Insights into the evolutionary history and epidemiological characteristics of the emerging lineage 1 porcine reproductive and respiratory syndrome viruses in China.

The newly emerged lineage 1 porcine reproductive and respiratory syndrome viruses (PRRSVs) (especially the NADC30-like and NADC34-like viruses) have posed a direct threat to the Chinese pig industry since 2013. The phylogenetic, epidemic, and recombinant properties of these viruses have not yet systematically analysed in China. This report presents regular surveillance and field epidemiological studies for PRRSV across China from 2007 to 2019. From over 4,000 detected clinical samples, 70 open reading frame five sequences and four complete genomes of lineage 1 viruses were successfully obtained. Combined with global data, we conducted an extensive and systematic molecular phylogeny analysis using a maximum likelihood tree. The Chinese lineage 1 viruses were clustered, and their temporal and spatial distribution was further explored. Multiple viral introductions of lineage 1 virus from the United States to China were detected, and some became endemic in China. There are three sub-lineage 1 clusters: lineage 1.5 (NADC34-like), lineage 1.6 and New Intro cluster (NADC30-like). These viruses show high genetic diversity and a wide distribution in China, with Henan Province showing the highest diversity. Moreover, Chinese lineage 1 viruses have developed an endemic NADC30-like cluster. The demographic feature of this cluster showed a more or less constant population expansion history with a recent decreasing trend. Moreover, the genome recombination of Chinese lineage 1 with two dominant clusters (Chinese HP-PRRSVs: lineage 8.7 and VR2332-like: lineage 5.1) was frequently detected, both of which have commercial vaccine strains available. Furthermore, recombination hotspots were discovered near NSP9 and ORF2-4 regions of the genome. Overall, these findings provide important insights into the evolution and geographical diversity of Chinese lineage 1 PRRSV. These results will facilitate the development of programmes for the control and prevention of the emerging lineage 1 viruses in China.

Avian-origin H3N2 canine influenza virus circulating in farmed dogs in Guangdong, China.

Since 2006, more and more cases of the infectious H3N2 canine influenza virus (CIV) in pet dogs have been reported in Southern China. However, little is known about the prevalence situation of H3N2 CIV infections in farmed dogs in China. This is the first systematic epidemiological surveillance of CIV in different dog populations in Southern China. Two virus strains A/Canine/Guangdong/1/2011(H3N2) and A/canine/Guangdong/5/2011(H3N2) were isolated from canine nasal swabs collected at one dog farm in Guangzhou and the other farm in Shenzhen. Sequence and phylogenetic analysis of eight gene segments of these viruses revealed that they were most similar to the newly isolated canine H3N2 viruses in dogs and cats from Korea and China, which originated from avian strain. This indicates that H3N2 CIV may be a common pathogen for pet and farmed dog populations in Southern China at present. Serological surveillance has shown that the infection rate of this avian-origin canine influenza in farmed dogs and in pet dogs were 12.22% and 5.3%, respectively; as determined by the ELISA. The data also suggested that transmission occurred, most probably by close contact, between H3N2 CIV infected dogs in different dog populations in recently years. As H3N2 outbreaks among dogs continue in the Guangdong Province (located very close to Hong Kong), the areas where is densely populated and with frequent animal trade, there is a continued risk for pet H3N2 CIV infections and for mutations or genetic reassortment leading to new virus strains with increased transmissibility among dogs. Further in-depth study is required as the H3N2 CIV has been established in different dog populations and posed potential threat to public health.

Serologic reports of H3N2 canine influenza virus infection in dogs in northeast China.

Reports of dogs with H3N2 canine influenza virus (CIV) have been documented frequently. To better understand the seroprevalence of H3N2 CIV among dogs in northeast China, here we report for the first time a relatively high seroprevalence of H3N2 CIV infection in dogs in northeast China. Forty-five of the 223 canine sera (20.2%) and 166 of the 500 canine sera (33.2%) tested feral dogs and pet dogs were seropositive by NP-ELISA, which is higher than that in southern China. The relative data provided in this report can be useful for small animal practitioners or public health policy makers to carry out relative measures for the prevention of this disease. Meanwhile, similar seroprevalence studies and prospective natural history and incidence studies should also be undertaken in other places.

Avian-origin H3N2 canine influenza virus circulating in farmed dogs in Guangdong, China.

Since 2006, more and more cases of the infectious H3N2 canine influenza virus (CIV) in pet dogs have been reported in southern China. However, little is known about the prevalence situation of H3N2 CIV infections in farmed dogs in China. This is the first systematic epidemiological surveillance of CIV in different dog populations in southern China. Two virus strains A/Canine/Guangdong/1/2011(H3N2) and A/canine/Guangdong/5/2011(H3N2) were isolated from canine nasal swabs collected at one dog farm in Guangzhou and the other farm in Shenzhen. Sequence and phylogenetic analysis of eight gene segments of these viruses revealed that they were most similar to the newly isolated canine H3N2 viruses in dogs and cats from Korea and China, which originated from avian strain. This indicates that H3N2 CIV may be a common pathogen for pet and farmed dog populations in southern China at present. Serological surveillance has shown that the infection rate of this avian-origin canine influenza in farmed dogs and in pet dogs were 12.22% and 5.3%, respectively; as determined by the ELISA. The data also suggested that transmission occurred, most probably by close contact, between H3N2 CIV infected dogs in different dog populations in recently years. As H3N2 outbreaks among dogs continue in the Guangdong province (located very close to Hong Kong), the areas where is densely populated and with frequent animal trade, there is a continued risk for pets H3N2 CIV infections and for mutations or genetic reassortment leading to new virus strains with increased transmissibility among dogs. Further in-depth study is required as the H3N2 CIV has been established in different dog populations and posed potential threat to public health.

Complete genome sequence of a novel field strain of rearranged porcine circovirus type 2 in southern China.

We report here the complete genomic sequence of a novel porcine circovirus type 2 (PCV2) strain, which is supposed to be the result of natural genetic recombination between the ORF1 gene of genotype PCV2b-1B and the ORF2 gene of PCV2b-1C. Further analyses revealed that this novel PCV2 strain arose from recombination between PCV2a and PCV2b strains within the ORF2 gene. To our knowledge, this is the first report of both inter- and intragenotype PCV2 gene rearrangement in the field, and it will help in understanding the epidemiology and molecular characteristics of porcine circovirus type 2(PCV2) in southern China.

Complete genome sequence of a novel duck hepatitis A virus discovered in southern China.

We report here the complete genomic sequence of a novel duck hepatitis A virus (DHAV) isolated from mixed infections with DHAV type 1 (DHAV-1) and DHAV-3 in ducklings in Southern China. The whole nucleotide sequence had the highest homology with the sequence of DHAV-3 (GenBank accession number DQ812093) (96.2%). To our knowledge, this is the first report of gene rearrangement between DHAV-1 and DHAV-3, and it will help to understand the epidemiology and molecular characteristics of duck hepatitis A virus in Southern China.

Complete Genome Sequence of a Novel Avian-Like H3N2 Swine Influenza Virus Discovered in Southern China.

We report here the complete genomic sequence of a novel avian-like H3N2 swine influenza virus containing an H5N1 highly pathogenic avian influenza virus segment that was obtained from swine in southern China. Phylogenetic analysis indicated that this virus might originate from domestic aquatic birds. The sequence information provided herein suggests that continuing study is required to determine if this virus can be established in the swine population and pose potential threats to public health.