Next Article in Journal
Diagnosis and Treatment of Local Allergic Rhinitis
Next Article in Special Issue
Long-Term Sequelae of COVID-19: A Systematic Review and Meta-Analysis of One-Year Follow-Up Studies on Post-COVID Symptoms
Previous Article in Journal
Odontogenic Cervicofacial Necrotizing Fasciitis: Microbiological Characterization and Management of Four Clinical Cases
Previous Article in Special Issue
Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Pathogens
Volume 11
Issue 1
10.3390/pathogens11010079
pathogens-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential

by
Fanzhi Kong
1,
Qiuhong Wang
2,3,*,
Scott P. Kenney
2,3,
Kwonil Jung
2,3,
Anastasia N. Vlasova
2,3 and
Linda J. Saif
2,3
1
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
2
Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
3
Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
*
Author to whom correspondence should be addressed.
Pathogens 2022, 11(1), 79; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11010079
Submission received: 9 December 2021 / Revised: 30 December 2021 / Accepted: 4 January 2022 / Published: 9 January 2022
(This article belongs to the Special Issue Emerging and/or Zoonotic Viral Infections)
Browse Figures
Versions Notes

Abstract

:
Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus of swine that causes acute diarrhoea, vomiting, dehydration and mortality in seronegative neonatal piglets. PDCoV was first reported in Hong Kong in 2012 and its etiological features were first characterized in the United States in 2014. Currently, PDCoV is a concern due to its broad host range, including humans. Chickens, turkey poults, and gnotobiotic calves can be experimentally infected by PDCoV. Therefore, as discussed in this review, a comprehensive understanding of the origin, evolution, cross-species transmission and zoonotic potential of epidemic PDCoV strains is urgently needed.

1. Introduction

Coronaviruses (CoVs) are single-stranded, positive-sense RNA viruses belonging to the subfamily Orthocoronavirinae within the family of Coronaviridae. They are classified into four genera: Alphacoronavirus (α-CoV), Betacoronavirus (β-CoV), Gammacoronavirus (γ-CoV), and Deltacoronavirus (δ-CoV). Coronaviruses are important pathogens of both humans and animals, causing diverse diseases. α-CoVs and β-CoVs infect mammals, while γ-CoVs and δ-CoVs primarily infect birds with some mammalian spill over [1,2,3]. Deltacoronaviruses were detected from the rectal swabs of mammalian species, including Asian leopard cats (Prionailurus bengalensis) and Chinese ferret badgers (Melogale moschata) in wet markets, during virological surveillance in southern China between 2005 and 2006 [4]. Since then, δ-CoVs have been detected from a wide range of birds and domestic pigs [5,6,7,8]. The Deltacoronavirus genus was defined by genomic sequence analysis of both avian and mammalian isolates [7]. The prototype porcine deltacoronavirus (PDCoV) HKU15 strain was reported in Hong Kong in 2012 [7]. However, its pathogenic potential was not recognized until 2014 when it was found to be the cause of pig diarrheic outbreaks, initially on several farms in Ohio, then spreading throughout the United States (US) and globally [9,10]. PDCoV infects the intestinal epithelial cells and causes acute watery diarrhoea, vomiting and dehydration in gnotobiotic and conventional piglets [9,11,12]. PDCoV causes clinical signs indistinguishable from those caused by other porcine enteric CoVs, such as porcine epidemic diarrhoea virus (PEDV) and transmissible gastroenteritis virus (TGEV) [13]. The clinical impact, prevalence, and disease severity of PDCoV in the field are lower than those of PEDV [14]. However, PDCoV has a broader host range and, unlike PEDV and TGEV, it could/can infect multiple species, including pigs, chickens, turkeys, cattle and humans [7,15,16,17,18]. This review focuses on the current knowledge on the origin, evolution, cross-species transmission and zoonotic potential of PDCoV. Additionally, we discuss the potential mechanisms for PDCoV interspecies transmission from birds to pigs, then to humans to help understand common mechanisms for the emergence of novel human CoVs, such as the highly pathogenic severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

2. Origin of PDCoV

The Deltacoronavirus genus was first established by The International Committee on Taxonomy of Viruses (ICTV) in 2012 after the identification of three novel avian coronaviruses (bulbul CoV HKU11, thrush CoV HKU12, and munia CoV HKU13) [6] and seven other novel δ-CoVs (porcine CoV HKU15, white-eye CoV HKU16, sparrow CoV HKU17, magpie robin CoV HKU18, night heron CoV HKU19, wigeon CoV HKU20, and common moorhen CoV HKU21) of birds or pigs [7]. Interestingly, the replicase polyprotein gene (partial cds) of PDCoV HKU15 is closely related (nucleotide identity ≥ 98.88%) to those δ-CoVs (GenBank accession no. EF584909–EF584912) detected in 2006 from the Chinese ferret badgers at wet markets. Similarly, the polyprotein (orf1b, partial cds), spike (S) protein, envelop (E) protein, membrane (M) protein, non-structure protein 6 (NS6), nucleocapsid (N) protein and non-structure protein 7 (NS7) genes of HKU15 share 98.70% nucleotide identity with those of the δ-CoV (GenBank accession no. EF584908) detected from an Asian leopard cat [7]. More importantly, a recent retrospective study has confirmed the presence of PDCoV (CHN/AH/2004) in diarrheic pigs as early as 2004 in Anhui Province, China [19]. These facts suggest that these mammalian δ-CoVs directly or indirectly evolved from avian δ-CoVs. The transmission direction between the small wild carnivores and pigs is still unknown: (1) The wild small carnivore mammals could have been infected through catching and eating δ-CoV-positive birds [20] and could/can act as the intermediate hosts to transmit PDCoV to pigs; or (2) the wild small carnivore mammals could have been infected as they were fed PDCoV-positive pig viscera, which was used as carnivore food in wet markets (Haitao Xiu, personal communication). Natural PDCoV infection of these two mammalian species has not been reported since 2007, even with additional surveillance attempts [7], further supporting the second possibility, although it needs to be validated with more data in the future. Phylogenetic and recombination analyses suggest that PDCoV might have resulted from several recombination events involving δ-CoVs from several avian species, such as sparrow δ-CoVs HKU17 and ISU73347, and quail δ-CoV HKU30 (Figure 1) [8,21]. Recent studies indicate that aquatic birds may serve as natural reservoirs for δ-CoVs, while terrestrial birds and mammalian species may represent spill over hosts [22,23]. Sparrows, one of the most common birds at pig farms during the wintertime, late fall, and early spring, could promote the transmission of δ-CoVs to pigs. For example, bird droppings in the farms or in contaminated feed grains may be consumed by pigs [24].
Because the S gene of CoVs is the main genetic determinant of CoV host, tissue, or cellular tropism [25,26,27], Niu et al. [28] and Alhamo et al. [29] tested whether the spike protein or receptor-binding domain (RBD) from the sparrow δ-CoVs could alter PDCoV host and tissue tropism. First, Niu et al. [28] generated an infectious cDNA clone of PDCoV OH-FD22 strain (icPDCoV) and constructed two chimeric icPDCoVs harbouring the spike protein of HKU17 (icPDCoV-SHKU17) or the RBD of ISU73347 (icPDCoV-RBDISU). Niu et al. [28] and Alhamo et al. [29] evaluated their replication in the porcine kidney cell line LLC-PK1 and chicken fibroblast cell line DF-1 and performed pathogenesis studies in 4-day-old gnotobiotic pigs, 8-day-old turkey poults, and 11-day-old embryonated chicken eggs (ECEs). Compared with icPDCoV, the two chimeric viruses replicated to lower titers in LLC-PK1 cells. They did not cause clinical signs in pigs and replicated weakly in the nasal cavity but not in the intestines of pigs, whereas icPDCoV replicated mainly in the pig intestines and weakly in the respiratory tract. The two chimeric viruses and icPDCoV did not replicate in DF-1 cells at a multiplicity of infection (MOI) of 0.01 and did not replicate in the turkey poults or ECEs. Thus, these data indicate that the spike protein of sparrow δ-CoV HKU17 and the RBD of sparrow δ-CoV ISU73347 reduced PDCoV replication in pigs, suggesting limited potential for direct cross-species spillover from current sparrow strains to pigs. Recent molecular clock analyses suggest that PDCoVs shared a common ancestor with sparrow CoVs around 1810 and PDCoVs emerged around the 1990s [21].
Collectively, these studies suggest that PDCoV could have originated from terrestrial birds (e.g., sparrows) or less likely from other unknown wild mammalian δ-CoVs (Figure 2). Clearly, a better understanding of PDCoV origin requires detailed epidemiological studies of δ-CoVs in different species of birds and mammals.

3. Molecular Epidemiology and Genetic Diversity of PDCoVs

3.1. Prevalence of PDCoV in Different Countries

To date, PDCoV has been detected in Hong Kong, the United States, Canada, South Korea, mainland China, Thailand, Vietnam, Laos, Taiwan, Japan, Mexico and Haiti. The first documented PDCoV HKU15-44 and HKU15-155 strains were detected from the faecal samples collected from healthy pigs in 2009–2010 from a large-scale animal surveillance study in Hong Kong [7]. Subsequently, in early 2014, PDCoV associated diarrhoea outbreaks were first reported in three states of the US (Ohio, Iowa and Illinois). Later studies showed that PDCoV had spread to many Asian countries (China, Japan, Korea, Laos, Thailand, and Vietnam) and North American countries (the US, Canada, and Mexico) [10,30,31]. In the US, a retrospective surveillance study using reverse transcription-PCR (RT-qPCR) showed that PDCoV RNA was detected as early as August 2013 in pig faecal samples collected from Minnesota, Iowa and Illinois [32]. Furthermore, an indirect PDCoV S1 protein-based enzyme linked immunosorbent assay (ELISA) test suggested an even earlier presence of PDCoV IgG antibody in four archived serum samples collected in 2010 from US pigs [33]. In response to the large number of Swine Enteric Coronavirus Disease (SECD) cases since 2014, the United States Department of Agriculture (USDA) issued a federal order in June 2014, making SECD (caused by PEDV or PDCoV) reportable diseases, which was rescinded on 6 March 2018. According to the last SECD weekly situation report on 8 March 2018, 300 confirmed PDCoV positive premises and 88 presumptive positive premises cumulated between June 2014 and March 2018 and were distributed in 18 states within the US (https://www.aasv.org/pedv/SECD_Situation_Report_180308.pdf; accessed on: 15 October 2021). To date, PDCoV diarrhea occurs at a relatively low reported case rate according to the Swine Health Information Center (https://www.swinehealth.org/domestic-disease-surveillance-reports/; accessed on: 15 October 2021).
In mainland China, PDCoV was first reported in 2015 [19,34,35,36]; however, retrospective studies have shown that PDCoV could have emerged as a swine pathogen as early as 2004 [19]. A recent PDCoV surveillance study reported that 94 (13.07%) of 719 porcine diarrhoea samples collected from 18 provinces in China from March 2016 to June 2018 were PDCoV-positive by RT-qPCR [37]. The complete S genes of 11 PDCoV strains were determined. Seven were expectedly grouped into the Chinese lineage. However, CH-WH-2017 (GenBank accession no. MK040451) exhibited a closer relationship to the US/Japan/South Korea lineage; CH-HA3-2017, CH-HA1-2017 and CH-HA2-2017 strains (GenBank accession no. MK040455, MK040453 and MK040454) were clustered into a new branch and separate from the Chinese lineage. The latter showed the closest relationship to the Vietnam/Laos/Thailand lineage [37]. As of October 2021, PDCoV has been detected in 26 provinces of China, including all swine producing areas [35,37,38,39,40,41,42]. From mid-March 2014 to January 2016, PDCoV related diarrhoea outbreaks were successively identified in Canada, South Korea, Thailand, Vietnam, and Laos [30,43,44,45]. Retrospective studies revealed that PDCoV has been circulating in Taiwan [46], Japan [47], Mexico [48] and Haiti [18] since 2011, late 2013, 2015 and 2014, respectively. PDCoVs or PDCoV-like δ-CoVs have not been detected in the Europe, South American, African, and Australian continents, although retrospective studies have been conducted in Brazil [49] and Spain [50] to identify CoVs in wild birds and pigs, respectively.

3.2. Genetic Diversity of Global PDCoV

To date, 122 complete genome sequences of PDCoVs are available in GenBank (Table 1 and Figure 3). Phylogenetic analysis of these PDCoV genome sequences showed that all US, South Korean and Japanese strains clustered together; and three Chinese isolates (CHN-GD16-05/2016; CHzmd2019; CH-HLJ-20/2020) and one Haiti isolate (PDCoV/Haiti/Human/0256-1/2015) appeared to be more closely related to US/South Korean/Japanese strains. Therefore, these latter four strains were classified into the US linage (Figure 3). Similarly, He et al. found two other newly sequenced Chinese strains (AH2019/H and SD2019/426, GenBank accession no. are not available) were also clustered into the US lineage [10]. The close genetic relatedness between Chinese and US PDCoVs is not surprising due to the frequent trade of pork and pork products and pig feed supplements (https://www.fas.usda.gov/china-2020-export-highlights; accessed on: 10 November 2021). Additionally, it is not surprising to see that one of the three Haitian PDCoVs detected from children grouped within US lineage because pigs were re-introduced from the US to Haiti after the local pig population was mostly wiped out following the African Swine Fever epidemic in 1970s–1980s [51]. The early Chinese lineage contains the earliest strain that was detected from a sample collected in the Anhui Province in 2004 (CHN-AH-2004) and the strains isolated in Hong Kong in 2009 (HKU15-44) and 2010 (HKU15-155). The Chinese lineage is also inclusive of the two Haiti PDCoVs (PDCoV/Haiti/Human/0081-4/2014 and PDCoV/Haiti/Human/0329-4/2015) and the currently circulating strains in mainland China. The two Haitian strains are closely related to a Chinese strain (CHN/Tianjin/2016). According to the pork trade data from the Observatory of Economic Complexity (OEC), Chinese pork was exported to Haiti from 2006 to 2011 (https://oec.world/en/visualize/tree_map/hs92/import/hti/show/10203/2012/; accessed on: 10 November 2021). This may have contributed to PDCoV transmission from China to Haiti. The Southeast Asian (or Vietnam/Laos/Thailand) lineage contains PDCoV strains prevailing in these countries and a novel strain detected in China (CHN/GX/1468B/2017), indicating that these strains may derive from common evolutionary ancestors [52]. In addition, another Thailand-like PDCoV isolate (CHN-GX81-2018) was also discovered in Guangxi Province of China [53]. Collectively, phylogenetic analysis demonstrated that multiple PDCoV lineages, including US lineage, early Chinese lineage, Chinese lineage, and Vietnam/Laos/Thailand lineage, coexist in mainland China. He et al. [10] reported that more frequent intra- and inter-lineage recombination and higher virus genetic diversity were identified among and within the Vietnam/Laos/Thailand and Chinese lineages than within the US lineage. Frequent recombination events between different lineages of PDCoV strains in China may complicate PDCoV epidemiology and result in the emergence of PDCoV strains with changed pathogenicity and host tropism.

3.3. Co-Infection of PDCoV with Other Porcine Enteric Viruses

Clinical signs associated with PDCoV infection were found to be less severe than PEDV infection, and the PDCoV prevalence rate in diarrheic pigs is about 30% [7,9,30]. Nevertheless, co-infection with other enteric viral pathogens, such as PEDV, transmissible gastroenteritis virus (TGEV) and porcine rotavirus (PRV), are common and may lead to more severe clinical disease [30,37,41,84,85]. Recent surveys conducted in the United States, Mexico, South Korea and mainland China found that PEDV is the most frequent co-infecting pathogen with PDCoV, with a detection rate ranging from 4.73% to 54.10% (Table 2). Furthermore, except for the US, multiple-infection cases with both PDCoV and two other viruses (PEDV, TGEV, or PRV) were identified in other countries, with a detection rate ranging from 0.12% to 18.80% (Table 2). Additionally, a recent study found the co-infection of PDCoV with 4 to 7 other viral pathogens in diarrhoea samples collected in China from 2015 to 2018. These pathogens were porcine astrovirus (PAstV), porcine teschovirus (PTV), porcine sapelovirus (PSV), porcine enterovirus (PEV) 9/10, torque teno sus virus 2 (TTSuV-2), mammalian reovirus (MRV), porcine torovirus (PToV), porcine kobuvirus (PKV) or porcine bocavirus (PBoV) (Table 2).

4. Cross-Species Transmission and Zoonotic Potential

4.1. Receptor Usage

To initiate infection, the interaction between CoV spike proteins and the host receptor(s) plays an important role and determines the extent of host cell susceptibility and interspecies transmission. Coronavirus spike proteins can bind to a wide variety of carbohydrates and protein receptors located at the cell surface, with receptor binding domains (RBDs) located in either the N-terminal domain (NTD) or the C-terminal domain (CTD) within the S1 subunit of the spike proteins [88]. Porcine aminopeptidase N (pAPN) has been identified as a PDCoV primary entry receptor [89,90]. PDCoV was shown to infect pig, human and chicken cells via APN and can use feline and human APN to infect nonpermissive cells [90]. The CTD of the S1 subunit of PDCoV spike protein binds to the interspecies conserved domain II of APN [90]. However, PDCoV may use additional receptors for cellular entry because pAPN knockout porcine intestinal epithelial (IPI-2I) cells can still be infected by PDCoV [91]. Furthermore, CD163 and pAPN double-gene-knockout pigs exhibited decreased susceptibility to PDCoV [92]. A recent study reported that sialic acids serve as a binding receptor of PDCoV [93]; however, whether sialic acids are PDCoV receptors or just attachment factors is still unknown. Additionally, lung fibroblast-like cells, derived from the pAPN knockout porcine alveolar macrophage (PAM) cultures, still supported PDCoV replication to high levels [94]. Similarly, Niu et al. [28] found that icPDCoV-RBDISU replicated to higher levels in APN knockout swine testis (ST) cells than in wild type ST cells, suggesting that the icPDCoV-RBDISU virus uses other unidentified host cell molecules, but not pAPN as the major receptor. In addition to receptor usage, other mechanisms might be involved in the cellular entry processes of PDCoVs. Recent studies have confirmed that macropinocytosis, clathrin-mediated endocytosis and pAPN-mediated endocytotic pathways play important roles in assisting PDCoV cellular entry and efficient viral replication [95,96,97].

4.2. Experimental Cross-Species Transmission of PDCoV

The host tropism of coronaviruses is largely determined by the spike protein owing to its receptor binding and membrane fusion functions. A critical step in cross-species transmission of CoVs is the capacity to bind to new receptors in a novel host, which occurs by the spike protein [90]. Due to their large RNA genomes, ranging from 26 to 32 kilobases in length, CoVs are genetically more tolerant to acquire non-lethal mutations, insertions and deletions, and recombination in S gene, increasing CoV capacity to cross host species barriers. The S gene of the δ-CoV identified in Asian leopard cats and Chinese ferret badgers share over 99.80% nucleotide identity with PDCoV, suggesting a potential cross-species transmission between these wild mammals and pigs [7]. Additionally, a recent study reported that PDCoV was detected in plasma samples of three Haitian children with an acute undifferentiated febrile illness [18]. In addition to natural cross-species transmission, PDCoV experimentally infected 3–7-day-old gnotobiotic calves with a high level of viral RNA in faeces and PDCoV-specific IgG antibody in convalescent sera [17]. Recent studies showed that chickens and turkey poults were also susceptible to PDCoV infection and passed the virus efficiently to contact chicks [15,16]. Additionally, PDCoV successfully (productively) infected a number of cells from an unusually broad species range (Table 3). Interestingly, Niu et al. [28] found that the chimeric PDCoVs with SpDCoV spike protein (HKU17) or the RBD (ISU73347) infected pigs but lost its virulence and intestinal tropism but retained respiratory tropism suggesting limited potential for direct cross-species spill over of current sparrow δ-CoVs to pigs. These observations indicate that PDCoV has the potential to infect diverse host species. More surveillance and sequence data and seroprevalence studies are needed to understand the mechanisms of cross-species transmission of PDCoVs among different species.

4.3. PDCoV Zoonotic Potential

In the last two decades, three zoonotic CoVs (SARS-CoV, MERS-CoV, and SARS-CoV-2) have posed a serious threat to public health and global security [102,103]. In addition, HCoV-HKU1, HCoV-229E, HCoV- NL63, HCoV-OC43 and HECV-4408 are also of zoonotic origin [104,105,106,107,108]. Recently, Vlasova et al. [109] first characterized a complete genome of novel canine-feline recombinant alphacoronavirus (CCoV-HuPn-2018, GenBank accession no. MW591993.2) which was isolated from a child with pneumonia in Malaysia. This report was followed by another study that identified and characterized a highly similar canine-feline recombinant alphacoronavirus in a member of a medical team that travelled to Haiti [110]. In November 2021, Lednicky et al. [18] reported the first evidence that PDCoV may have jumped from pigs to three children in Haiti. The three children had mild symptoms (febrile, cough, and/or abdominal pain) and recovered. Genomic sequence analyses showed that Haiti/Human/0256-1/2015 and USA/Porcine/Arkansas61/2015 shared 99.40% nucleotide identity; and Haiti/Human/0081-4 and Haiti/Human/0329-4/2015 had 99.80% and 99.97% nucleotide identities with the CHN/ Porcine/Tianjin/2016, respectively [18]. These data suggest that at least two independent cross-species transmission events of PDCoV from pigs to humans occurred. It is still unknown whether PDCoV is transmissible among humans. Currently, PDCoV has only been demonstrated to cause asymptomatic or mild disease in humans and does not seem to pose a major health risk to human health. However, continued surveillance and seroprevalence studies of PDCoV in humans, especially those in close contact with pigs (e.g., swine farm families and workers and slaughterhouse workers), may provide a clearer answer in the future. Collectively, it appears inevitable that similar spill over events will occur again in the future, so more epidemiological studies are needed to clarify the origin, epidemiology, and cross-species transmission mechanisms of CoVs for improved CoV disease control and prevention.

5. Conclusions, Challenges, and Future Perspectives

Coronaviruses are an important group of pathogens that can have a devastating impact on human and animal health, with new zoonotic CoVs continually emerging or re-emerging. PDCoV is an emerging pathogen of pigs that can also infect birds, and several mammalian species, including humans. PDCoV likely evolved directly or indirectly from avian δ-CoVs, although the exact origin pathway of PDCoV is still unknown. While its prevalence and disease severity are lower than those of PEDV, PDCoV co-infections with other porcine enteric pathogens are common, posing a threat to the swine industry. All PDCoV strains share >96.70% nucleotide identity at the genomic level, suggesting their recent emergence. Since the evidence of δ-CoVs infections of small carnivore mammals and humans is limited to one report, respectively, and these δ-CoVs are genetically indistinguishable from PDCoVs from pigs, it may indicate that PDCoVs are still in the process of adaption to different species, including humans. Currently, PDCoV strains form four lineages and all lineages of PDCoVs have been detected in China. The large pig population and low biosecurity in the swine farms in China [111,112] and the relatively mild diseases caused by PDCoVs can contribute to the frequent recombination and generation of new PDCoV variants, consequently facilitating interspecies transmission to other species.
Although pAPN has been shown to be the major receptor for PDCoV infection, additional minor receptors exist that remain to be identified. There are still intriguing questions to be clarified about PDCoV, such as whether PDCoV could/can naturally infect other mammal species; whether frequent spill overs of PDCoV occur between birds and pigs and other mammals, such as MERS-CoV between camels and humans [113,114]; and whether PDCoV has spread to Europe, South America, Africa or Australia. These questions cannot be fully answered due to the unavailability of comprehensive epidemiological data. Therefore, additional studies to evaluate the genetic diversity of δ-CoVs in avian and mammalian hosts are needed to better understand their ecology and evolution. Furthermore, experimental studies on PDCoV interspecies transmission and host adaptation are needed to evaluate its pathogenicity in various hosts. Additionally, seroprevalence studies in pigs can provide useful information highlighting the actual prevalence of PDCoV globally. Finally, continued surveillance and seroprevalence studies of PDCoV in humans are needed to define its impact on public health. Safe and effective vaccines may be needed for pigs to prevent infection, to reduce the PDCoV gene pool that contribute to spill overs [18], and may be needed for humans if severe cases emerge.

Author Contributions

Conceptualization, F.K. and Q.W.; writing—original draft preparation, F.K. and Q.W.; writing—review and editing, Q.W., S.P.K., K.J., A.N.V. and L.J.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by a SEEDS grant (2020-009, Q.W., principal investigator) from College of Food, Agricultural and Environmental Sciences, The Ohio State University. Salaries and research support were provided by state and federal funds appropriated to The Ohio State University.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data presented in this study are openly available at GenBank (https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/nucleotide/, accessed on: 15 October 2021) and the websites provided in this manuscript.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

References

  1. Geoghegan, J.L.; Duchene, S.; Holmes, E.C. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog. 2017, 13, e1006215. [Google Scholar] [CrossRef] [PubMed]
  2. Kenney, S.P.; Wang, Q.; Vlasova, A.; Jung, K.; Saif, L. Naturally Occurring Animal Coronaviruses as Models for Studying Highly Pathogenic Human Coronaviral Disease. Vet. Pathol. 2021, 58, 438–452. [Google Scholar] [CrossRef]
  3. King, A.M.Q.; Lefkowitz, E.J.; Mushegian, A.R.; Adams, M.J.; Dutilh, B.E.; Gorbalenya, A.E.; Harrach, B.; Harrison, R.L.; Junglen, S.; Knowles, N.J.; et al. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018). Arch. Virol. 2018, 163, 2601–2631. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Dong, B.Q.; Liu, W.; Fan, X.H.; Vijaykrishna, D.; Tang, X.C.; Gao, F.; Li, L.F.; Li, G.J.; Zhang, J.X.; Yang, L.Q.; et al. Detection of a novel and highly divergent coronavirus from asian leopard cats and Chinese ferret badgers in Southern China. J. Virol. 2007, 81, 6920–6926. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  5. Chu, D.K.; Leung, C.Y.; Gilbert, M.; Joyner, P.H.; Ng, E.M.; Tse, T.M.; Guan, Y.; Peiris, J.S.; Poon, L.L. Avian coronavirus in wild aquatic birds. J. Virol. 2011, 85, 12815–12820. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  6. Woo, P.C.; Lau, S.K.; Lam, C.S.; Lai, K.K.; Huang, Y.; Lee, P.; Luk, G.S.; Dyrting, K.C.; Chan, K.H.; Yuen, K.Y. Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J. Virol. 2009, 83, 908–917. [Google Scholar] [CrossRef] [Green Version]
  7. Woo, P.C.; Lau, S.K.; Lam, C.S.; Lau, C.C.; Tsang, A.K.; Lau, J.H.; Bai, R.; Teng, J.L.; Tsang, C.C.; Wang, M.; et al. 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 Deltacoronavirus. J. Virol. 2012, 86, 3995–4008. [Google Scholar] [CrossRef] [Green Version]
  8. Lau, S.K.P.; Wong, E.Y.M.; Tsang, C.C.; Ahmed, S.S.; Au-Yeung, R.K.H.; Yuen, K.Y.; Wernery, U.; Woo, P.C.Y. Discovery and Sequence Analysis of Four Deltacoronaviruses from Birds in the Middle East Reveal Interspecies Jumping with Recombination as a Potential Mechanism for Avian-to-Avian and Avian-to-Mammalian Transmission. J. Virol. 2018, 92, e00265-18. [Google Scholar] [CrossRef] [Green Version]
  9. Wang, L.; Byrum, B.; Zhang, Y. Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA, 2014. Emerg. Infect. Dis. 2014, 20, 1227–1230. [Google Scholar] [CrossRef] [PubMed]
  10. He, W.T.; Ji, X.; He, W.; Dellicour, S.; Wang, S.; Li, G.; Zhang, L.; Gilbert, M.; Zhu, H.; Xing, G.; et al. Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus. Mol. Biol. Evol. 2020, 37, 2641–2654. [Google Scholar] [CrossRef]
  11. Jung, K.; Hu, H.; Eyerly, B.; Lu, Z.; Chepngeno, J.; Saif, L.J. Pathogenicity of 2 porcine deltacoronavirus strains in gnotobiotic pigs. Emerg. Infect. Dis. 2015, 21, 650–654. [Google Scholar] [CrossRef]
  12. Chen, Q.; Gauger, P.; Stafne, M.; Thomas, J.; Arruda, P.; Burrough, E.; Madson, D.; Brodie, J.; Magstadt, D.; Derscheid, R.; et al. Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets. Virology 2015, 482, 51–59. [Google Scholar] [CrossRef] [Green Version]
  13. Wang, Q.; Vlasova, A.N.; Kenney, S.P.; Saif, L.J. Emerging and re-emerging coronaviruses in pigs. Curr. Opin. Virol. 2019, 34, 39–49. [Google Scholar] [CrossRef] [PubMed]
  14. Jung, K.; Hu, H.; Saif, L.J. Porcine deltacoronavirus infection: Etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis. Virus Res. 2016, 226, 50–59. [Google Scholar] [CrossRef] [PubMed]
  15. Boley, P.A.; Alhamo, M.A.; Lossie, G.; Yadav, K.K.; Vasquez-Lee, M.; Saif, L.J.; Kenney, S.P. Porcine Deltacoronavirus Infection and Transmission in Poultry, United States. Emerg. Infect. Dis. 2020, 26, 255–265. [Google Scholar] [CrossRef] [Green Version]
  16. Liang, Q.; Zhang, H.; Li, B.; Ding, Q.; Wang, Y.; Gao, W.; Guo, D.; Wei, Z.; Hu, H. Susceptibility of Chickens to Porcine Deltacoronavirus Infection. Viruses 2019, 11, 573. [Google Scholar] [CrossRef] [Green Version]
  17. Jung, K.; Hu, H.; Saif, L.J. Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus. Arch. Virol. 2017, 162, 2357–2362. [Google Scholar] [CrossRef]
  18. Lednicky, J.A.; Tagliamonte, M.S.; White, S.K.; Elbadry, M.A.; Alam, M.M.; Stephenson, C.J.; Bonny, T.S.; Loeb, J.C.; Telisma, T.; Chavannes, S.; et al. Independent infections of porcine deltacoronavirus among Haitian children. Nature 2021, 600, 133–137. [Google Scholar] [CrossRef] [PubMed]
  19. Dong, N.; Fang, L.; Zeng, S.; Sun, Q.; Chen, H.; Xiao, S. Porcine Deltacoronavirus in Mainland China. Emerg. Infect. Dis. 2015, 21, 2254–2255. [Google Scholar] [CrossRef]
  20. Lo, C.L.C.; Fernandez, D.A.P.; de Luna, M.C.T.; de Guia, A.P.O.; Paller, V.G.V. Diet, parasites, and other pathogens of Sunda leopard cats (Prionailurus javanensis Desmarest 1816) in Aborlan, Palawan Island, Philippines. J. Parasit. Dis. 2021, 45, 627–633. [Google Scholar] [CrossRef]
  21. Ye, X.; Chen, Y.; Zhu, X.; Guo, J.; Da, X.; Hou, Z.; Xu, S.; Zhou, J.; Fang, L.; Wang, D.; et al. Cross-Species Transmission of Deltacoronavirus and the Origin of Porcine Deltacoronavirus. Evol. Appl. 2020, 13, 2246–2253. [Google Scholar] [CrossRef]
  22. Vlasova, A.N.; Kenney, S.P.; Jung, K.; Wang, Q.; Saif, L.J. Deltacoronavirus Evolution and Transmission: Current Scenario and Evolutionary Perspectives. Front. Vet. Sci. 2020, 7, 626785. [Google Scholar] [CrossRef] [PubMed]
  23. Wille, M.; Holmes, E.C. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiol. Rev. 2020, 44, 631–644. [Google Scholar] [CrossRef] [PubMed]
  24. Chen, Q.; Wang, L.; Yang, C.; Zheng, Y.; Gauger, P.C.; Anderson, T.; Harmon, K.M.; Zhang, J.; Yoon, K.J.; Main, R.G.; et al. The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17. Emerg. Microbes Infect. 2018, 7, 105. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Kuo, L.; Godeke, G.J.; Raamsman, M.J.; Masters, P.S.; Rottier, P.J. Retargeting of coronavirus by substitution of the spike glycoprotein ectodomain: Crossing the host cell species barrier. J. Virol. 2000, 74, 1393–1406. [Google Scholar] [CrossRef] [Green Version]
  26. Haijema, B.J.; Volders, H.; Rottier, P.J. Switching species tropism: An effective way to manipulate the feline coronavirus genome. J. Virol. 2003, 77, 4528–4538. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  27. Sanchez, C.M.; Pascual-Iglesias, A.; Sola, I.; Zuniga, S.; Enjuanes, L. Minimum Determinants of Transmissible Gastroenteritis Virus Enteric Tropism Are Located in the N-Terminus of Spike Protein. Pathogens 2019, 9, 2. [Google Scholar] [CrossRef] [Green Version]
  28. Niu, X.; Hou, Y.J.; Jung, K.; Kong, F.; Saif, L.J.; Wang, Q. Chimeric Porcine Deltacoronaviruses with Sparrow Coronavirus Spike Protein or the Receptor-Binding Domain Infect Pigs but Lose Virulence and Intestinal Tropism. Viruses 2021, 13, 122. [Google Scholar] [CrossRef]
  29. Alhamo, M.A.; Boley, P.A.; Niu, X.; Yadav, K.K.; Lee, C.; Wang, Q.; Saif, L.; Kenney, S.P. Characterization of the Cross-Species Transmission Potential for Porcine Deltacoronaviruses Expressing Sparrow Coronavirus Spike Protein in Commercial Poultry. Viruses 2021. accepted. [Google Scholar]
  30. Marthaler, D.; Raymond, L.; Jiang, Y.; Collins, J.; Rossow, K.; Rovira, A. Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus. Emerg. Infect. Dis. 2014, 20, 1347–1350. [Google Scholar] [CrossRef] [Green Version]
  31. Ma, Y.; Zhang, Y.; Liang, X.; Lou, F.; Oglesbee, M.; Krakowka, S.; Li, J. Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. mBio 2015, 6, e00064. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  32. Sinha, A.; Gauger, P.; Zhang, J.; Yoon, K.J.; Harmon, K. PCR-based retrospective evaluation of diagnostic samples for emergence of porcine deltacoronavirus in US swine. Vet. Microbiol. 2015, 179, 296–298. [Google Scholar] [CrossRef]
  33. Thachil, A.; Gerber, P.F.; Xiao, C.T.; Huang, Y.W.; Opriessnig, T. Development and application of an ELISA for the detection of porcine deltacoronavirus IgG antibodies. PLoS ONE 2015, 10, e0124363. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Chen, F.; Zhu, Y.; Wu, M.; Ku, X.; Yao, L.; He, Q. Full-Length Genome Characterization of Chinese Porcine Deltacoronavirus Strain CH/SXD1/2015. Genome Announc. 2015, 3, e01284-15. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Song, D.; Zhou, X.; Peng, Q.; Chen, Y.; Zhang, F.; Huang, T.; Zhang, T.; Li, A.; Huang, D.; Wu, Q.; et al. Newly Emerged Porcine Deltacoronavirus Associated with Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis. Transbound Emerg. Dis. 2015, 62, 575–580. [Google Scholar] [CrossRef]
  36. Wang, Y.W.; Yue, H.; Fang, W.; Huang, Y.W. Complete Genome Sequence of Porcine Deltacoronavirus Strain CH/Sichuan/S27/2012 from Mainland China. Genome Announc. 2015, 3, e00945-15. [Google Scholar] [CrossRef] [Green Version]
  37. Zhang, Y.; Cheng, Y.; Xing, G.; Yu, J.; Liao, A.; Du, L.; Lei, J.; Lian, X.; Zhou, J.; Gu, J. Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018. Infect. Genet. Evol. 2019, 73, 151–158. [Google Scholar] [CrossRef]
  38. Zhai, S.L.; Wei, W.K.; Li, X.P.; Wen, X.H.; Zhou, X.; Zhang, H.; Lv, D.H.; Li, F.; Wang, D. Occurrence and sequence analysis of porcine deltacoronaviruses in southern China. Virol. J. 2016, 13, 136. [Google Scholar] [CrossRef] [Green Version]
  39. Li, D.; Feng, H.; Liu, Y.; Chen, Y.; Wei, Q.; Wang, J.; Liu, D.; Huang, H.; Su, Y.; Wang, D.; et al. Molecular evolution of porcine epidemic diarrhea virus and porcine deltacoronavirus strains in Central China. Res. Vet. Sci. 2018, 120, 63–69. [Google Scholar] [CrossRef]
  40. Li, B.; Zheng, L.; Li, H.; Ding, Q.; Wang, Y.; Wei, Z. Porcine deltacoronavirus causes diarrhea in various ages of field-infected pigs in China. Biosci. Rep. 2019, 39, BSR20190676. [Google Scholar] [CrossRef] [Green Version]
  41. Zhang, F.; Luo, S.; Gu, J.; Li, Z.; Li, K.; Yuan, W.; Ye, Y.; Li, H.; Ding, Z.; Song, D.; et al. Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from 2012 to 2018. BMC Vet. Res. 2019, 15, 470. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  42. Tang, P.; Cui, E.; Song, Y.; Yan, R.; Wang, J. Porcine deltacoronavirus and its prevalence in China: A review of epidemiology, evolution, and vaccine development. Arch. Virol. 2021, 166, 2975–2988. [Google Scholar] [CrossRef]
  43. Lee, S.; Lee, C. Complete Genome Characterization of Korean Porcine Deltacoronavirus Strain KOR/KNU14-04/2014. Genome Announc. 2014, 2, e01191-14. [Google Scholar] [CrossRef] [Green Version]
  44. Lorsirigool, A.; Saeng-Chuto, K.; Temeeyasen, G.; Madapong, A.; Tripipat, T.; Wegner, M.; Tuntituvanont, A.; Intrakamhaeng, M.; Nilubol, D. The first detection and full-length genome sequence of porcine deltacoronavirus isolated in Lao PDR. Arch. Virol. 2016, 161, 2909–2911. [Google Scholar] [CrossRef] [Green Version]
  45. Saeng-Chuto, K.; Lorsirigool, A.; Temeeyasen, G.; Vui, D.T.; Stott, C.J.; Madapong, A.; Tripipat, T.; Wegner, M.; Intrakamhaeng, M.; Chongcharoen, W.; et al. Different Lineage of Porcine Deltacoronavirus in Thailand, Vietnam and Lao PDR in 2015. Transbound Emerg. Dis. 2017, 64, 3–10. [Google Scholar] [CrossRef]
  46. Hsu, T.H.; Liu, H.P.; Chin, C.Y.; Wang, C.; Zhu, W.Z.; Wu, B.L.; Chang, Y.C. Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan. Arch. Virol. 2018, 163, 3113–3117. [Google Scholar] [CrossRef] [Green Version]
  47. Suzuki, T.; Shibahara, T.; Imai, N.; Yamamoto, T.; Ohashi, S. Genetic characterization and pathogenicity of Japanese porcine deltacoronavirus. Infect. Genet. Evol. 2018, 61, 176–182. [Google Scholar] [CrossRef]
  48. Perez-Rivera, C.; Ramirez-Mendoza, H.; Mendoza-Elvira, S.; Segura-Velazquez, R.; Sanchez-Betancourt, J.I. First report and phylogenetic analysis of porcine deltacoronavirus in Mexico. Transbound Emerg. Dis. 2019, 66, 1436–1441. [Google Scholar] [CrossRef]
  49. Barbosa, C.M.; Durigon, E.L.; Thomazelli, L.M.; Ometto, T.; Marcatti, R.; Nardi, M.S.; de Aguiar, D.M.; Pinho, J.B.; Petry, M.V.; Neto, I.S.; et al. Divergent coronaviruses detected in wild birds in Brazil, including a central park in Sao Paulo. Braz. J. Microbiol. 2019, 50, 547–556. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  50. Puente, H.; Arguello, H.; Mencia-Ares, O.; Gomez-Garcia, M.; Rubio, P.; Carvajal, A. Detection and Genetic Diversity of Porcine Coronavirus Involved in Diarrhea Outbreaks in Spain. Front. Vet. Sci. 2021, 8, 651999. [Google Scholar] [CrossRef] [PubMed]
  51. Alexander, F.C. Experiences with African swine fever in Haiti. Ann. N. Y. Acad. Sci. 1992, 653, 251–256. [Google Scholar] [CrossRef]
  52. Wang, H.; Qin, Y.; Zhao, W.; Yuan, T.; Yang, C.; Mi, X.; Zhao, P.; Lu, Y.; Lu, B.; Chen, Z.; et al. Genetic Characteristics and Pathogenicity of a Novel Porcine Deltacoronavirus Southeast Asia-Like Strain Found in China. Front. Vet. Sci. 2021, 8, 701612. [Google Scholar] [CrossRef] [PubMed]
  53. Huang, H.; Yin, Y.; Wang, W.; Cao, L.; Sun, W.; Shi, K.; Lu, H.; Jin, N. Emergence of Thailand-like strains of porcine deltacoronavirus in Guangxi Province, China. Vet. Med. Sci. 2020, 6, 854–859. [Google Scholar] [CrossRef]
  54. Marthaler, D.; Jiang, Y.; Collins, J.; Rossow, K. Complete Genome Sequence of Strain SDCV/USA/Illinois121/2014, a Porcine Deltacoronavirus from the United States. Genome Announc. 2014, 2, e00218-14. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  55. Li, G.; Chen, Q.; Harmon, K.M.; Yoon, K.J.; Schwartz, K.J.; Hoogland, M.J.; Gauger, P.C.; Main, R.G.; Zhang, J. Full-Length Genome Sequence of Porcine Deltacoronavirus Strain USA/IA/2014/8734. Genome Announc. 2014, 2, e00278-14. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  56. Wang, L.; Zhang, Y.; Byrum, B. Complete Genome Sequence of Porcine Coronavirus HKU15 Strain IN2847 from the United States. Genome Announc. 2014, 2, e00291-14. [Google Scholar] [CrossRef] [Green Version]
  57. Wang, L.; Byrum, B.; Zhang, Y. Porcine coronavirus HKU15 detected in 9 US states, 2014. Emerg. Infect. Dis. 2014, 20, 1594–1595. [Google Scholar] [CrossRef] [PubMed]
  58. Wang, L.; Hayes, J.; Sarver, C.; Byrum, B.; Zhang, Y. Porcine deltacoronavirus: Histological lesions and genetic characterization. Arch. Virol. 2016, 161, 171–175. [Google Scholar] [CrossRef]
  59. Hu, H.; Jung, K.; Vlasova, A.N.; Chepngeno, J.; Lu, Z.; Wang, Q.; Saif, L.J. Isolation and characterization of porcine deltacoronavirus from pigs with diarrhea in the United States. J. Clin. Microbiol. 2015, 53, 1537–1548. [Google Scholar] [CrossRef] [Green Version]
  60. Chung, H.C.; Nguyen, V.G.; Oh, W.T.; My Le, H.T.; Moon, H.J.; Lee, J.H.; Kim, H.K.; Park, S.J.; Park, B.K. Complete Genome Sequences of Porcine Deltacoronavirus Strains DH1/2016 and DH2/2016 Isolated in South Korea. Genome Announc. 2017, 5, e01706-16. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  61. Jang, G.; Kim, S.H.; Lee, Y.J.; Kim, S.; Lee, D.S.; Lee, K.K.; Lee, C. Isolation and characterization of Korean porcine deltacoronavirus strain KNU16-07. J. Vet. Sci. 2018, 19, 577–581. [Google Scholar] [CrossRef] [PubMed]
  62. Jang, G.; Lee, K.K.; Kim, S.H.; Lee, C. Prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in South Korea, 2014–2016. Transbound Emerg. Dis. 2017, 64, 1364–1370. [Google Scholar] [CrossRef]
  63. Suzuki, T.; Hayakawa, J.; Ohashi, S. Complete Genome Characterization of the Porcine Deltacoronavirus HKD/JPN/2016, Isolated in Japan, 2016. Genome Announc. 2017, 5, e00795-17. [Google Scholar] [CrossRef] [Green Version]
  64. Mai, K.; Li, D.; Wu, J.; Wu, Z.; Cheng, J.; He, L.; Tang, X.; Zhou, Z.; Sun, Y.; Ma, J. Complete Genome Sequences of Two Porcine Deltacoronavirus Strains, CHN-GD16-03 and CHN-GD16-05, Isolated in Southern China, 2016. Genome Announc. 2018, 6, e01545-17. [Google Scholar] [CrossRef] [Green Version]
  65. Dong, N.; Fang, L.; Yang, H.; Liu, H.; Du, T.; Fang, P.; Wang, D.; Chen, H.; Xiao, S. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014. Vet. Microbiol. 2016, 196, 98–106. [Google Scholar] [CrossRef]
  66. Wang, M.; Wang, Y.; Baloch, A.R.; Pan, Y.; Tian, L.; Xu, F.; Shivaramu, S.; Chen, S.; Zeng, Q. Detection and genetic characterization of porcine deltacoronavirus in Tibetan pigs surrounding the Qinghai-Tibet Plateau of China. Transbound Emerg. Dis. 2018, 65, 363–369. [Google Scholar] [CrossRef]
  67. Liang, Q.; Li, B.; Zhang, H.; Hu, H. Complete Genome Sequences of Two Porcine Deltacoronavirus Strains from Henan Province, China. Microbiol. Resour. Announc. 2019, 8, e01517-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  68. Zhao, F.; Sun, Y.; Qian, B.; Zhang, X.; Wu, Y. Complete Genome Characterization of Chinese Porcine Deltacoronavirus Strain CHN/Tianjin/2016. Genome Announc. 2017, 5, e00237-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  69. Zhang, M.; Ye, Y.; Gong, W.; Guo, N.; Zhang, F.; Li, A.; Zhou, X.; Huang, D.; Song, D.; Tang, Y. Complete Genome Sequence of Porcine Deltacoronavirus Strain CH/JXJGS01/2016, Isolated in Jiangxi Province, China, 2016. Genome Announc. 2017, 5, e00832-17. [Google Scholar] [CrossRef] [Green Version]
  70. Yang, D.; Ju, H.; Wang, J.; Bai, Y.; Ge, F.; Liu, J.; Li, X.; Sun, Q.; Yang, X.C.; Zhu, J.; et al. Genome sequencing and analysis of a porcine delta coronavirus from eastern China. Eur. J. Exp. Biol. 2017, 7, 25. [Google Scholar] [CrossRef]
  71. Zhang, M.J.; Liu, D.J.; Liu, X.L.; Ge, X.Y.; Jongkaewwattana, A.; He, Q.G.; Luo, R. Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China. Arch. Virol. 2019, 164, 413–425. [Google Scholar] [CrossRef] [Green Version]
  72. Xu, Z.; Zhong, H.; Zhou, Q.; Du, Y.; Chen, L.; Zhang, Y.; Xue, C.; Cao, Y. A Highly Pathogenic Strain of Porcine Deltacoronavirus Caused Watery Diarrhea in Newborn Piglets. Virol. Sin. 2018, 33, 131–141. [Google Scholar] [CrossRef] [Green Version]
  73. Liu, B.J.; Zuo, Y.Z.; Gu, W.Y.; Luo, S.X.; Shi, Q.K.; Hou, L.S.; Zhong, F.; Fan, J.H. Isolation and phylogenetic analysis of porcine deltacoronavirus from pigs with diarrhoea in Hebei province, China. Transbound Emerg. Dis. 2018, 65, 874–882. [Google Scholar] [CrossRef] [Green Version]
  74. Zhou, X.; Zhou, L.; Zhang, P.; Ge, X.; Guo, X.; Han, J.; Zhang, Y.; Yang, H. A strain of porcine deltacoronavirus: Genomic characterization, pathogenicity and its full-length cDNA infectious clone. Transbound Emerg. Dis. 2021, 68, 2130–2146. [Google Scholar] [CrossRef]
  75. Zhang, H.; Liang, Q.; Li, B.; Cui, X.; Wei, X.; Ding, Q.; Wang, Y.; Hu, H. Prevalence, phylogenetic and evolutionary analysis of porcine deltacoronavirus in Henan province, China. Prev. Vet. Med. 2019, 166, 8–15. [Google Scholar] [CrossRef] [PubMed]
  76. Zhao, Y.; Qu, H.; Hu, J.; Fu, J.; Chen, R.; Li, C.; Cao, S.; Wen, Y.; Wu, R.; Zhao, Q.; et al. Characterization and Pathogenicity of the Porcine Deltacoronavirus Isolated in Southwest China. Viruses 2019, 11, 1074. [Google Scholar] [CrossRef] [Green Version]
  77. Qian, S.; Jia, X.; Gao, Z.; Zhang, W.; Xu, Q.; Li, Z. Isolation and Identification of Porcine Deltacoronavirus and Alteration of Immunoglobulin Transport Receptors in the Intestinal Mucosa of PDCoV-Infected Piglets. Viruses 2020, 12, 79. [Google Scholar] [CrossRef] [Green Version]
  78. Janetanakit, T.; Lumyai, M.; Bunpapong, N.; Boonyapisitsopa, S.; Chaiyawong, S.; Nonthabenjawan, N.; Kesdaengsakonwut, S.; Amonsin, A. Porcine Deltacoronavirus, Thailand, 2015. Emerg. Infect. Dis. 2016, 22, 757–759. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  79. Madapong, A.; Saeng-Chuto, K.; Lorsirigool, A.; Temeeyasen, G.; Srijangwad, A.; Tripipat, T.; Wegner, M.; Nilubol, D. Complete Genome Sequence of Porcine Deltacoronavirus Isolated in Thailand in 2015. Genome Announc. 2016, 4, e00408-16. [Google Scholar] [CrossRef] [Green Version]
  80. Saeng-Chuto, K.; Stott, C.J.; Wegner, M.; Senasuthum, R.; Tantituvanont, A.; Nilubol, D. Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015. Arch. Virol. 2017, 162, 2103–2108. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  81. Le, V.P.; Song, S.; An, B.H.; Park, G.N.; Pham, N.T.; Le, D.Q.; Nguyen, V.T.; Vu, T.T.H.; Kim, K.S.; Choe, S.; et al. A novel strain of porcine deltacoronavirus in Vietnam. Arch. Virol. 2018, 163, 203–207. [Google Scholar] [CrossRef] [Green Version]
  82. Saeng-Chuto, K.; Jermsutjarit, P.; Stott, C.J.; Vui, D.T.; Tantituvanont, A.; Nilubol, D. Retrospective study, full-length genome characterization and evaluation of viral infectivity and pathogenicity of chimeric porcine deltacoronavirus detected in Vietnam. Transbound Emerg. Dis. 2020, 67, 183–198. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  83. Nakamura, T.; Yamada, K.D.; Tomii, K.; Katoh, K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2018, 34, 2490–2492. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  84. Saeng-Chuto, K.; Madapong, A.; Kaeoket, K.; Pineyro, P.E.; Tantituvanont, A.; Nilubol, D. Coinfection of porcine deltacoronavirus and porcine epidemic diarrhea virus increases disease severity, cell trophism and earlier upregulation of IFN-alpha and IL12. Sci. Rep. 2021, 11, 3040. [Google Scholar] [CrossRef] [PubMed]
  85. Zhang, H.; Han, F.; Shu, X.; Li, Q.; Ding, Q.; Hao, C.; Yan, X.; Xu, M.; Hu, H. Co-infection of porcine epidemic diarrhoea virus and porcine deltacoronavirus enhances the disease severity in piglets. Transbound Emerg. Dis. 2021. [Google Scholar] [CrossRef]
  86. Animal and Plant Health Inspection Service. Available online: https://www.aasv.org/pedv/SECD_Situation_Report_180308.pdf (accessed on 15 October 2021).
  87. Su, M.; Qi, S.; Yang, D.; Guo, D.; Yin, B.; Sun, D. Coinfection and Genetic Characterization of Porcine Astrovirus in Diarrheic Piglets in China from 2015 to 2018. Front. Vet. Sci. 2020, 7, 462. [Google Scholar] [CrossRef]
  88. Millet, J.K.; Jaimes, J.A.; Whittaker, G.R. Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol. Rev. 2021, 45, fuaa057. [Google Scholar] [CrossRef]
  89. Wang, B.; Liu, Y.; Ji, C.M.; Yang, Y.L.; Liang, Q.Z.; Zhao, P.; Xu, L.D.; Lei, X.M.; Luo, W.T.; Qin, P.; et al. Porcine Deltacoronavirus Engages the Transmissible Gastroenteritis Virus Functional Receptor Porcine Aminopeptidase N for Infectious Cellular Entry. J. Virol. 2018, 92, e00318-18. [Google Scholar] [CrossRef] [Green Version]
  90. Li, W.; Hulswit, R.J.G.; Kenney, S.P.; Widjaja, I.; Jung, K.; Alhamo, M.A.; van Dieren, B.; van Kuppeveld, F.J.M.; Saif, L.J.; Bosch, B.J. Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility. Proc. Natl. Acad. Sci. USA 2018, 115, E5135–E5143. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  91. Zhu, X.; Liu, S.; Wang, X.; Luo, Z.; Shi, Y.; Wang, D.; Peng, G.; Chen, H.; Fang, L.; Xiao, S. Contribution of porcine aminopeptidase N to porcine deltacoronavirus infection. Emerg. Microbes Infect. 2018, 7, 65. [Google Scholar] [CrossRef]
  92. Xu, K.; Zhou, Y.; Mu, Y.; Liu, Z.; Hou, S.; Xiong, Y.; Fang, L.; Ge, C.; Wei, Y.; Zhang, X.; et al. CD163 and pAPN double-knockout pigs are resistant to PRRSV and TGEV and exhibit decreased susceptibility to PDCoV while maintaining normal production performance. eLife 2020, 9, e57132. [Google Scholar] [CrossRef] [PubMed]
  93. Yuan, Y.; Zu, S.; Zhang, Y.; Zhao, F.; Jin, X.; Hu, H. Porcine Deltacoronavirus Utilizes Sialic Acid as an Attachment Receptor and Trypsin Can Influence the Binding Activity. Viruses 2021, 13, 2442. [Google Scholar] [CrossRef] [PubMed]
  94. Stoian, A.; Rowland, R.R.R.; Petrovan, V.; Sheahan, M.; Samuel, M.S.; Whitworth, K.M.; Wells, K.D.; Zhang, J.; Beaton, B.; Cigan, M.; et al. The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV). Virology 2020, 541, 136–140. [Google Scholar] [CrossRef]
  95. Zhang, J.; Chen, J.; Shi, D.; Shi, H.; Zhang, X.; Liu, J.; Cao, L.; Zhu, X.; Liu, Y.; Wang, X.; et al. Porcine deltacoronavirus enters cells via two pathways: A protease-mediated one at the cell surface and another facilitated by cathepsins in the endosome. J. Biol. Chem. 2019, 294, 9830–9843. [Google Scholar] [CrossRef]
  96. Fang, P.; Zhang, J.; Zhang, H.; Xia, S.; Ren, J.; Tian, L.; Bai, D.; Fang, L.; Xiao, S. Porcine deltacoronavirus enters porcine IPI-2I intestinal epithelial cells via macropinocytosis and clathrin-mediated endocytosis dependent on pH and dynamin. J. Virol. 2021, 95, e01345-21. [Google Scholar] [CrossRef]
  97. Yang, Y.L.; Liu, J.; Wang, T.Y.; Chen, M.; Wang, G.; Yang, Y.B.; Geng, X.; Sun, M.X.; Meng, F.; Tang, Y.D.; et al. Aminopeptidase N Is an Entry Co-factor Triggering Porcine Deltacoronavirus Entry via an Endocytotic Pathway. J. Virol. 2021, 95, e0094421. [Google Scholar] [CrossRef] [PubMed]
  98. Jung, K.; Miyazaki, A.; Hu, H.; Saif, L.J. Susceptibility of porcine IPEC-J2 intestinal epithelial cells to infection with porcine deltacoronavirus (PDCoV) and serum cytokine responses of gnotobiotic pigs to acute infection with IPEC-J2 cell culture-passaged PDCoV. Vet. Microbiol. 2018, 221, 49–58. [Google Scholar] [CrossRef]
  99. Wang, X.; Fang, L.; Liu, S.; Ke, W.; Wang, D.; Peng, G.; Xiao, S. Susceptibility of porcine IPI-2I intestinal epithelial cells to infection with swine enteric coronaviruses. Vet. Microbiol. 2019, 233, 21–27. [Google Scholar] [CrossRef]
  100. Fang, P.; Zhang, H.; Sun, H.; Wang, G.; Xia, S.; Ren, J.; Zhang, J.; Tian, L.; Fang, L.; Xiao, S. Construction, Characterization and Application of Recombinant Porcine Deltacoronavirus Expressing Nanoluciferase. Viruses 2021, 13, 1991. [Google Scholar] [CrossRef]
  101. Jung, K.; Vasquez-Lee, M.; Saif, L.J. Replicative capacity of porcine deltacoronavirus and porcine epidemic diarrhea virus in primary bovine mesenchymal cells. Vet. Microbiol. 2020, 244, 108660. [Google Scholar] [CrossRef] [PubMed]
  102. Hu, B.; Guo, H.; Zhou, P.; Shi, Z.L. Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol. 2021, 19, 141–154. [Google Scholar] [CrossRef]
  103. de Wit, E.; van Doremalen, N.; Falzarano, D.; Munster, V.J. SARS and MERS: Recent insights into emerging coronaviruses. Nat. Rev. Microbiol. 2016, 14, 523–534. [Google Scholar] [CrossRef]
  104. Corman, V.M.; Baldwin, H.J.; Tateno, A.F.; Zerbinati, R.M.; Annan, A.; Owusu, M.; Nkrumah, E.E.; Maganga, G.D.; Oppong, S.; Adu-Sarkodie, Y.; et al. Evidence for an Ancestral Association of Human Coronavirus 229E with Bats. J. Virol. 2015, 89, 11858–11870. [Google Scholar] [CrossRef] [Green Version]
  105. Corman, V.M.; Eckerle, I.; Memish, Z.A.; Liljander, A.M.; Dijkman, R.; Jonsdottir, H.; Juma Ngeiywa, K.J.; Kamau, E.; Younan, M.; Al Masri, M.; et al. Link of a ubiquitous human coronavirus to dromedary camels. Proc. Natl. Acad. Sci. USA 2016, 113, 9864–9869. [Google Scholar] [CrossRef] [Green Version]
  106. Su, S.; Wong, G.; Shi, W.; Liu, J.; Lai, A.C.K.; Zhou, J.; Liu, W.; Bi, Y.; Gao, G.F. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol. 2016, 24, 490–502. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  107. Tao, Y.; Shi, M.; Chommanard, C.; Queen, K.; Zhang, J.; Markotter, W.; Kuzmin, I.V.; Holmes, E.C.; Tong, S. Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History. J. Virol. 2017, 91, e01953-16. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  108. Zhang, X.M.; Herbst, W.; Kousoulas, K.G.; Storz, J. Biological and genetic characterization of a hemagglutinating coronavirus isolated from a diarrhoeic child. J. Med. Virol. 1994, 44, 152–161. [Google Scholar] [CrossRef]
  109. Vlasova, A.N.; Diaz, A.; Damtie, D.; Xiu, L.; Toh, T.H.; Lee, J.S.; Saif, L.J.; Gray, G.C. Novel Canine Coronavirus Isolated from a Hospitalized Pneumonia Patient, East Malaysia. Clin. Infect. Dis. 2021, ciab456. [Google Scholar] [CrossRef]
  110. Lednicky, J.A.; Tagliamonte, M.S.; White, S.K.; Blohm, G.M.; Alam, M.M.; Iovine, N.M.; Salemi, M.; Mavian, C.; Morris, J.G. Isolation of a Novel Recombinant Canine Coronavirus from a Visitor to Haiti: Further Evidence of Transmission of Coronaviruses of Zoonotic Origin to Humans. Clin. Infect. Dis. 2021, ciab924. [Google Scholar] [CrossRef] [PubMed]
  111. Li, Y.; Edwards, J.; Wang, Y.; Zhang, G.; Cai, C.; Zhao, M.; Huang, B.; Robertson, I.D. Prevalence, distribution and risk factors of farmer reported swine influenza infection in Guangdong Province, China. Prev. Vet. Med. 2019, 167, 1–8. [Google Scholar] [CrossRef]
  112. Li, Y.; Edwards, J.; Huang, B.; Shen, C.; Cai, C.; Wang, Y.; Zhang, G.; Robertson, I. Risk of zoonotic transmission of swine influenza at the human-pig interface in Guangdong Province, China. Zoonoses Public Health 2020, 67, 607–616. [Google Scholar] [CrossRef] [PubMed]
  113. Alagaili, A.N.; Briese, T.; Mishra, N.; Kapoor, V.; Sameroff, S.C.; Burbelo, P.D.; de Wit, E.; Munster, V.J.; Hensley, L.E.; Zalmout, I.S.; et al. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. mBio 2014, 5, e00884-14. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  114. Reusken, C.B.; Haagmans, B.L.; Muller, M.A.; Gutierrez, C.; Godeke, G.J.; Meyer, B.; Muth, D.; Raj, V.S.; Smits-De Vries, L.; Corman, V.M.; et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: A comparative serological study. Lancet Infect. Dis. 2013, 13, 859–866. [Google Scholar] [CrossRef] [Green Version]
Pathogens 11 00079 g001 550
Figure 1. Identification of PDCoV-AH2004 strain as potential recombinant strain using Recombination Identification Program (http://www.hiv.lanl.gov/content/sequence/RIP/RIP.html, accessed on: 28 November 2021). At each position of the window, the query sequence PDCoV-AH2004 was compared with background sequences for 5 avian δ-CoVs (sparrow δ-CoVs HKU17 and ISU73347, quail δ-CoV HKU30, munia δ-CoV HKU13, and bulbul δ-CoV HKU11). The x-axis represents the length of the PDCoV genome, and the y-axis represents the similarity value. When the query sequence is like the background sequence, the homologous regions are indicated as thick dashed lines (of the corresponding color) on the top of the plot. Arrows represent potential recombination breakpoints.
Figure 1. Identification of PDCoV-AH2004 strain as potential recombinant strain using Recombination Identification Program (http://www.hiv.lanl.gov/content/sequence/RIP/RIP.html, accessed on: 28 November 2021). At each position of the window, the query sequence PDCoV-AH2004 was compared with background sequences for 5 avian δ-CoVs (sparrow δ-CoVs HKU17 and ISU73347, quail δ-CoV HKU30, munia δ-CoV HKU13, and bulbul δ-CoV HKU11). The x-axis represents the length of the PDCoV genome, and the y-axis represents the similarity value. When the query sequence is like the background sequence, the homologous regions are indicated as thick dashed lines (of the corresponding color) on the top of the plot. Arrows represent potential recombination breakpoints.
Pathogens 11 00079 g001
Pathogens 11 00079 g002 550
Figure 2. Likely origin and routes of cross-species transmission of PDCoV. The red dashed line indicates potential, but unknown, transmission of δ-CoVs from avian to mammalian species; the blue dashed line indicates potential transmission of PDCoV based on epidemiology or experimental studies.
Figure 2. Likely origin and routes of cross-species transmission of PDCoV. The red dashed line indicates potential, but unknown, transmission of δ-CoVs from avian to mammalian species; the blue dashed line indicates potential transmission of PDCoV based on epidemiology or experimental studies.
Pathogens 11 00079 g002
Pathogens 11 00079 g003 550
Figure 3. Phylogenetic analyses of PDCoV based on 122 complete genomes. Genome sequences were aligned with MAFFT v.7.490 [83]. The phylogenetic tree was constructed using the neighbour-joining method of MEGA 11, and bootstrap values (1000 replicates) above 70% are shown. The bar represents a corrected genetic distance. The red circles indicate PDCoV strains from China but that fall into non-Chinese lineages; the blue circles indicate PDCoV strains from humans in Haiti.
Figure 3. Phylogenetic analyses of PDCoV based on 122 complete genomes. Genome sequences were aligned with MAFFT v.7.490 [83]. The phylogenetic tree was constructed using the neighbour-joining method of MEGA 11, and bootstrap values (1000 replicates) above 70% are shown. The bar represents a corrected genetic distance. The red circles indicate PDCoV strains from China but that fall into non-Chinese lineages; the blue circles indicate PDCoV strains from humans in Haiti.
Pathogens 11 00079 g003
Table
Table 1. Complete genome information on PDCoV strains.
Table 1. Complete genome information on PDCoV strains.
LineageGenBank Accession No.Strain NameCountriesCollection DateHostReference
USKJ462462.1OH1987USA31-Jan-2014Pig[9]
KJ481931.1PDCoV/USA/Illinois121/2014USA04-Jan-2014Pig[54]
KJ567050.18734/USA-IA/2014USA20-Feb-2014Pig[55]
KJ569769.1IN2847USA13-Feb-2014Pig[56]
KJ584355.1IL2768USA12-Feb-2014Pig[57]
KJ584356.1SD3423USA20-Feb-2014Pig[57]
KJ584357.1KY4813USA07-Mar-2014Pig[57]
KJ584358.1PA3148USA18-Feb-2014Pig[57]
KJ584359.1NE3579USA21-Feb-2014Pig[57]
KJ620016.1MI6148USA18-Mar-2014Pig[57]
KM012168.1Michigan/8977/2014USA17-Mar-2014PigUnpublished
KR150443.1USA/Arkansas61/2015USA24-Mar-2015PigUnpublished
KR265847.1USA/Minnesota442/2014USA06-Mar-2014PigUnpublished
KR265848.1USA/Minnesota214/2014USA14-Mar-2014PigUnpublished
KR265849.1USA/Michigan447/2014USA02-Apr-2014PigUnpublished
KR265850.1USA/Michigan448/2014USA02-Apr-2014PigUnpublished
KR265851.1USA/Indiana453/2014USA13-May-2014PigUnpublished
KR265852.1USA/Illinois449/2014USA21-Apr-2014PigUnpublished
KR265853.1USA/Minnesota/2013USA14-Oct-2013PigUnpublished
KR265854.1USA/Minnesota454/2014USA21-May-2014PigUnpublished
KR265855.1USA/Minnesota455/2014USA21-May-2014PigUnpublished
KR265856.1USA/Illinois272/2014USA23-Feb-2014PigUnpublished
KR265857.1USA/Illinois273/2014USA23-Feb-2014PigUnpublished
KR265858.1USA/NorthCarolina452/2014USA06-May-2014PigUnpublished
KR265859.1USA/Minnesota159/2014USA11-Feb-2014PigUnpublished
KR265860.1USA/Nebraska209/2014USA05-Feb-2014PigUnpublished
KR265861.1USA/Nebraska210/2014USA05-Feb-2014PigUnpublished
KR265862.1USA/Ohio444/2014USA26-Mar-2014PigUnpublished
KR265863.1USA/Ohio445/2014USA27-Mar-2014PigUnpublished
KR265864.1USA/Minnesota292/2014USA14-Mar-2014PigUnpublished
KR265865.1USA/Iowa459/2014USA05-Jun-2014PigUnpublished
KT381613.1OH11846USA07-May-2014Pig[58]
KX022602.1PDCoV/USA/Iowa136/2015USA15-Oct-2015PigUnpublished
KX022603.1PDCoV/USA/Minnesota140/2015USA18-Dec-2015PigUnpublished
KX022604.1PDCoV/USA/Nebraska137/2015USA27-Nov-2015PigUnpublished
KX022605.1PDCoV/USA/Nebraska145/2015USA21-Dec-2015PigUnpublished
MZ291567.1OH-FD22 P7USA2014Pig[59]
KY354363.1DH1South Korea01-Apr-2016Pig[60]
KY354364.1DH2South Korea01-Apr-2016Pig[60]
KY364365.1KNU16-07South KoreaJul-2014Pig[61]
KY926512.1KNU16-11South KoreaNov-2016Pig[62]
KM820765.1KNU14-04South KoreaApr-2014Pig[43]
LC260038.1AKT/JPN/2014JapanMay-2014Pig[47]
LC260039.1GNM-1/JPN/2014JapanMay-2014Pig[47]
LC260040.1GNM-2/JPN/2014JapanMay-2014Pig[47]
LC260041.1IWT/JPN/2014JapanMay-2014Pig[47]
LC260042.1MYZ/JPN/2014JapanMay-2014Pig[47]
LC260043.1OKN/JPN/2014JapanAug-2014Pig[47]
LC260044.1YMG/JPN/2014JapanDec-2014Pig[47]
LC260045.1HKD/JPN/2016JapanSep-2016Pig[63]
KY363868.1CHN-GD16-05China05-Jan-2016Pig[64]
MN781985.1CHzmd2019ChinaUnknownPigUnpublished
MZ802955.1CH-HLJ-20ChinaSep-2020PigUnpublished
MW685623.1PDCoV/Haiti/Human/0256-1/2015Haiti16-Mar-2015Human[18]
Early
Chinese		KP757890.1CHN-AH-2004China24-May-2004Pig[19]
KP757891.1CHN-HB-2014China26-Dec-2014Pig[19]
JQ065042.2HKU15-44China: Hong Kong2009Pig[7]
JQ065043.2HKU15-155China: Hong Kong2010Pig[7]
KT336560.1CHN-HN-2014China24-Nov-2014Pig[65]
KY513725.1CH/Jiangsu/2014China2014PigUnpublished
MF431742.1GDChina2015PigUnpublished
MF642322.1CHN/GS/2016/1ChinaAug-2016Pig[66]
MF642323.1CHN/GS/2016/2ChinaAug-2016Pig[66]
MF642324.1CHN/GS/2017/1ChinaApr-2017Pig[66]
MF642325.1CHN/QH/2017/1ChinaMar-2017Pig[66]
ChineseKP757892.1CHN-JS-2014China20-Dec-2014Pig[19]
KR131621.1PDCoV/CHJXNI2/2015ChinaMar-2015Pig[35]
KT021234.1CH/SXD1/2015China20-Mar-2015Pig[34]
KT266822.1CH/Sichuan/S27/2012China2012Pig[36]
KU665558.1CHN-LYG-2014China26-Jun-2014PigUnpublished
KU981059.1NHChina16-Feb-2015PigUnpublished
KX443143.2CH-01China2016Pig[67]
KY065120.1CHN/Tianjin/2016China2016Pig[68]
KY293677.1CH/JXJGS01/2016China23-May-2016Pig[69]
KY293678.1CH/JXJGS02/2016China23-May-2016PigUnpublished
KY363867.1CHN-GD16-03China18-Mar-2016Pig[64]
KY513724.1CH/Hunan/2014China2014PigUnpublished
MF041982.1SHJS/SL/2016China23-Dec-2016Pig[70]
MF095123.1CHN-HG-2017China15-Feb-2017Pig[71]
MF280390.1CHN-GD-2016China2016Pig[72]
MF431743.1SDChina2014PigUnpublished
MF948005.1HB-BDChina10-Aug-2017Pig[73]
MG242062.1CHN-HeB1-2017China2017PigUnpublished
MG832584.1CHN-HN-1601ChinaJul-2016Pig[74]
MH708123.1HNZK-02China20-Mar-2018Pig[67]
MH708124.1HNZK-04China20-Mar-2018Pig[75]
MH708125.1HNZK-06China20-Mar-2018Pig[75]
MH715491.1PDCoV/CHGD/2016China2016PigUnpublished
MK005882.1Swine/CHN/SC/2018/1ChinaMar-2018PigUnpublished
MK211169.1CHN/Sichuan/2017China24-Dec-2017PigUnpublished
MK330604.1CHN/Sichuan/2017ChinaFeb-2017PigUnpublished
MK330605.1CHN/Sichuan/2018ChinaJan-2018PigUnpublished
MK355396.1CHN-SC2015China20-Feb-2016Pig[76]
MK359104.1CHN-GX01-2018China2018Pig[53]
MK572803.1SCNC201705ChinaJun-2017PigUnpublished
MK625638.1CH/JXJGS01/2016ChinaOct-2018Pig[69]
MK625639.1CH/JXJGS01/2016ChinaOct-2018Pig[69]
MK625640.1CH/JXJGS01/2016ChinaOct-2018Pig[69]
MK625641.1CH/JXJGS01/2016ChinaOct-2018Pig[69]
MK993519.1CHN/Sichuan/2019ChinaJan-2019PigUnpublished
MN173779.1CHN-GX11-2018China2018Pig[53]
MN173780.1CHN-GX12-2018China2018Pig[53]
MN173781.1CHN-GX81-2018China2018Pig[53]
MN173782.1CHN-GX09-2018China2018Pig[53]
MN249445.1CHN-JS-2017China11-Dec-2017Pig[77]
MN942260.1PDCoV HeN/swine/2015China2015PigUnpublished
MW854634.1104-553China: TaiwanJun-2015Pig[46]
MT663769.1CHN-TS1-2019China23-Jul-2019PigUnpublished
MW685622.1PDCoV/Haiti/Human/0081-4/2014Haiti15-Dec-2014Human[18]
MW685624.1PDCoV/Haiti/Human/0329-4/2015Haiti13-Apr-2015Human[18]
Vietnam/
Laos/
Thailand		KU051641.1PDCoV/Swine/Thailand/S5011/2015Thailand10-Jun-2015Pig[78]
KU051649.1PDCoV/Swine/Thailand/S5015L/2015Thailand30-Jun-2015Pig[78]
KU984334.1TT_1115ThailandNov-2015Pig[79]
KX118627.1P1_16_BTL_0115/PDCoV/2016/LaoLaos20-Jan-2016Pig[44]
KX361343.1P1_13_ST1_0213/PDCoV/0213/ThailandThailandFeb-2013Pig[80]
KX361344.1P2_13_ST2_0313/PDCoV/0213/ThailandThailandMar-2013Pig[80]
KX361345.1P24_15_NT1_1215/PDCoV/2015/ThailandThailandDec-2015Pig[80]
KX834351.1PDCoV/Swine/Vietnam/HaNoi6/2015Vietnam10-Oct-2015Pig[81]
KX834352.1PDCoV/Swine/Vietnam/Binh21/2015Vietnam08-Dec-2015Pig[81]
KX998969.1P29_15_VN_1215VietnamDec-2015PigUnpublished
MH118332.1P19_16_VN_0416VietnamUnknownPig[82]
MN025260.1CH/GX/1468B/2017China18-Jan-2017Pig[52]
Table
Table 2. Co-infection of PDCoV with other porcine enteric viruses in pig farms or diarrheic samples from 2012 to 2018.
Table 2. Co-infection of PDCoV with other porcine enteric viruses in pig farms or diarrheic samples from 2012 to 2018.
YearCountryPathogensPositive Farms/Samples
(Positive Rate)		References
2014–2018United StatesPDCoV + PEDV307[86]
2014–2017MexicoPDCoV + PEDV46 (54.1%)[48]
PDCoV + TGEV9 (10.6%)
PDCoV + PEDV + TGEV16 (18.8%)
2014–2016South KoreaPDCoV + PEDV43 (6.3%)[62]
PDCoV + PRV19 (2.78%)
PDCoV + PEDV + PRV2 (0.29%)
2016–2018ChinaPDCoV + PEDV34 (4.73%)[37]
2012–2018PDCoV + PEDV380 (46.74%)[41]
PDCoV + TGEV30 (3.69%)
PDCoV + PEDV + PRV3 (0.37%)
PDCoV + PEDV + TGEV1 (0.12%)
2015–2018PDCoV + PAstV + PEV + TTSuV-2 + MRV + PKV1 (1.12%)[87]
PDCoV + PAstV + PEV + PKV + PBoV1 (1.12%)
PDCoV + PAstV + PTV + PSV + PEV + PKV + PBoV1 (1.12%)
PDCoV + PAstV + PTV + PSV + PKV + PBoV1 (1.12%)
PDCoV + PAstV + PTV + PSV + PEV + TTSuV-2 + PKV + PBoV1 (1.12%)
PDCoV + PAstV + PTV + PEV + TTSuV-2 + PToV + PBoV1 (1.12%)
PDCoV + PAstV + PEV + TTSuV-2 + PBoV1 (1.12%)
Table
Table 3. Cells susceptible to PDCoV infection in vitro.
Table 3. Cells susceptible to PDCoV infection in vitro.
Cell or Cell LineOriginReferences
LLC-PK1Porcine kidney proximal tubular epithelials cells[59]
STSwine testicular cells[59]
IPEC-J2Porcine small intestinal epithelial cells[98]
IPI-2IPorcine ileum epithelial cells[99]
IPAMImmortalized porcine cell line of pulmonary alveolar macrophages[100]
Huh7Human hepatoma cells[90]
A549Human lung carcinoma cells[100]
LMHChicken leghorn male hepatoma cells[90]
DF-1Chicken fibroblast cells[90]
White-feather broiler embryosWhite-feather broiler[16]
Hyline layer embryosHyline layer[16]
PBKPrimary bovine kidney cells[101]
PBHPrimary bovine heart cells[101]
MDBKMadin Darby bovine kidney cells[100]
VeroAfrican green monkey kidney epithelial cells[100]
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Kong, F.; Wang, Q.; Kenney, S.P.; Jung, K.; Vlasova, A.N.; Saif, L.J. Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential. Pathogens 2022, 11, 79. https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11010079

AMA Style

Kong F, Wang Q, Kenney SP, Jung K, Vlasova AN, Saif LJ. Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential. Pathogens. 2022; 11(1):79. https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11010079

Chicago/Turabian Style

Kong, Fanzhi, Qiuhong Wang, Scott P. Kenney, Kwonil Jung, Anastasia N. Vlasova, and Linda J. Saif. 2022. "Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential" Pathogens 11, no. 1: 79. https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11010079

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop