like (OASL), CC chemokine ligand (CCL)19, CCL21, interest on CoVs. One important finding was the identifica-
MDA5, TLR7, and IFN-a, are expressed in duck lungs as tion of bats as the natural animal reservoir and civet and
early as 1 day after H5N1 virus inoculation [29–31]. Proin- other mammals as the intermediate amplifying hosts of
flammatory cytokines were lower in duck than in chicken SARS-CoV [4]. These discoveries revolutionized the ‘hunt-
embryonic fibroblasts infected with H5N1 virus [32]. Major ing’ strategy for novel CoVs and redefined the classification
differences in the immune system between ducks and of CoVs based on their updated phylogeny and the critical
chickens may account for the differential susceptibility role of bats in inter- and intra-species transmissions of CoVs.
to highly pathogenic avian influenza. Whereas chicken With the new wealth of knowledge on CoV phylogeny gen-
cells naturally lack RIG-I or RIG-I activity, duck RIG-I erated after the SARS epidemic, the Coronavirus Study
has a similar structure and function to its human ortholog. Group of the International Committee for Taxonomy of
It was shown that transfection of duck RIG-I into a chicken Viruses changed the classification into four genera, Alpha-
embryonic fibroblast cell line augments the IFN response coronavirus, Betacoronavirus, Gammacoronavirus, and Del-
and suppresses viral replication [33]. Chicken cells appar- tacoronavirus to replace the traditional antigenic groups of
ently rely upon MDA5 and LGP2 to sense influenza virus 1, 2, and 3 (Figure 2A) (http://www.ictvonline.org/virus
infection [34]. Furthermore, the duck TLR7 differs from Taxonomy.asp?bhcp=1). This remarkable diversity of spe-
chicken in the ligand binding LRR domains [35]. When cies and genotypes, as well as the emergence of novel species
infected by influenza virus or stimulated with TLR7 ago- capable of adapting to new hosts and ecological niches, is the
nists, chickens and ducks differentially activate the pro- result of environmental, viral, and host factors that favor
duction of MDA5, TLR7, and IFN-a [31]. Notably, TLR8 interspecies transmission.
and IFNv, which are present in bats, are either disrupted
or not found in birds. Environmental factors
The adaptive immune system is particularly unique in Environmental factors have played a key role in the emer-
ducks. Influenza virus elicits a short-lived antibody re- gence of SARS-CoV. The open door policy and economic
sponse in ducks [36]. Unlike mammals, ducks have three boom in China after 1978 is naturally associated with an
types of antibody, namely IgA, IgM, and IgY (human IgG increasing population and mobility as well as an increasing
counterpart). The predominant antibody response in cultural demand for food and game animals in South China.
infected ducks is the truncated form of IgY, which The density of both animals and humans in South China
lacks the Fc region and does not exhibit hemagglutination provided an ideal incubator for brewing novel viruses that
Miniopterus bat coronavirus 1A; Mi-BatCoV 1B, Miniopterus bat coronavirus 1B; Mi-BatCoV HKU7, Miniopterus bat coronavirus HKU7; Mi-BatCoV HKU8, Miniopterus bat
coronavirus HKU8; MRCoV HKU18, magpie robin coronavirus HKU18; MunCoV HKU13, munia coronavirus HKU13; My-BatCoV HKU6, Myotis bat coronavirus HKU6; NHCoV
HKU19, night heron coronavirus HKU19; PCoV, pigeon coronavirus; PEDV, porcine epidemic diarrhea virus; PhCoV, Pheasant coronavirus; PHEV, porcine hemagglutinating
encephalomyelitis virus; Pi-BatCoV HKU5, Pipistrellus bat coronavirus HKU5; PorCoV HKU15, porcine coronavirus HKU15; PRCV, porcine respiratory coronavirus; RCoV, rat
coronavirus; RbCoV HKU14, rabbit coronavirus HKU14; Rh-BatCoV HKU2, Rhinolophus bat coronavirus HKU2; Ro-BatCoV HKU9, Rousettus bat coronavirus HKU9; Ro-
BatCoV HKU10, Rousettus bat coronavirus HKU10; Sc-BatCoV 512, Scotophilus bat coronavirus 512; TEGV, transmissible gastroenteritis virus; SARS-CoV, severe acute
respiratory syndrome coronavirus; SARSr-CiCoV, SARS-related civet coronavirus; SARSr-CoV-CFB, SARS-related Chinese ferret badger coronavirus; SARSr-Rh-BatCoV
HKU3, SARS-related Rhinolophus bat coronavirus HKU3; TCoV, turkey coronavirus; SpCoV HKU17, sparrow coronavirus HKU17; ThCoV HKU12, thrush coronavirus HKU12;
Ty-BatCoV HKU4, Tylonycteris bat coronavirus HKU4; WECoV HKU16, white-eye coronavirus HKU16; WiCoV HKU20, wigeon coronavirus HKU20.
549
Review Trends in Microbiology October 2013, Vol. 21, No. 10
could adapt to new hosts. Phylogenetic analysis and epide- Viral and host factors
miological data revealed that SARS-CoV has likely emerged Besides the importance of abundant animal reservoirs as
from its natural animal reservoir, the bats, to civets and gene sources and favorable environmental conditions,
other game food mammals during their caging in the over- three major viral factors are instrumental in allowing
crowded and unhygienic wildlife markets of South China CoVs to cross species barriers [41]. First, their unusually
before further crossing the species barrier to humans [4]. high estimated mutation rate associated with RNA repli-