Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World

He, Wanting; Bollen, Nena; Xu, Yi; Zhao, Jin; Dellicour, Simon; Yan, Ziqing; Gong, Wenjie; Zhang, Cheng; Zhang, Letian; Lu, Meng; Lai, Alexander; Suchard, Marc A.; Ji, Xiang; Tu, Changchun; Lemey, Philippe; Baele, Guy; Su, Shuo

doi:10.1093/molbev/msab364

Cited by 45 publications

(55 citation statements)

References 95 publications

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“…The seasonality for the prevalence of PEDV has been gradually decreasing [ 37 , 38 ], and many provinces showed high incidence throughout the year, suggesting that the prevention and control of the epidemic should be strengthened in the summer and autumn when PEDV was low in the past. Furthermore, we found that Hunan and Hubei were the provinces with the most severe PEDV epidemics in south-central China, which is consistent with the study of He et al [ 39 ]. In addition, our results revealed that the GII-a subgroup has been increasing rapidly and has become dominant in recent years.…”

Section: Discussionsupporting

confidence: 92%

Epidemic and Evolutionary Characteristics of Swine Enteric Viruses in South-Central China from 2018 to 2021

Geng

et al. 2022

Viruses

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Swine enteric viruses are a major cause of piglet diarrhea, causing a devastating impact on the pork industry. To further understand the molecular epidemiology and evolutionary diversity of swine enteric viruses, we carried out a molecular epidemiological investigation of swine enteric viruses (PEDV, PDCoV, PoRVA, and TGEV) on 7107 samples collected from pig farms in south-central China. The results demonstrated that PEDV is the predominant pathogen causing piglet diarrhea, and its infection occurs mainly in relatively cold winter and spring in Hunan and Hubei provinces. The positive rate of PEDV showed an abnormal increase from 2020 to 2021, and that of PoRVA and PDCoV exhibited gradual increases from 2018 to 2021. PEDV-PoRVA and PEDV-PDCoV were the dominant co-infection modes. A genetic evolution analysis based on the PEDV S1 gene and ORF3 gene revealed that the PEDV GII-a is currently epidemic genotype, and the ORF3 gene of DY2020 belongs to a different clade relative to other GII-a strains isolated in this study. Overall, our results indicated that the variant PEDV GII-a is the main pathogen of piglet diarrhea with a trend of outbreak. G9 is the dominant PoRVA genotype and has the possibility of outbreak as well. It is therefore critical to strengthen the surveillance of PEDV and PoRVA, and to provide technical reserves for the prevention and control of piglet diarrhea.

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Section: Discussionsupporting

confidence: 92%

Epidemic and Evolutionary Characteristics of Swine Enteric Viruses in South-Central China from 2018 to 2021

Geng

et al. 2022

Viruses

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“…Considering the dependence of the virus on host cell mechanisms, codon usage patterns can help us understand molecular evolution and expression levels and help vaccine design [17]. Recombination analysis of other pathogens with other DNA [18] and RNA [19] viruses, including recombination outages and evolutionary rates.…”

Section: Introductionmentioning

confidence: 99%

Codon Usage for Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Parvoviruses 2 through 7 (PPV2–PPV7)

Xie

Tao

Zhang

et al. 2022

Viruses

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Porcine parvovirus (PPV) is the main pathogen of reproductive disorders. In recent years, a new type of porcine parvovirus has been discovered and named porcine parvovirus 2 to 7 (PPV2–PPV7), and it is associated with porcine circovirus type 2 in pigs. Codon usage patterns and their effects on the evolution and host adaptation of different PPV sub-types are still largely unknown. Here, we define six main sub-types based on the Bayesian method of structural proteins of each sub-type of PPV, including PPV2, PPV3, PPV4, PPV5, PPV6, and PPV7, which show different degrees of codon usage preferences. The effective number of codons (ENC) indicates that all PPV sub-types have low codon bias. According to the codon adaptation index (CAI), PPV3 and PPV7 have the highest similarity with the host, which is related to the main popular tendency of the host in the field; according to the frequency of optimal codons (FOP), PPV7 has the highest frequency of optimal codons, indicating the most frequently used codons in its genes; and according to the relative codon deoptimization index (RCDI), PPV3 has a higher degree. Therefore, it is determined that mutational stress has a certain impact on the codon usage preference of PPV genes, and natural selection plays a very decisive and dominant role in the codon usage pattern. Our research provides a new perspective on the evolution of porcine parvovirus (PPV) and may help provide a new method for future research on the origin, evolutionary model, and host adaptation of PPV.

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“…The texture of the food given is not appropriate, some babies still get a mashed texture when babies should be given soft food, so the process of eating is not successful, and the baby is not trained to chew properly (He, 2022). Following the theory of MP-ASI should be introduced at the age of 6 months because it is a critical period for infants to be introduced to solid foods gradually as stimulation of oromotor skills.…”

Section: Resultsmentioning

confidence: 99%

relationship of supplementary feeding, breast milk (MP-ASI) to infants with the event of diarrhea

Anggraeni¹,

Wati²,

Nambiar³

et al. 2022

ijhs

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Background: Diarrhea is one of the causes of death in toddlers, one of the factors that causes diarrhea is MP ASI. Based on the largest proportion of diarrhea sufferers at the Baros Health Center in the last 3 months of October, November, and December, there were 87 infants aged 0-12 months, 29 infants aged 12-24 months, and 31 infants aged 25-60 months. Objective: To determine the relationship between complementary feeding and the incidence of diarrhea in infants aged 3-12 months in the working area of the Baros Public Health Center, Sukabumi City. Methods: The study used a cross-sectional population and the total sampling was 48 infants aged 3-12 months. Data processing using Chi-Square. Results: The inappropriate provision of complementary feeding to infants aged 3-12 months was 26 respondents (54.2%) and the appropriate ones were 22 respondents (45.8 %), the incidence of diarrhea in infants aged 3-12 months who had diarrhea as many as 28 respondents (58.6%) and who did not have diarrhea as many as 20 respondents (41.7%). Research shows that there is a relationship between giving complementary feeding to infants aged 3-12 months with the incidence of diarrhea with a value of 0.00 (<0.05).

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Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World

Cited by 45 publications

References 95 publications

Epidemic and Evolutionary Characteristics of Swine Enteric Viruses in South-Central China from 2018 to 2021

Epidemic and Evolutionary Characteristics of Swine Enteric Viruses in South-Central China from 2018 to 2021

Codon Usage for Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Parvoviruses 2 through 7 (PPV2–PPV7)

relationship of supplementary feeding, breast milk (MP-ASI) to infants with the event of diarrhea

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