On November 29, 2025, Professor Yan Qigui's team from the College of Veterinary Medicine, Sichuan Agricultural University, and the Juxing Agricultural and Animal Husbandry Research Institute published a new study in the international journal *Veterinary Sciences* on the molecular epidemiological characteristics and virus isolation and identification of porcine rotavirus (PoRV) in Southwest China.
This study systematically revealed the epidemiological characteristics, genotypic changes, and cross-species recombination of PoRV in Southwest China from 2024 to 2025, providing crucial scientific evidence for the prevention and control of swine diarrhea and vaccine upgrades.
Research Highlights
* **Severe Situation:** The PoRV infection rate in Southwest China is as high as 57.14%, far exceeding other regions in China (Guangdong 36.44%, Guangxi 37.13%), making it the leading pathogen of viral diarrhea in pigs in the region.
* **Major Genotypic Reshuffling:** The traditionally dominant G5 genotype has been replaced by G9 (35.71%) and G4 (39.28%), while current commercial vaccines only contain the G5 genotype, raising questions about their protective efficacy.
• Cross-species recombination alert: A rare G1P[7] strain was isolated for the first time in Sichuan. Genomic analysis confirmed that its NSP2-NSP4 gene fragments originated from human rotavirus, posing a risk of cross-species transmission.
• Coexistence of multiple pathogens: Group C rotavirus was detected in 33.04% of samples, and 7.14% were mixed infections of Group B and Group C, indicating an unprecedented level of complexity in the epidemic.
This study aims to systematically investigate the prevalence and molecular characteristics of porcine rotavirus (PoV) in large-scale pig farms in Southwest China from 2024 to 2025, filling a research gap in this field.
The research team collected 196 clinical diarrhea samples from 29 large-scale pig farms in Southwest China during 2024-2025. Using techniques such as RT-qPCR, RT-PCR, virus isolation, whole-genome sequencing, and phylogenetic analysis, they conducted in-depth analysis of the prevalence, genotype distribution, whole-genome characteristics, and genetic evolutionary relationships of PoV.
Introduction
Porcine rotavirus is one of the main pathogens causing acute diarrhea in piglets, often resulting in co-infection with other diarrheal pathogens and causing serious economic losses. In the past, it received insufficient attention due to its low mortality rate. However, in recent years, its prevalence has increased significantly, and its genotypes have become increasingly complex, posing new challenges to prevention and control.
In 2023, the detection rate of porcine rotavirus in pig herds in my country exceeded that of porcine epidemic diarrhea virus (PEDV) for the first time, becoming the "number one diarrheal pathogen." Southwest my country, a major pig-farming region, is particularly affected by the epidemic, but systematic molecular epidemiological data is lacking.
Research Results
1. Sample Detection and Epidemiological Characteristics:
From 2024 to 2025, the research team collected 196 diarrhea samples (100 intestinal tissue samples and 96 fecal samples) from 29 large-scale pig farms in Southwest China. RT-qPCR testing revealed:
· The overall PoRV positivity rate was 57.14% (112/196), with group A (PoRVA) accounting for the highest proportion (46.43%), making it the absolute dominant group;
· The positive rates for group B (PoRVB) and group C (PoRVC) were 10.71% and 33.04%, respectively, with a mixed infection rate of 9.82%, and the PoRVB+PoRVC combination being the most common (7.14%).
Table 1. Positive rates in different PoRV groups.
2. Genotype distribution and evolutionary analysis:
Sequencing analysis of VP4 and VP7 genes in 52 PoRVA positive samples showed that:
· VP4 genotypes were classified into four P genotypes: P[13] (77.78%), P[7] (14.81%), P[6] (3.7%), and P[23] (3.7%), with P[13] being the absolute dominant genotype;
Figure 1. ML tree of VP4 gene in PoRVA samples.
· VP7 gene was classified into 6 G genotypes: G4 (39.28%), G9 (35.71%), G5 (10.71%), G1 (7.14%), G3 (3.57%), and G11 (3.57%);
· The dominant G/P combinations were G9P[13] and G4P[13] (each accounting for 33.33%), which were significantly different from the traditionally popular G5P[7] and G3P[13].
Figure 2. ML tree of VP7 gene in PoRVA sample.
3. Virus isolation and genomic characteristics:
One PoRV strain (RVA/Pig-wt/SCLS-JW/2024/G1P [7]) was successfully isolated. Its typical rotavirus morphology and infectivity were verified by transmission electron microscopy and indirect immunofluorescence (IFA):
· The genomic constellation is G1-P [7]-I5-R1-C1-M1-A8-N1-T1-E1-H1, and the structural genes (VP1-VP4, VP6-VP7) are highly homologous to porcine strains;
Figure 3. Phylogenetic tree of VP1 to VP4, VP6, and VP7 genes in the RVA/SCLS-JW/2024 isolate.
• The non-structural genes NSP2-NSP4 show 94%-98% similarity to human rotavirus, confirming it as a human-porcine recombinant strain;
Figure 4. Phylogenetic tree of NSP1 to NSP5 genes in the RVA/SCLS-JW/2024 isolate.
· This strain replicated well in MA104 cells, reaching a viral titer of 10⁶ TCID₅₀/mL after 24 hours, indicating strong replication ability.
Figure 5. Virus isolation and identification results.
Summary
This study systematically revealed the latest epidemiological characteristics of porcine rotavirus in Southwest China from 2024 to 2025, clarifying that the G9 and G4 genotypes have replaced the traditional G5 as the dominant circulating strains, filling a gap in recent molecular epidemiological data for this region.
The results indicate a significant antigenic mismatch between existing vaccine strains and circulating strains, which may affect the effectiveness of immune protection. Meanwhile, the identified human-porcine recombinant strains suggest a risk of cross-species transmission, highlighting the importance of continuous surveillance and vaccine updates for the control of porcine viral diarrhea.
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