ABSTRACT
To develop a multiplex fluorescent quantitative RT-PCR for the detection of porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV) and swine acute diarrhea syndrome coronavirus (SADS-CoV), in this study, specific primers/probes were designed based on the conserved regions of M, M and N gene sequences of PEDV, PDCoV and SADS-CoV, respectively. After optimization of the reaction conditions, a multiplex fluorescent quantitative RT-PCR for PEDV, PDCoV and SADS-CoV was established. The results of specificity assay showed that the method was positive for detection of PEDV, PDCoV and SADS-CoV, and negative for detection of porcine transmissible gastroenteritis virus, porcine rotavirus, porcine reproductive and respiratory syndrome virus, porcine pseudorabies virus, porcine circovirus type 2, porcine parvovirus, classical swine fever virus and foot-and-mouth disease virus. The results of sensitivity assay showed that the detection limit of this method for PEDV, PDCoV, and SADS-CoV plasmids standard was 1.0x101 copies/L, and had a good linear relationship with their Ct values in the range of 101 copies/L to 106 copies/L. The results of repeatability assay showed that the coefficients of variation (CVs) of intra- and inter-assay reproducibility ranged from 0.33% to 2.53%, indicating good repeatability and stability. To evaluate the effects of the developed method, 100 clinical samples collected from different parts of Henan province were used for detection of these three viruses and compared with those of single RT-PCR and standard methods. The results of multiplex fluorescent quantitative RT-PCR showed that the positive rates of PEDV, PDCoV and SADS-CoV were 38% (38/100), 14% (14/100) and 5% (5/100), respectively. There was no mixed infection. The coincidence rate with the standard detection methods of PEDV and PDCoV was 100%, and the sensitivity was higher than that of single RT-PCR. In this study, a specific, sensitive and rapid multiplex fluorescent quantitative RTPCR method was established for the first time, which could be used for the differential detection of PEDV, PDCoV and SADS-CoV, and laid a foundation for the differential diagnosis and control of porcine diarrheal diseases.
ABSTRACT
The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.
ABSTRACT
Many restrictive measures were implemented in China from January-February 2020 to control the rapid spread of COVID-19. Many studies reported that the COVID-19 lockdown impacted PM2.5, SO2, volatile organic compounds (VOCs), etc. VOCs play important roles in the production of ozone and PM2.5. Ambient VOCs in Xiong'an were measured from December 25, 2019 to January 24, 2020 (prior to epidemic prevention, P1) and from January 25, 2020 to February 24, 2020 (during epidemic prevention, P2) through a VOCs online instrument. In the study, VOCs characteristics and ozone generation potential (OFP) of ambient VOCs were analyzed, and source apportionment of VOCs were analyzed by using Positive Matrix Factorization (PMF). The results showed that φ(TVOCs) during epidemic prevention and control was 45.1×10-9, which was approximately half of that before epidemic prevention and control (90.5×10-9). The chemical composition of VOCs showed significant changes after epidemic prevention and control, the contribution rate of alkanes increased from 37.6% to 53.8%, and the contribution rate of aromatic hydrocarbons and halogenated hydrocarbons decreased from 13.3% and 12.0% to 7.5% and 7.8%, respectively. Aromatic hydrocarbons, halogenated hydrocarbons, and OVOCs decreased by more than 60%. Seven types of the top ten species were the same before and during the epidemic prevention and control, mainly low-carbon alkanes, olefins, aldehydes, and ketones. Dichloromethane, trichloromethane, and BTEXs decreased significantly. The OPP was 566 µg·m-3 and 231 µg·m-3 in P1 and P2, respectively. The OPP of VOCs decreased by more than 30%. The proportion of OFP contribution of aromatic hydrocarbons decreased significantly after the epidemic prevention and control, and the proportion of OFP contribution of alkanes and alkynes increased significantly. Positive matrix factorization (PMF) was then applied for VOCs sources apportionment. Six sources were identified, including background sources, oil-gas volatile sources, combustion sources, industrial sources, solvent use sources, and vehicle exhaust sources. The results showed that after the epidemic prevention and control, the contribution rate of solvent use sources to TVOCs decreased from 24% to 9%. The contribution rates of background sources, oil-gas volatile sources, and combustion sources increased from 13%, 34%, and 24% to 6%, 14%, and 13%, respectively. The relative contributions of vehicle exhaust sources before and after epidemic prevention and control were 21% and 18%, respectively. The observation points were affected by the emission of VOCs from paroxysmal industrial sources before the epidemic prevention and control. The emission was stopped after the epidemic prevention and control, and its contribution rate was reduced from 22% before the epidemic prevention and control to 1%. The concentrations of industrial sources, solvent sources, motor vehicle tail gas sources, and combustion sources decreased by 97%, 82%, 61%, and 15%, respectively, after the epidemic prevention and control. The concentration of background sources remained stable, and the concentration of oil and gas volatile sources increased by 7%. The control of production and traffic activities cannot reduce the emission of VOCs from oil and gas volatile sources, which is the focus of VOCs control in Xiong'an.