The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17

Chen, Qi; Wang, Leyi; Yang, Chang Yeol; Gauger, Phillip C.; Anderson, Tavis K.; Harmon, Karen M.; Zhang, Jianqiang; Yoon, Kyoung‐Jin; Main, Rodger; Li, Ganwu

doi:10.1038/s41426-018-0108-z

Cited by 36 publications

(43 citation statements)

References 7 publications

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“…The true incidence rates for PDCoV infection, natural host range, reservoirs, and routes of transmission are still relatively unknown, and no plans for vaccine development have been reported (37). DCoV RNA has been detected in fecal samples from wild birds (38,39), Chinese ferret badgers (Melogale moschata), and leopard cats (40). In addition to swine, calves have been shown by experimental testing to be susceptible to PDCoV infection (41).…”

Section: Discussionmentioning

confidence: 99%

Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1

Boley¹,

Alhamo²,

Lossie³

et al. 2020

Emerg. Infect. Dis.

124

101

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Section: Discussionmentioning

confidence: 99%

Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1

Boley¹,

Alhamo²,

Lossie³

et al. 2020

Emerg. Infect. Dis.

124

101

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“…Li et al [40] found a shared epitope, EXE/DPPFG, among six flaviviruses and verified the cross-reactivity by positive sera detection. Chen et al [41] found that PDCoV N gene-based PCR cross-reacts with SpDCoV because of their relatively conserved regions. The relationship between PDCoV and other animal-originated deltacoronavirus needs further exploration and whether PDCoV EP-4E88 cross-reacts with HKU17, ALCCoV, HKU30, or SpDCoV should be analyzed using two-way serum cross-reactivity.…”

Section: Discussionmentioning

confidence: 99%

Identification of a Novel Linear B-Cell Epitope on the Nucleocapsid Protein of Porcine Deltacoronavirus

Rui

et al. 2020

IJMS

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Porcine deltacoronavirus (PDCoV), first identified in 2012, is a swine enteropathogen now found in many countries. The nucleocapsid (N) protein, a core component of PDCoV, is essential for virus replication and is a significant candidate in the development of diagnostics for PDCoV. In this study, monoclonal antibodies (mAbs) were generated and tested for reactivity with three truncations of the full protein (N1, N2, N3) that contained partial overlaps; of the five monoclonals chosen tested, each reacted with only the N3 truncation. The antibody designated 4E88 had highest binding affinity with the N protein and was chosen for in-depth examination. The 4E88 epitope was located to amino acids 308-AKPKQQKKPKK-318 by testing the 4E88 monoclonal for reactivity with a series of N3 truncations, then the minimal epitope, 309-KPKQQKKPK-317 (designated EP-4E88), was pinpointed by testing the 4E88 monoclonal for reactivity with a series of synthetic peptides of this region. Homology analysis showed that the EP-4E88 sequence is highly conserved among PDCoV strains, and also shares high similarity with sparrow coronavirus (HKU17), Asian leopard cat coronavirus (ALCCoV), quail coronavirus (UAE-HKU30), and sparrow deltacoronavirus (SpDCoV). Of note, the PDCoV EP-4E88 sequence shared very low similarity (<22.2%) with other porcine coronaviruses (PEDV, TGEV, PRCV, SADS-CoV, PHEV), demonstrating that it is an epitope that can be used for distinguishing PDCoV and other porcine coronavirus. 3D structural analysis revealed that amino acids of EP-4E88 were in close proximity and may be exposed on the surface of the N protein.

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“…Next-generation sequencing and genome assembly. To obtain whole genomic sequences, the 102 samples from the United States were subjected to next-generation sequencing (NGS) on a MiSeq platform (Illumina, San Diego, CA, USA) as previously described (27). Specifically, the DNA from the extracted sample DNA/RNA was cleared with the RNase-free DNase set (Qiagen, Valencia, CA), and residual reagent was then removed from the remaining RNA with the Agencourt RNAClean XP kit (Beckman Coulter, Indianapolis, IN) according to the manual.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetics, Genomic Recombination, and NSP2 Polymorphic Patterns of Porcine Reproductive and Respiratory Syndrome Virus in China and the United States in 2014–2018

Yan

Shī

et al. 2020

J Virol

Self Cite

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Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen that affects the pig industry, is a highly genetically diverse RNA virus. However, the phylogenetic and genomic recombination properties of this virus have not been completely elucidated. In this study, comparative analyses of all available genomic sequences of North American (NA)-type PRRSVs (n = 355, including 138 PRRSV genomes sequenced in this study) in China and the United States during 2014–2018 revealed a high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and the GP2 to GP3 regions. Lineage 1 (L1) PRRSV was found to be susceptible to recombination among PRRSVs both in China and the United States. The recombinant major parent between the 1991–2013 data and the 2014–2018 data showed a trend from complex to simple. The major recombination pattern changed from an L8 to L1 backbone during 2014–2018 for Chinese PRRSVs, whereas L1 was always the major backbone for US PRRSVs. Intralineage recombination hot spots were not as concentrated as interlineage recombination hot spots. In the two main clades with differential diversity in L1, NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, NADC34-like PRRSVs have been relatively stable in population genetic diversity for years. Systematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patterns, which could generate novel references for the classification of PRRSVs. The results of this study contribute to a deeper understanding of the recombination of PRRSVs and indicate the need for coordinated epidemiological investigations among countries. IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.

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The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17

Cited by 36 publications

References 7 publications

Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1

Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1

Identification of a Novel Linear B-Cell Epitope on the Nucleocapsid Protein of Porcine Deltacoronavirus

Phylogenetics, Genomic Recombination, and NSP2 Polymorphic Patterns of Porcine Reproductive and Respiratory Syndrome Virus in China and the United States in 2014–2018

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