Development of A Super-Sensitive Diagnostic Method for African Swine Fever Using CRISPR Techniques.

African swine fever (ASF) is an infectious disease caused by African swine fever virus (ASFV) with clinical symptoms of high fever, hemorrhages and high mortality rate, posing a threat to the global swine industry and food security. Quarantine and control of ASFV is crucial for preventing swine industry from ASFV infection. In this study, a recombinase polymerase amplification (RPA)-CRISPR-based nucleic acid detection method was developed for diagnosing ASF. As a highly sensitive method, RPA-CRISPR can detect even a single copy of ASFV plasmid and genomic DNA by determining fluorescence signal induced by collateral cleavage of CRISPR-lwCas13a (previously known as C2c2) through quantitative real-time PCR (qPCR) and has the same or even higher sensitivity than the traditional qPCR method. A lateral flow strip was developed and used in combination with RPA-CRISPR for ASFV detection with the same level of sensitivity of TaqMan qPCR. Likewise, RPA-CRISPR is capable of distinguishing ASFV genomic DNA from viral DNA/RNA of other porcine viruses without any cross-reactivity. This diagnostic method is also available for diagnosing ASFV clinical DNA samples with coincidence rate of 100% for both ASFV positive and negative samples. RPA-CRISPR has great potential for clinical quarantine of ASFV in swine industry and food security.

Genetic and Molecular Characterization of H9N2 Avian Influenza Viruses Isolated from Live Poultry Markets in Hubei Province, Central China, 2013-2017.

H9N2 subtype avian influenza virus (AIV) is an influenza A virus that is widely spread throughout Asia, where it jeopardizes the poultry industry and provides genetic material for emerging human pathogens. To better understand the epidemicity and genetics of H9 subtype AIVs, we conducted active surveillance in live poultry markets (LPMs) in Hubei Province from 2013 to 2017. A total of 4798 samples were collected from apparent healthy poultry and environment. Real-time RT-PCR revealed that the positivity rate of influenza A was 26.6% (1275/4798), of which the H9 subtype accounted for 50.3% (641/1275) of the positive samples. Of the 132 H9N2 viral strains isolated, 48 representative strains were subjected to evolutionary analysis and genotyping. Phylogenetic analysis revealed that all H9N2 viral genes had 91.1%-100% nucleotide homology, clustered with genotype 57, and had high homology with human H9N2 viruses isolated from 2013 to 2017 in China. Using a nucleotide divergence cutoff of 95%, we identified ten distinct H9N2 genotypes that continued to change over time. Molecular analysis demonstrated that six H9N2 isolates had additional potential glycosylation sites at position 218 in the hemagglutinin protein, and all isolates had I155T and Q226L mutations. Moreover, 44 strains had A558V mutations in the PB2 protein and four had E627V mutations, along with H9N2 human infection strains A/Beijing/1/2016 and A/Beijing/1/2017. These results emphasize that the H9N2 influenza virus in Hubei continues to mutate and undergo mammalian adaptation changes, indicating the necessity of strengthening the surveillance of the AIV H9N2 subtype in LPMs.

Coexistence of multiple genotypes of porcine epidemic diarrhea virus with novel mutant S genes in the Hubei Province of China in 2016.

The emergence of highly virulent porcine epidemic diarrhea virus (PEDV) variants in China caused huge economic losses in 2010. Since then, large-scale sporadic outbreaks of PED caused by PEDV variants have occasionally occurred in China. However, the molecular diversity and epidemiology of PEDV in different provinces has not been completely understood. To determine the molecular diversity of PEDV in the Hubei Province of China, we collected 172 PED samples from 34 farms across the province in 2016 and performed reverse transcription polymerase chain reaction (RT-PCR) by targeting the nucleocapsid (N) gene. Seventy-four samples were found to be PEDV-positive. We further characterized the complete spike (S) glycoprotein genes from the positive samples and found 21 different S genes with amino acid mutations. The PEDV isolates here presented most of the genotypes which were found previously in field isolates in East and South-East Asia, North America, and Europe. Besides the typical Genotypes I and II, the INDEX groups were also found. Importantly, 58 new amino acids mutant sites in the S genes, including 44 sites in S1 and 14 sites in S2, were first described. Our results revealed that the S genes of PEDV showed variation and that diverse genotypes of PEDV coexisted and were responsible for the PED outbreaks in Hubei in 2016. This work highlighted the complexity of the epidemiology of PEDV and emphasized the need for reassessing the efficacy of classic PEDV vaccines against emerging variant strains and developing new vaccines to facilitate the prevention and control of PEDV in fields.

An adhesion molecule-based colloidal gold immunochromatography assay strip for rapidly and specifically detecting chicken antibodies against Mycoplasma gallisepticum.

The fragment of the VlhA1.2 gene was cloned from a Mycoplasma gallisepticum (MG) DNA library by serial PCRs after the same-sense mutagenesis of three TGA codons encoding tryptophan (Trp). Following transforming the generated plasmid of pKG-VlhA1.2, the recombinant VlhA1.2-GST fusion protein of 92kDa was induced and recognized by anti-MG sera. After GST-affinity chromatographic purification, the VlhA-based colloidal gold immunochromatography assay (GICA) strips were generated. The GICA strips specifically detected anti-MG antibodies, but not antibodies against Mycoplasma synoviae and other positive sera against non-MG pathogens tested. The GICA strips were 128-fold more sensitive to detect anti-MG antibodies, as compared with traditional serological methods and were stored at 4° C for 15 months without loss of their sensitivity and specificity. Analysis of sample revealed that, the GICA strips were highly sensitive, specific and stable for the on-site surveillance of MG infections by unskilled users.

Development of an immunochromatographic strip for rapid detection of H9 subtype avian influenza viruses.

An immunochromatographic strip was developed for the detection of the H9 subtype of avian influenza viruses (H9AIVs) in poultry, using two monoclonal antibodies (MAb), 4C4 for H9AIV hemagglutinin (HA) and 4D4 for nucleoprotein. The 4C4 MAb was labeled with colloidal gold as the detection reagent, and the 4D4 MAb was blotted on the test line while a goat anti-mouse antibody was used on the control line of the nitrocellulose membrane. In comparison with the HA and HA inhibition (HI) tests, the strip was specific for the detection of H9AIV, with a sensitivity at 0.25 HA units within 10 min. Storage of the strips at room temperature for 6 months or at 4 degrees C for 12 months did not change their sensitivity and specificity. Evaluation of the strip with experimental tracheal and cloacal swab samples collected from H9N2-infected chickens revealed that the strip detected the H9N2 viruses on day 3 postinoculation, earlier than the appearance of clinical symptoms. Application of the strip for the analysis of 157 tracheal or cloacal samples from potentially infected chickens on five poultry farms showed that four farms had chickens that were infected with H9AIV. Further characterization of 10 positive and 30 negative randomly selected samples showed that no single sample was false positive or negative, as determined by the standard virus isolation and HI assays. Therefore, the immunochromatographic strip for the detection of H9AIVs has high specificity, sensitivity, and stability. This finding, together with the advantages of rapid detection and easy operation and without the requirement for special skills and equipment, makes the strip suitable for onsite detection and the differentiation of H9AIVs from other viruses in poultry.

Development and validation of an immunochromatographic assay for rapid detection of sulfadiazine in eggs and chickens.

A rapid immunochromatographic assay (ICA) was developed and validated for the detection of sulfadiazine in eggs and chickens. Based on the competitive reaction mechanism, the competitor of sulfadiazine (sulfadiazine-BSA conjugate) was immobilized to the defined detection zone on a nitrocellulose membrane which acted as the capture reagent, and the monoclonal antibody against sulfadiazine was conjugated to colloidal gold particles which served as the detection reagent for the preparation of the immunochromatographic strips to test sulfadiazine. With this method, the semi-quantitative detection of sulfadiazine was accomplished in less than 15min, with high sensitivity to sulfadiazine (5ng/g) and low cross-reactivities with other sulfonamides. With experimental egg and chicken samples spiked with sulfadiazine at concentrations of 10, 20, and 100ng/g, recoveries were demonstrated to be from 71% to 97% in egg samples and 71% to 95% in chicken samples. This method was compared with the enzyme-linked immunosorbent assay by testing 52 egg samples from the animal experiment, and compared with the high-performance liquid chromatographic method by testing 56 chicken samples, with an agreement rate of 100% for both comparisons, by using the maximum allowed residue of sulfadiazine (i.e. 100ng/g) as the cut-off level as set by the European Union and China. The accuracy of ICA was also confirmed in an initial study with marketed egg and chicken samples. In conclusion, the method is rapid and accurate for the detection of sulfadiazine in eggs and chickens.