Genomic analysis reveals G3P[13] porcine rotavirus A interspecific transmission to human from pigs in a swine farm with diarrhoea outbreak.

Nan Yan1 Hua Yue2,1 Yuanwei Wang1 Bin Zhang2,1 Cheng Tang1,2
Affiliations 2 institutions
  1. College of Life Science and Technology, Southwest Minzu University, Chengdu, PR China.
  2. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, PR China.

Abstract

Rotavirus A (RVA) is a major diarrhoea-causing pathogen in young animals and children. The zoonotic potential of RVA has received extensive attention in recent years. In May 2018, an outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, PR China. RVA was detected in 95.7 % (22/23) of piglet samples, 60 % (9/15) of sow samples and 100 % (3/3) of pig-breeder faecal samples. The predominant RVA genotype on this swine farm was G3P[13], and G3P[13] RVA was also detected in the three breeder faecal samples. Three G3P[13] RVA strains were isolated from a piglet faecal sample, a sow faecal sample and a pig-breeder faecal sample, and were named SCLS-X1, SCLS-3 and SCLS-R3, respectively. The complete sequences of 11 gene segments of these three isolates were derived. Phylogenetic analysis showed that ten gene segments (VP7, VP4, VP1-VP3 and NSP1-NSP5) of pig-breeder isolate SCLS-R3 were closely related to pig isolates SCLS-X1 and SCLS-3 from this farm. Only the VP6 gene shared higher homology with human RVA strain I321. Therefore, a G3P[13] porcine RVA strain most likely infected pig breeders. These results provided the first complete epidemiological link demonstrating interspecies transmission of G3P[13] RVA from pigs to human. Our data contribute to an improved understanding of the genetic evolution and interspecies transmission of RVA.

Supporting text Virus Host Location
genome 8 interspecies transmission 51 pig 10 rotavirus A 12 Adult 71 Animals 1948 Diarrhea 29 Disease Outbreaks 170 Farms 30 Feces 113 Female 289 Genome, Viral 317 Humans 1440 Male 224 Phylogeny 805 Rotavirus 65 Rotavirus Infections 61 Swine 258 Swine Diseases 153 Viral Nonstructural Proteins 28

Evidence records

5 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type
1 records
OVE4347
Key finding

G3P[13] rotavirus A strains were successfully isolated from piglet, sow, and human pig-breeder faecal samples in Sichuan province, China.

Virus
Host
Location
Not specified
Supporting text

Three G3P[13] RVA strains were isolated from a piglet faecal sample, a sow faecal sample and a pig-breeder faecal sample, and were named SCLS-X1, SCLS-3 and SCLS-R3, respectively.

Sample type
faecal sample
Evidence type
1 records
OVE4346
Key finding

Rotavirus A (RVA) was detected in faecal samples from diarrhoeic piglets, sows, and pig-breeders during a swine farm outbreak in Sichuan province, PR China.

Virus
Host
Location
Supporting text

In May 2018, an outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, PR China. RVA was detected in 95.7 % (22/23) of piglet samples, 60 % (9/15) of sow samples and 100 % (3/3) of pig-breeder faecal samples.

Method
viral RNA detection | genomic analysis
Sample type
faecal samples
Geographic raw
Sichuan province, PR China
Country inferred
CHN
Transmission Evidence
2 records · 2 evidence types
Evidence type
1 records
OVE4348
Key finding

A G3P[13] porcine rotavirus A strain spilled over from pigs to human pig breeders.

Virus
Host
Location
Supporting text

In May 2018, an outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, PR China. Therefore, a G3P[13] porcine RVA strain most likely infected pig breeders.

Method
phylogenetic analysis | virus isolation | genomic sequencing
Study design
epidemiological and genomic investigation of diarrhoea outbreak on swine farm
Transmission direction
animal-to-human
Geographic raw
Sichuan province, PR China
Country inferred
CHN
Evidence type
1 records
OVE4351
Key finding

An outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, China, in May 2018, and Rotavirus A (RVA) was detected in most piglet samples collected during the outbreak.

Virus
Host
Location
Supporting text

In May 2018, an outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, PR China. RVA was detected in 95.7 % (22/23) of piglet samples, 60 % (9/15) of sow samples and 100 % (3/3) of pig-breeder faecal samples.

Method
outbreak investigation | sampling | virus detection
Transmission direction
same-species transmission
Geographic raw
Sichuan province, PR China
Country inferred
CHN
Outbreak setting
swine farm
Outbreak time
May 2018
Outbreak scale
outbreak of diarrhoea among piglets
Genomic Evolution
1 records · 1 evidence types
Evidence type
1 records
OVE4349
Key finding

Phylogenetic analysis showed that ten gene segments of the pig-breeder G3P[13] rotavirus isolate were closely related to pig isolates from the same farm, indicating host-associated genomic relatedness and cross-species evolutionary linkage.

Virus
Host
Location
Not specified
Supporting text

Phylogenetic analysis showed that ten gene segments (VP7, VP4, VP1–VP3 and NSP1–NSP5) of pig-breeder isolate SCLS-R3 were closely related to pig isolates SCLS-X1 and SCLS-3 from this farm.

Genes or proteins
VP7 | VP4 | VP1 | VP2 | VP3 | NSP1 | NSP2 | NSP3 | NSP4 | NSP5
Analysis methods
phylogenetic analysis