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A total of 472 samples from domestic pigs collected in China from 2015 to 2018 were tested for the presence of porcine circovirus types 2 and 3 (PCV2 and PCV3, respectively) by conventional polymerase chain reaction analysis. The prevalence of PCV2, PCV3, and PCV2/3 co-infection was 50.0%, 13.3%, and 6.78%, respectively. The complete genomic sequences of 66 PCV2 isolates and four PCV3 isolates were determined. Based phylogenetic analysis, the PCV2 isolates were assigned to three genotypes, PCV2a, PCV2b, and PCV2d, representing 13.6% (9/66), 25.8% (17/66), and 60.6% (40/66) of the total, respectively. All four PCV3 isolates shared a high degree of similarity in their complete nucleotide sequences (98.8–99.8% identity) and ORF2 amino acid sequences (98.6–99.5% identity). These results indicate that all three PCV2 genotypes (PCV2a, PCV2b, and PCV2d) are present on pig farms and that PCV2d has become the predominant genotype. The predicted amino acid sequences of the four PCV3 isolates indicated that PCV3-CN-JL53/PCV3-CN-LN56, PCV3-CN-HLJ3, and PCV3-CN-0710, belonged to the genotypes PCV3a, PCV3b, and PCV3a-IM, respectively. In view of the great harm that PCV2 causes to the pig industry, the epidemic trend of PCV3 should continue to be closely monitored. This study provides information about the prevalence, genetic diversity, and molecular epidemiology of PCV2 and PCV3 in China from 2015 to 2018. [ABSTRACT FROM AUTHOR]

In an effort to trace the evolution of porcine epidemic diarrhea virus (PEDV), S1 and ORF3 genes of viruses identified in 41 pig farms from seven regions (North, Northeast, Northwest, Central, East, South West, and South, respectively) of China in 2015 were sequenced and analyzed. Sequence analysis revealed that the 41 ORF3 genes and 29 S1 genes identified in our study exhibited nucleotide homologies of 98.2%–100% and 96.6%–100%, respectively; these two genes exhibited low nucleotide sequence similarities with classical CV777 strain and early Chinese strain LZC. Phylogenetic analysis indicated that the identified PEDV strains belonged to global non S-INDEL strains, and exhibited genetic diversity; S1 gene of the HLJ2015/DP1-1 strain harbored an unique deletion of 12 nucleotides (A1130CAACTCCACTG1141); while the Chinese PEDV S-INDEL reference strains included two types of the “CV777” S-INDEL as well as the “US” S-INDEL, and all co-circulated with Chinese non S-INDEL strains. Of 29 identified S1 genes, the SS2 epitope (Y748SNIGVCK755) was highly conserved, while the SS6 epitope (L764QDGQVKI771) and pAPN receptor-binding region (aa 490–615) exhibited amino substitutions. Nine possible recombination events were identified between the 29 identifed S1 genes and the 3 S1 reference genes from early Chinese PEDV strains. The complete S genes of selected Chinese PEDV field strains (2011–2015) showed 5.18%–6.07% nucleotide divergence, which is far higher than the divergence observed in early Chinese PEDV strains (3.1%) (P<0.05). Our data provide evidence that PEDV non S-INDEL strains with genetic diversities and potential recombination circulate in seven regions of China in 2015; Chinese PEDV S-INDEL strains exhibit genetic diversity and co-circulate with non S-INDEL strains. [ABSTRACT FROM AUTHOR]

In this study, we report the complete nucleotide sequence of porcine kobuvirus CH/HZ/2011 (CH/HZ) isolated from infected piglets in China. Dendrograms indicated that CH/HZ is closely related to other porcine kobuviruses. The complete genome sequence of CH/HZ has an adenine insertion at position 124, an 18-nt deletion in the 5′UTR, and a 90-nt deletion in the 2B coding region. A neighbor-joining tree based on the VP1 gene indicated that 31 porcine kobuvirus strains are divided into four clusters (Thai-Japanese group, Hungarian group, Chinese group I and Chinese group II). The strain CH/HZ was included in Chinese group II. [ABSTRACT FROM AUTHOR]

Porcine epidemic diarrhea virus (PEDV) poses a great threat to the Chinese swine industry. During 2006-2011, 74.0 % (94/127) of samples from 32 swine-raising farms in 15 provinces were positive for PEDV by reverse transcription nested polymerase chain reaction (RT-nested PCR). The sequences of nucleocapsid (N) genes of 32 representative field strains were determined, and the open reading frames (ORFs) of these N genes were 1326 nucleotides long. The N gene sequences were found to be more than 95 % identical to each other. The number of potential phosphorylation sites in the N protein varied from 5 to 12. A phylogenetic tree based on the N genes showed that the 32 Chinese field strains formed three groups. [ABSTRACT FROM AUTHOR]

The fifth most important G genotype, G9 rotavirus, is recognized as an emerging genotype that is spreading around the world. Sequence analysis was completed of a rare group A rotavirus, strain G9P[23], that was designated rotavirus A pig/China/NMTL/2008/G9P[23] and abbreviated as NMTL. It was isolated from a piglet with diarrhea in China. Nucleotide sequence analysis revealed that the VP7 gene clustered within the G9 lineage VId. The VP4 gene clustered within the rare P[23] genotype. NMTL is the first porcine G9 stain reported in China. Thus, to further characterize the evolutionary diversity of the NMTL strain, all gene segments were used to draw a phylogenetic tree. Based on the new classification system of rotaviruses, the NMTL sequence revealed a G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotype with close similarity to human Wa-like and porcine strains. The results showed that (i) NSP2 and NSP4 genes of NMTL exhibited higher genetic relatedness to human group A rotaviruses than to porcine strains, (ii) the VP2 and VP4 genes clustered with porcine and porcine-like human strains, and (iii) VP1 genes clustered apart from the Wa-like human and porcine clusters. In view of rotavirus evolution, this report provides additional evidence to support the notion that the human and porcine rotavirus genomes might be related. [ABSTRACT FROM AUTHOR]

Abstract: Since April 2006, swine herds have experienced the outbreaks of a highly pathogenic porcine reproductive and respiratory syndrome (PRRS) in China. To explore the possible mechanism of the emergence of the highly pathogenic PRRS and more fully understand the extent of genetic diversity of PRRSV in China, we analyzed the ORF5 gene sequences of 159 representative PRRSV isolates in 16 provinces from 2006 to 2008. Sequence and phylogenetic analyses showed that all these 159 isolates belonged to the North American genotype and were further divided into six subgenotypes; 140 of 159 isolates were closely related to the highly pathogenic PRRSV with 98.5–100% nucleotide and 98.3–100% amino acid sequence identities and belonged to Subgenotype I; and 3, 8, 4, 3, 1 of 159 isolates were part of Subgenotypes II–VI, respectively. Amino acid analysis of the GP5 protein revealed that all the isolates in Subgenotypes I–III were found to be highly variable in the primary neutralizing epitope; most of the isolates in Subgenotypes I and IV had more glycosylation sites than those in Subgenotypes II, III, V and VI; and 1, 5, and 9 unique amino acid mutations were observed in Subgenotypes I, IV and VI, respectively. In conclusion, our study provides the evidence of coexistence of six different subgenotype isolates in pigs in China from 2006 to 2008, and emphasizes the importance of reinforcing PRRSV surveillance, especially after the emergence of highly pathogenic PRRS in China. [Copyright &y& Elsevier]

Abstract: Objective: To determine the prevalence and genotype distribution of human papillomavirus (HPV) infection among Chinese patients with mucopurulent cervicitis (MPC) or cervical cancer (CC). Methods: In total, 191 cases of CC (n=66), acute MPC (n=84), and healthy cervix controls (n=41) were initially included; samples were collected between May 21, 2008, and October 9, 2011. Cervical specimens were screened for HPV using a nested polymerase chain reaction assay and DNA sequencing. Results: Overall prevalence of HPV infection was 20.0% in the control group, 53.3% in the MPC group, and 93.8% in the CC group. The predominant genotype detected in all 3 groups was the oncogenic variant HPV 16 (87.7%, 18.7%, and 10.0% in the CC, MPC and control specimens, respectively). The second most frequent genotype among patients with MPC was HPV 58. This variant is also oncogenic and was detected at a higher rate in the MPC group (9.3%) than in the control (2.5%) and CC (1.5%) groups. Conclusion: Infection with HPV was prevalent among Chinese women with MPC or CC. Furthermore, the high prevalence of oncogenic genotypes observed among HPV-positive patients with MPC suggests that this group is at increased risk of developing CC. [Copyright &y& Elsevier]

Amur virus was recently identified as the causative agent of hemorrhagic fever with renal syndrome. Here we report the complete genome sequence of an Amur virus isolated from Apodemus peninsulae in Northeastern China. The sequence information provided here is critical for the molecular epidemiology and evolution of Amur virus in China. [ABSTRACT FROM AUTHOR]

Here we report the complete genome sequence of a dengue virus serotype 2 (DENV-2) strain, GZ40, isolated in Guangdong, China, in 2010. A phylogenetic analysis classified GZ40 into the Cosmopolitan genotype, while previous Chinese DENV-2 isolates belong to the Asian I genotype. The reemergence of the Cosmopolitan genotype of DENV-2 in China deserves further investigation. [ABSTRACT FROM AUTHOR]