Two novel recombinant porcine reproductive and respiratory syndrome viruses belong to sublineage 3.5 originating from sublineage 3.2

Porcine reproductive and respiratory syndrome virus (PRRSV) is an agent of porcine reproductive and respiratory syndrome (PRRS), which causes substantial economic losses to the swine industry. PRRSV displays rapid variation, and five lineages coexist in mainland China. Lineage 3 PRRSVs emerged in mainland China in 2005 and prevailed in southern China after 2010. In the present study, two lineage 3 PRRSV strains, which are named SD110‐1608 and SDWH27‐1710, were isolated from northern China in 2017. To explore the characteristics and origins of the two strains, we divided lineage 3 into five sublineages (3.1–3.5) based on 146 open reading frame (ORF) 5 sequences. Both strains and the strains isolated from mainland China were classified into sublineage 3.5. Lineage 3 PRRSVs isolated from Taiwan and Hong Kong were classified into sublineages 3.1–3.3 and sublineage 3.4, respectively. Recombination analysis revealed that SD110‐1608 and SDWH27‐1710 were derived from recombination of QYYZ (major parent strain) and JXA1 (minor parent strain). Sequence alignment showed that SD110‐1608 and SDWH27‐1710 shared a 36‐aa insertion in Nsp2 with QYYZ isolated from Guangdong Province in 2010. Based on the evolutionary relationship among GP2a, GP3, GP4, GP5 and N proteins between sublineages 3.2 (FJ‐1) and 3.5 (FJFS), we speculated that sublineage 3.5 (mainland China) originated from sublineage 3.2 (Taiwan, China). This study provides important information regarding the classification and transmission of lineage 3 PRRSVs.     

Phylogeography,phylodynamics and the recent outbreak of lineage 3 porcine reproductive and respiratory syndrome viruses in China

Novel highly pathogenic porcine reproductive and respiratory syndrome viruses (PRRSVs) have attracted increasing attention owing to their continual high emergence and recent re‐emergence. Recently, lineage 3 PRRSVs, belonging to the type 2 viruses, with novel characteristics and increased virulence have been continuously re‐emerging in China, thereby posing a great threat to pig farming. However, available information about lineage 3 is limited. Here, we carried out molecular epidemiological investigations for PRRSV surveillance in most regions of China from 2007 to 2017. More than 3,000 samples were obtained, amounting to 73 sequences of lineage 3 viruses. The origin, demographic history and spread pattern of lineage 3 PRRSVs were investigated combining with the database globally. Phylogeography and phylodynamic analyses within a Bayesian statistical framework revealed that lineage 3 viruses originated in Taiwan. Followed by subsequent propagation to different areas and geography, it dichotomized into two endemic clusters. South China has become an epicentre for these viruses, which diffused into China's interiors in recent years. Furthermore, viral dispersal route analysis revealed the risk of viral diffusion. Overall, the origin, epidemic history and geographical evolution of lineage 3 PRRSVs were comprehensively analysed in this study. In particular, the epicentre of southern China and the diffusion routines of the viruses are highlighted in this study, and the possible continuous transmission of the novel lineages poses the biggest threat to pig farmers.     

Emergence of a novel highly pathogenic porcine reproductive and respiratory syndrome virus in China

From 2014 to 2015, four novel highly pathogenic PRRS virus (HP‐PRRSV) strains named 14LY01‐FJ, 14LY02‐FJ 15LY01‐FJ, and 15LY02‐FJ were isolated from high morbidity (100%) and mortality (40%–80%) in piglets and sows in Fujian Province. To further our knowledge about these novel virus strains, we characterized their complete genomes and determined their pathogenicity in piglets. Full‐length genome sequencing analysis showed that these four isolates were closely related to type 2 (North American type, NA‐type) isolates, with 88.1%–96.3% nucleotide similarity, but only 60.6%–60.8% homology to the Lelystad virus (LV) (European type, EU‐type). The full length of the four isolates was determined to be 15017 or 15018 nucleotides (nt), excluding the poly(A) tail. Furthermore, the four isolates had three discontinuous deletions (aa 322–432, aa 483, and aa 504–522) within hypervariable region II (HV‐II) of Nsp2, as compared to the reference strain VR‐2332. This deletion pattern in the four isolates is consistent with strain MN184 and strain NADC30 isolated from America. Phylogenetic and molecular evolutionary analyses indicated that these virulent strains originated from a natural recombination event between the JXA1‐like HP‐PRRSV (JXA‐1 is one of the earliest Chinese HP‐PRRSV strains; sublineage 8.7) and the NADC30‐like (lineage 1) PRRSV. Animal experiments demonstrated that these four strains caused significant weight loss and severe histopathological lung lesions as compared to the negative control group. High mortality rate (40% or 80%) was found in piglets infected with any one of the four strains, similar to that found with other Chinese HP‐PRRSV strains. This study showed that the novel variant PRRSV was HP‐PRRSV, and it is therefore critical to monitor PRRSV evolution in China and develop a method for controlling PRRS.     

Emergence of a virulent porcine reproductive and respiratory syndrome virus in Taiwan in 2018

In March 2018, an abortion storm caused by porcine reproductive and respiratory syndrome virus was confirmed in a farrow‐to‐finish pig herd in Taiwan. Open reading frame 5 and non‐structural protein 2 of the virus confirmed that the virus is closely related to the virulent strains circulating in the United States.     

Genetic characterization of a novel recombinant PRRSV2 from lineage 8, 1 and 3 in China with significant variation in replication efficiency and cytopathic effects

There are four major porcine reproductive and respiratory syndrome virus 2 (PRRSV2) lineages circulating in China based on classification system, including lineages 1 (NADC30‐like), 3 (QYYZ‐like), 5.1 (VR2332‐like) and 8 (JXA1‐like/CH‐1a‐Like), which leads to the potential recombination. In the present study, a novel variant of PRRSV2 strain named JS18‐3 was isolated from piglets suffering severe breathing difficulties in Jiangsu Province of China in 2018. Full‐length genome analysis indicated that JS18‐3 shared 86.5%, 87.9%, 84.2%, 82.2% and 86.4% nucleotide similarity with PRRSVs CH‐1a, JXA1, VR2332, QYYZ and NADC30, respectively. 4871–6635 of JS18‐3 shared the highest identity of 99.3% in nucleotide sequence with HP‐PRRSV representative strain JXA1 indicating ongoing evolution to HP‐PRRSV. JS18‐3 was classified into classical lineage 8 of PRRSV2 based on phylogenetic analysis of complete genome and ORF5. Genomic break points in structural (ORF3) and non‐structural (NSP2, NSP3) regions of genomes were detected in recombination analysis. JS18‐3 is a recombinant isolate from lineages 8, 1 and 3. Replication enhancement and severe cytopathic effects caused by JS18‐3 were observed in Marc‐145 cells and porcine alveolar macrophages (PAMs) as compared to JX07, a typical strain of lineage 8. Pathogenicity results indicated that piglets inoculated with JS18‐3 presented persistent fever, dyspnoea, serious microscopic lung lesions and lymph node congestion. The study suggests that lineage 8 of PRRSV2 is involved in continuing evolution by genetic recombination and mutation leading to outbreaks in vaccinated pigs in China.     

Pathogenicity of porcine reproductive and respiratory syndrome virus (ORF5 RFLP 1‐7‐4 viruses) in China

Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus that causes reproductive failure in sows and respiratory problems in piglets. PRRSV infection leads to substantial pig mortality and causing huge economic losses so that disease outbreaks caused by the new PRRSV strain from other regions have caused great concern in China. In this study, we analysed the pathogenicity of the novel ORF5 RFLP 1‐7‐4‐like PRRSV strain, named PRRSV‐ZDXYL‐China‐2018‐1 in pigs. The viral challenge test showed that PRRSV‐ZDXYL‐China‐2018‐1 infection can cause persistent fever, moderate dyspnoea, serum viraemia and interstitial pneumonia in piglets. The levels of viral loads in serum and PRRSV‐specific antigen were also detected in lung tissues were used one‐step Taq‐Man RT‐qPCR and Immunohistochemistry, respectively. At 28dpi, the level of specific antibodies was increased among infected piglets. Importantly, the new virus appeared be a moderately virulent isolate with pathogenicity compared to HP‐PRRSV strain LQ (JXA1‐like strain). Histological examination revealed severe monocyte haemorrhage and interstitial pneumonia associated with monocyte infiltration in the lung tissue of pigs infected with PRRSV‐ZDXYL‐China‐2018‐1 and LQ‐JXA1 strains. Immunohistochemistry (IHC) results showed positive brown‐red epithelial cells and macrophages in pig lungs. Therefore, it is critical to establish an effective strategy to control the spread of PRRSV in China.     

Visual detection of porcine reproductive and respiratory syndrome virus using CRISPR‐Cas13a

Porcine reproductive and respiratory syndrome virus (PRRSV) has varied constantly and circulated in the pig industry worldwide. The prevention and control of porcine reproductive and respiratory syndrome (PRRS) is complicated. A visual, sensitive and specific diagnostic method is advantageous to the control of PRRS. The collateral cleavage activity of LwCas13a is activated to degrade non‐targeted RNA, when crRNA of LwCas13a bond to target RNA. The enhanced Cas13a detection is the combination of collateral cleavage activity of LwCas13a and recombinase polymerase amplification (RPA). In this study, the enhanced Cas13a detection for PRRSV was established. The novel method was an isothermal detection at 37°C, and the detection can be used for real‐time analysis or visual readout. The detection limit of the enhanced Cas13a detection was 172 copies/μl, and there were no cross‐reactions with porcine circovirus 2, porcine parvovirus, classical swine fever virus and pseudorabies virus. The enhanced Cas13a detection can work well in clinical samples. In summary, a visual, sensitive and specific nucleic acid detection method based on CRISPR‐Cas13a was developed for PRRSV.     

The prevalence of novel porcine circovirus type 3 isolates in pig farms in China

The emerging porcine circovirus type 3 (PCV3) has been reported in Chinese swine herds since 2017. We performed a nationwide investigation on the prevalence of PCV3 in pig breeding farms and slaughterhouses in China. A total of 4,040 tonsil samples were collected from 89 farms in 25 provinces, and 1,419 lymph node samples were collected from 50 slaughterhouses in 27 provinces. The PCR results showed that in pig breeding farms, the positive rate was 41.6% (37/89) at the farm level and 5.0% (201/4040) at the individual level. In the slaughterhouses, the positive rate was 62.0% (31/50) at the farm level and 8.0% (114/1419) at the individual level. The PCR‐positive samples were further sequenced, and 19 new PCV3 isolates were identified. The complete genomes of the 19 virus isolates showed 97.4%–99.7% nucleotide identity with other PCV3 isolates. The phylogenetic analysis revealed that the 19 isolates were divided into PCV3a and PCV3b genotype clusters based on the PCV3 complete genome sequences. This study indicated that PCV3 has spread extensively in both pig breeding farms and slaughterhouses. The positive rate of PCV3 was higher in eastern China compared to other regions in China. Furthermore, this study will help us understand the prevalence and genetic variation of PCV3 in Chinese swine herds.     

A recombination between two Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV‐1) vaccine strains has caused severe outbreaks in Danish pigs

Porcine reproductive and respiratory syndrome virus (PRRSV) is prevalent in Danish swine herds. In July 2019, PRRSV‐1 was detected in a PRRSV‐negative boar station and subsequently spread to more than 38 herds that had received semen from the boar station. Full genome sequencing revealed a sequence of 15.098 nucleotides. Phylogenetic analyses showed that the strain was a recombination between the Amervac strain (Unistrain PRRS vaccine; Hipra) and the 96V198 strain (Suvaxyn PRRS; Zoetis AH). The major parent was the 96V198 strain that spanned ORFs 1–2 and part of ORF 3 and the minor parent was the Amervac strain, which constituted the remaining part of the genome. The virus seems to be highly transmissible and has caused severe disease in infected herds despite a high level of genetic identity to the attenuated parent strains. The source of infection was presumable a neighbouring farm situated 5.8 km from the boar station.     

Sequence and phylogenetic analyses of Nsp2‐HVII,ORF5, and ORF7 coding regions of highly pathogenic porcine reproductive and respiratory syndrome virus from Myanmar

In this study, PRRSVs that spread during the outbreaks of 2011 in Myanmar were investigated. Sequences and phylogenetic analyses of the Nsp2 middle hypervariable region (Nsp2‐HVII) encoding gene, ORF5, and ORF7 showed that they belonged to the North American (NA) genotype and were clustered with HP‐PRRSV strains from other Southeast Asian countries. The discontinuous 30‐amino acid deletions at positions 481 and 533–561 were found in the Nsp2‐HVII of all Myanmarese PRRSVs, implying their derivation from HP‐PRRSV. The phylogenetic trees also showed that Myanmarese strains were in the same group as other Southeast Asian strains from Cambodia, Thailand, and Laos suggesting their close relationships. Conversely, Vietnamese 07QN was in the same group as Chinese JXA1. The unique amino acid mutations found only in Myanmarese PRRSVs were L292F, P431S, and V621M in Nsp2‐HVII and E170G in GP5, which may be used as a marker for monitoring genetic diversity of newly emerging HP‐PRRSV strains.     

Assessment of area spread of porcine reproductive and respiratory syndrome (PRRS) virus in three clusters of swine farms

Despite decades of porcine reproductive and respiratory syndrome (PRRS ) research, outbreaks with emerging and re‐emerging PRRS virus (PRRSV ) strains are not uncommon in North America. The role of area spread, commonly referred but not limited to airborne transmission, in originating such outbreaks is currently unknown. The main objective of this study was to explore the role of area spread on the occurrence of new PRRSV cases by combining information on genetic similarity among recovered PRRSV isolate's open‐reading frame (ORF ) 5 sequences and publicly available weather data. Three small regions were enrolled in the study for which high farm‐level participation rate was achieved, and swine sites within those regions were readily sampled after reporting of an outbreak in a sow farm. Oral fluid PCR testing was used to determine PRRSV status of farms, and wind roses were generated for assessment of prevailing wind directions during 2–14 days preceding the outbreak. Under the conditions of this study, the data did not support the area spread theory as the main cause for these outbreaks. We suggest that for future studies, analysis of animal movement and other links between farms such as personnel, equipment and sharing of service providers should be incorporated for better insights on source of the virus. Furthermore, the development of rapid and easy diagnostic methods for ruling out resident PRRSV is urgently needed.     

Development of universal and quadruplex real‐time RT‐PCR assays for simultaneous detection and differentiation of porcine reproductive and respiratory syndrome viruses

Porcine reproductive and respiratory syndrome virus 1 (PRRSV1) and 2 (PRRSV2) (including 3 major subtypes: classical (CA‐PRRSV2), highly pathogenic (HP‐PRRSV2) and NADC30‐like (NL‐PRRSV2)) are currently coexisting in Chinese swine herds but with distinct virulence. Reliable detection and differentiation assays are crucial to monitor the prevalence of PRRSV and to adopt effective control strategies. However, current diagnostic methods cannot simultaneously differentiate the four major groups of PRRSV in China. In this study, universal and quadruplex real‐time RT‐PCR assays using TaqMan‐MGB probes were developed for simultaneous detection and differentiation of Chinese PRRSV isolates. The newly developed real‐time RT‐PCR assays exhibited good specificity, sensitivity, repeatability and reproducibility. In addition, the newly developed real‐time RT‐PCR assays were further validated by comparing with a universal PRRSV conventional RT‐PCR assay on the detection of 664 clinical samples collected from 2016 to 2019 in China. Based on the clinical performance, the agreements between the universal and quadruplex real‐time RT‐PCR assays and the conventional RT‐PCR assay were 99.55% and 99.40%, respectively. Totally 90 samples were detected as PRRSV‐positive, including 2 samples that were determined to be co‐infected with NL‐PRRSV2 and HP‐PRRSV2 isolates by the quadruplex real‐time RT‐PCR assay. ORF5 sequencing confirmed the real‐time RT‐PCR results that 2, 6, 27 and 57 of the 92 sequences were PRRSV1, CA‐PRRSV2, NL‐PRRSV2 and HP‐PRRSV2, respectively. This study provides promising alternative tools for simultaneous detection and differentiation of PRRSV circulating in Chinese swine herds.     

A modified‐live porcine reproductive and respiratory syndrome virus (PRRSV)‐1 vaccine protects late‐term pregnancy gilts against heterologous PRRSV‐1 but not PRRSV‐2 challenge

The objective of this study was to determine the efficacy of a commercially available porcine reproductive and respiratory syndrome virus (PRRSV )‐1 modified‐live virus (MLV ) vaccine against PRRSV ‐1 and PRRSV ‐2 challenge in late‐term pregnancy gilts. Gilts were vaccinated with the PRRSV ‐1 MLV vaccine at 4 weeks prior to breeding and then challenged intranasally with PRRSV ‐1 or PRRSV ‐2 at 93 days of gestation. After PRRSV ‐1 challenge, vaccinated pregnant gilts had a significantly longer gestation period, significantly higher numbers of live‐born and weaned piglets and a significantly lower number of stillborn piglets at birth compared to unvaccinated pregnant gilts. No significant improvement in reproductive performance was observed between vaccinated and unvaccinated pregnant gilts following PRRSV ‐2 challenge. Vaccinated pregnant gilts also exhibited a significantly improved reproductive performance after challenge with PRRSV ‐1 compared to vaccinated pregnant gilts following PRRSV ‐2 challenge. The PRRSV ‐1 MLV vaccine was able to reduce PRRSV ‐1 but not PRRSV ‐2 viremia in pregnant gilts. Vaccinated gilts also showed a significantly higher number of PRRSV ‐1‐specific IFN ‐γ‐secreting cells (IFN ‐γ‐SC ) compared to PRRSV ‐2‐specific IFN ‐γ‐SC . The data presented here suggest that the vaccination of pregnant gilts with a PRRSV ‐1 MLV vaccine provides good protection against PRRSV ‐1 but only limited protection against PRRSV ‐2 challenge in late‐term pregnancy gilts based on improvement of reproductive performance, reduction in viremia and induction of IFN ‐γ‐SC .     

Comparative Analysis of Immune Responses in Pigs to High and Low Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses Isolated in China

The CH‐1a and HuN4 strains of porcine reproductive and respiratory syndrome virus (PRRSV) show different pathogenicities in pigs. To understand host immune responses against these viruses, we investigated the dynamic changes in cytokine levels produced in peripheral blood of piglets infected with the highly pathogenic PRRSV HuN4 strain or the CH‐1a strain. Clinical signs, virus loads and serum cytokine levels [interferon(IFN)‐α, Interleukin (IL)‐1, TNF‐α, IL‐6, IL‐12, IFN‐γ, IL‐10 and TGF‐β] were tested. The results showed that while piglets developed effective cellular immune responses against CH‐1a infection, those infected with HuN4 displayed ineffective cellular immunity, organ lesions and persistent elevated levels of immunoregulatory cytokines (IL‐10 and TGF‐β), which delayed the development of PRRSV‐specific immune responses. These results demonstrated that HuN4 infection induced higher cytokine levels than that of CH‐1a infection induced. The changes in inflammatory cytokines intensified the inflammatory reaction and damaged the tissues and organs.     

Updated phylogenetic analysis of the spike gene and identification of a novel recombinant porcine epidemic diarrhoea virus strain in Taiwan

New variants of porcine epidemic diarrhoea virus (PEDV) causing a highly contagious intestinal disease, porcine epidemic diarrhoea virus (PED), have resulted in high mortality in suckling pigs across several countries since 2013. After 2015, the prevalence of the genogroup 2b (G2b) PEDVs decreased in a cyclical pattern with endemic seasonal outbreaks occasionally seen. To better understand the genetic diversity of PEDVs recently circulating in Taiwan, full‐length spike (S) genes of 31 PEDV strains from 28 pig farms collected during 2016–2018 were sequenced. While the majority of S gene sequences (from 27/28 farms) were closely related to the previous G2b PEDV strains, increased genetic diversities leading to several nonsynonymous mutations scattering in the neutralizing epitopes of the S gene were detected in PEDVs recently circulating in Taiwan. Furthermore, novel recombinant variants, the PEDV TW/Yunlin550/2018 strains exhibiting recombinant events between a previously isolated Taiwan PEDV G2b strain and a wild‐type PEDV G1a strain, were identified and further classified into a new genogroup, G1c. These results provide updated information about the genetic diversity of currently circulating PEDVs in the field and could help to develop more suitable strategies for controlling this disease.     

The detection of porcine circovirus 3 in Guangxi,China

Porcine circovirus type 3 (PCV 3) is a novel circovirus that was firstly detected in the USA . PCV 3 is associated with porcine dermatitis and nephropathy syndrome (PDNS ), reproductive failure and cardiac and multisystemic inflammation. Latterly, PCV 3 was detected in Guangxi, China. Forty‐one of 108 (37.96%) samples and nine of 47 (19.14%) samples were PCV 3 positive in pig farms and pig slaughter houses, respectively. Three PCV 3 strains were sequenced and designated PCV 3‐China/GX 2016‐1, PCV 3‐China/GX 2016‐2 and PCV 3‐China/GX 2016‐3. The complete genome of PCV 3‐China/GX 2016‐2 and PCV 3‐China/GX 2016‐3 is both 2,000 bp in length, while PCV 3‐China/GX 2016‐1 is of 1,999 bp and has a G deletion at position of 1,155 in its genome. The complete genome and capsid nucleotide of the three PCV 3 strains identified in this study shared 97.5%–99.4% and 96.7%–99.1% identities with that of the other PCV 3 strains available in NCBI , respectively. Phylogenetic analysis based on complete genome and capsid gene of 35 PCV 3 strains showed that the three PCV 3 sequences from Guangxi Province were divided into two clusters. The results of this study contribute to the understanding of PCV 3 molecular epidemiology.     

Phylogenetic and genomic characterization of a novel atypical porcine pestivirus in China

Atypical porcine pestivirus (APPV ) has been considered a novel pestivirus and causative agent of congenital tremor type A‐II . An APPV CH ‐GX 2016 strain was characterized from newly born piglets with clinical symptoms of congenital tremor in Guangxi, China. The genome of APPV CH ‐GX 2016 strain was 11,475 bp in length and encoded a polyprotein composed of the 3,635 amino acids. This genome sequence exhibited 88.0% to 90.8% nucleotide sequence homology with other APPV reference sequences in GenBank. Phylogenetic analysis further showed that APPV CH ‐GX is a novel pestivirus compared with previously described classical pestivirus strains. Therefore, APPV is present in pigs in China.     

A natural recombinant PRRSV between HP‐PRRSV JXA1‐like and NADC30‐like strains

Porcine reproductive and respiratory syndrome virus (PRRSV ) is a major economically significant pathogen that has adversely affected China's swine industry. Currently, a novel type 2 PRRSV , called the NADC 30‐like strain, is epidemic in numerous provinces of China, and commercial vaccines provide limited protection for infected animals. The extensive recombination phenomenon among NADC 30‐like PRRSV s is identified as a unique molecular characteristic of the virus. However, our understanding of how recombination influences NADC 30‐like PRRSV s is largely inadequate. In this study, we analysed the genetic characteristics of a recombinant NADC 30‐like PRRSV (SC ‐d) and examined its pathogenicity compared with a non‐recombinant NADC 30‐like PRRSV (SD ‐A19) and a highly pathogenic PRRSV (HuN4). SC ‐d has three discontinuous deletions in nsp2, consistent with NADC 30 isolated from the United States in 2008. Furthermore, we identified four recombination breakpoints in the SC ‐d genome, which separated the SC ‐d genome into four regions (regions A, B, C and D). Regions A and C are closely related to the JXA 1‐like strain, one of the earliest Chinese HP ‐PRRSV strains, and regions B and D are closely related to the NADC 30 strain. Moreover, SC ‐d inoculated piglets exhibited a persistent fever, moderate weight loss, mild thymus atrophy and obvious microscopic lung lesions. In summary, the recombinant NADC 30‐like PRRSV SC ‐d strain displayed a higher pathogenicity than the non‐recombinant NADC 30‐like PRRSV SD ‐A19 strain; however, the pathogenicity of the NADC 30‐like PRRSV SC ‐d was lower compared with the HP ‐PRRSV HuN4 strain in piglets. Our findings demonstrate that recombination is responsible for the enormous genetic diversity and pathogenicity variance of the NADC 30‐like PRRSV in China. This study provides a theoretical basis for developing a more reasonable PRRSV control and prevention strategy.     

Genome characterization of a porcine circovirus type 3 in South China

Porcine circovirus type 3 (PCV 3) is a novel circovirus that was associated with porcine dermatitis and nephropathy syndrome, reproductive failure, and multisystemic inflammation. Recently, a PCV 3 strain was identified from pyretic and pneumonic piglets in Guangdong province, China. This virus strain was sequenced and designated PCV 3‐China/GD 2016. The complete genome of PCV 3‐China/GD 2016 is 2,000 bp in length and shared 99.1% and 99.1% nucleotide identities with PCV 3/29160 and PCV 3/2164, respectively. [Corrections added after initial online publication on 13 March 2017: The numbers ‘98.5%’ and ‘97.4%’ has been changed to ‘99.1%’ and ‘99.1%’ in the previous sentence.] Phylogenetic analysis based on the complete genome showed that PCV 3‐China/GD 2016 clustered with the emerging PCV 3 and separated with other virus in genus Circovirus . The results of this study suggest that PCV 3 has existed within the pigs of China. It is urgent to investigate the pathogenicity and epidemiology of this novel circovirus China.