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Simple SummaryDuring the long-term co-evolution of the virus and the host, even closely related vaccines may emerge with incomplete protective immunity due to the mutations or deletions of amino acids at specific antigenic sites. The mutation of PEDV was accelerated by the recombination of different strains and the mutation of the strains adapting to the environment. These mutations either cause immune escape from conventional vaccines or affect the virulence of the virus. Therefore, researching and developing new vaccines with cross-protection through continuous monitoring, isolation and sequencing are important to determine whether their genetic characteristics are changed and to evaluate the protective efficacy of current vaccines. The porcine epidemic diarrhea virus (PEDV) can cause severe piglet diarrhea or death in some herds. Genetic recombination and mutation facilitate the continuous evolution of the virus (PEDV), posing a great challenge for the prevention and control of porcine epidemic diarrhea (PED). Disease materials of piglets with PEDV vaccination failure in some areas of Shanxi, Henan and Hebei provinces of China were collected and examined to understand the prevalence and evolutionary characteristics of PEDV in these areas. Forty-seven suspicious disease materials from different litters on different farms were tested by multiplex PCR and screened by hematoxylin-eosin staining and immunohistochemistry. PEDV showed a positivity rate of 42.6%, infecting the small and large intestine and mesenteric lymph node tissues. The isolated strains infected Vero, PK-15 and Marc-145 multihost cells and exhibited low viral titers in all three cell types, as indicated by their growth kinetic curves. Possible putative recombination events in the isolates were identified by RDP4.0 software. Sequencing and phylogenetic analysis showed that compared with the classical vaccine strain, PEDV SX6 contains new insertion and mutations in the S region and belongs to genotype GIIa. Meanwhile, ORF3 has the complete amino acid sequence with aa80 mutated wild strains, compared to vaccine strains CV777, AJ1102, AJ1102-R and LW/L. These results will contribute to the development of new PEDV vaccines based on prevalent wild strains for the prevention and control of PED in China.
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Infectious bronchitis virus (IBV) is distributed worldwide and causes significant losses in the poultry industry. In recent decades, lineages GI-19 and GI-7 have become the most prevalent IBV strains in China. However, the molecular evolution and phylodynamics of the lineage GI-7 IBV strains remain largely unknown. In this study, we identified 19 IBV strains from clinical samples from January 2021 to June 2022 in China, including 12 strains of GI-19, 3 strains of GI-7, and 1 strain each of GI-1, GI-9, GI-13, and GI-28. These results indicated that lineages GI-19 and GI-7 IBVs are still the most prevalent IBVs in China. Here, we investigated the evolution and transmission dynamics of lineage GI-7 IBVs. Our results revealed that the Taiwan province might be the origin of lineage GI-7 IBVs and that South China plays an important role in the spread of IBV. Furthermore, we found low codon usage bias of the S1 gene in lineage GI-7 IBVs. This allowed IBV to replicate in the host during evolution as a result of reduced competition, mainly driven by natural selection and mutational pressure, where the role of natural selection is more prominent. Collectively, our results reveal the genetic diversity and evolutionary dynamics of lineage GI-7 IBVs, which could assist in the prevention and control of viral infection.
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Diarrhea outbreaks in piglets on pig farms are commonly attributed to porcine epidemic diarrhea virus (PEDV) infection. This research analyzed the S gene prevalence variation and recombination patterns in PEDV GII strains. Throughout the previous two years, 172 clinical samples of piglet diarrhea have been collected, from which 24 PEDV isolates have been isolated. Analysis of the evolutionary relationships among all 24 S genes revealed that 21 were most closely related to strains within the GII-a subgroup. The 2 isolates grouped into one clade with the GII-b subgroup. According to the mutation analysis of the amino acids (aa) that encode the S protein, 43 of the common aa in strains of the GII subtype were found to have undergone a change in polarity or charge, and 36 of these aa had a mutation frequency of more than 90%. Three different aa mutation sites were identified as exclusive to GII-a subtype strains. The genomes of three PEDV isolates were sequenced, and the resulting range in genome length was 28,035−28,041 nt. The results of recombination analysis showed that the SD1 isolate is a novel strain recombinant from the foreign S-INDEL strain and a domestic GII subtype strain. Based on the findings, the PEDV GII-a strain has been the most circulating strain in several parts of China during the previous two years. Our study reveals for the first time the unique change of aa mutations in the S protein of the GII-a subtype strain and the new characteristics of the recombination of foreign strains and domestic GII subtype strains, indicating that it is crucial to monitor the epidemic dynamics of PEDV promptly to prevent and control the occurrence of PED effectively.
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Porcine sapelovirus (PSV) is an emerging swine enteric virus that can cause various disorders including acute diarrhea, respiratory distress, reproductive failure, and polioencephalomyelitis in pigs. In this study, we isolated a PSV strain HNHB-01 from a clinical porcine deltacoronavirus- (PDCoV-) positive intestinal content of a diarrheic piglet. PSV was first identified using the small RNA deep sequencing and assembly, and further identified by the electron microscopic observation and the immunofluorescence assay. Subsequently, this virus was serially passaged in swine testis (ST) cells, and the complete genomics of PSV HNHB-01 passage 5 (P5), P30, P60, and P100 were sequenced and analyzed. 9 nucleotide mutations and 7 amino acid changes occurred in the PSV HNHB-01 P100 strain when compared with the PSV HNHB-01 P5. Pathogenicity investigation showed that orally inoculation of PSV HNHB-01 P30 could cause obvious clinical symptoms and had broad tissue tropism in 5-day-old piglets. Epidemiological investigation revealed that PSV infections and the coinfections of diarrhea coronaviruses were highly prevalent in swine herds. The complete genomes of 8 representative PSV epidemic strains were sequenced and analyzed. Phylogenetic analysis revealed that the PSV epidemic strains were closely related to other PSV reference strains that located in the Chinese clade. Furthermore, recombination analysis revealed that the recombination events were occurred in downstream of the 2C region in our sequenced PSV HNNY-02/CHN/2018 strain. Our results provided theoretical basis for future research studies of the pathogenic mechanism, evolutionary characteristics, and the development of vaccines against PSV.
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Objective To identify the pathogen and track the genetic source of a cluster of cases with fever in a kindergarten in Fengtai district during the normalization of COVID-19 prevention and control in Beijing.Methods A descriptive analysis method was used to investigate this cluster of cases with fever in April 2021.Pharyngeal swabs were collected and viral nucleic acid was extracted, real-time PCR was performed to identify SARS-CoV-2 and other common respiratory virus. G gene of human metapneumovirus（hMPV） was amplified by RT-PCR and was then sequenced. BioEdit was used for G gene sequence analysis and the Neighbor-Joining model in MEGA 5. 0 software was used to construct the phylogenic tree of G gene. Results A total of 16 cases were reported in one class with the incidence of 53. 3%（16/30） during 8 days of a cluster outbreak. All pharyngeal swabs collected from 12 cases were tested SARS-CoV-2 negative, six were found to be hMPV positive by multiplex-PCR, and one was positive for both human adenovirus and hMPV. Full-length sequences of G genes were obtained from 2 strains of hMPV. Sequence analysis showed that both strains were hMPV B2 and the nucleic acid homology of G gene was 96. 73%-98. 01% with strains from Japan（LC337940, LC337935, LC1922349） in 2016 and over 98. 40%with strains from Shandong（OL625642, OL625644） in 2019, Henan MN944096 in 2019.Compared with the amino acid sequence of hMPV-B2 reference strain（AY297748）, six amino acid insertions containing EKEKEK were identified between 161-166 amino acid location and N-glycosylation of G protein analysis showed that the two strains had four N-glycosylation sites. Conclusions The leading pathogen for this cluster outbreak is found to be hMPV-B2, which are highly homologous with strains from Japan, Shandong and Henan. Therefore, a non-stop surveillance of hMPV is necessary during the normalization control and prevention period for COVID-19.
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Kefir is a fermented milk beverage different in consistency and taste from other popular milk-product yogurt. Unlike yogurt prepared using lactic acid bacteria in fermentation, milk is fermented for kefir production using preculture in the form of kefir grains. Therefore, the metabolic activities of a mixed culture, including strains of bacteria and yeast, contribute to the probiotic characteristics in kefir. This article is based on the review of published studies on the functionality and nutraceutical properties of kefir. The therapeutic and dietary properties of kefir beverage and its probiotic strains have been discussed for their several health benefits. Concise selected information mostly from recent reports has been presented for two categories of kefir products: milk used for the production of dairy-based traditional kefir beverages for the lactose-tolerant population, and the plant-sourced substrates used for the production of dairy-free kefir beverages for lactose-intolerant and vegan consumers.
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The recent COVID-19 pandemic has once again caught the attention of people on the probable zoonotic transmission from animals to humans, but the role of companion animals in the coronavirus (CoV) epidemiology still remains unknown. The present study was aimed to investigate epidemiology and molecular characterizations of CoVs from companion animals in Chengdu city, Southwest China. 523 clinical samples from 393 animals were collected from one veterinary hospital between 2020 and 2021, and the presence of CoVs was detected by end-point PCR using pan-CoV assay targeting the RdRp gene. Partial and complete S genes were sequenced for further genotyping and genetic diversity analysis. A total of 162 (31.0%, 162/523) samples and 146 (37.2%, 146/393) animals were tested positive for CoVs. The positive rate in rectal swabs was higher than that in eye/nose/mouth swabs and ascitic fluid but was not statistically different between clinically healthy and diseased ones. Genotyping identified twenty-two feline enteric coronavirus (FCoV) I, four canine enteric coronavirus (CECoV) I, fourteen CECoV IIa, and one CECoV IIb, respectively. Eight complete S genes, including one canine respiratory coronavirus (CRCoV) strain, were successfully obtained. FCoV strains (F21071412 and F21061627) were more closely related to CECoV strains than CRCoV, and C21041821-2 showed potential recombination event. In addition, furin cleavage site between S1 and S2 was identified in two strains. The study supplemented epidemiological information and natural gene pool of CoVs from companion animals. Further understanding of other functional units of CoVs is needed, so as to contribute to the prevention and control of emerging infectious diseases.
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Porcine transmissible gastroenteritis virus is the major pathogen that causes fatal diarrhea in newborn piglets. In this study, a TGEV strain was isolated from the small intestine of diarrhea piglets in Sichuan Province, China, and designated SC2021. The complete genomic sequence of TGEV SC2021 was 28561 bp, revealing a new natural deletion TGEV strain. Based on phylogenetic analyses, TGEV SC2021 belonged to the Miller cluster and was closely related to CN strains. The newborn piglets orally challenged with TGEV SC2021 showed typical watery diarrhea. In addition, macro and micropathological changes in the lungs and intestines were observed. In conclusion, we isolated a new natural deletion virus strain and confirmed that the virus strain has high pathogenicity in newborn piglets. Moreover, macroscopic and microscopic lesions were observed in the lungs and intestines of all TGEV SC2021-infected piglets. In summary, we isolated a new natural deletion TGEV strain and demonstrated that the natural deletion strain showed high pathogenicity in newborn piglets. These data enrich the diversity of TGEV strains and help us to understand the genetic evolution and molecular pathogenesis of TGEV.
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Background: Today, SARS-CoV-2 (COVID-19), a viral disease caused by the novel coronavirus (a tiny crowned virus), has become one of the threats for human beings all over the world and caused the death of millions of people worldwide. Many vaccines have been developed and administered to people in several countries;however, due to their propensity to create new strains, it appears that curing all corona strains will be challenging. So, it is necessary to identify the structure of the virus, mechanism of action, and its antiviral activities against drugs and other functional materials. Methods: AgNPs have unique physicochemical and antimicrobial properties. This review describes the structure and nature of the virus and the mechanism of action of an antiviral drug such as silver nanoparticles (AgNPs) with the virus. In addition, different methods for synthesis of AgNPs, application of AgNPs as an antiviral agent against influenza virus, human immuno deficiency virus (HIV), herpes simplex virus type 1 (HSV-1), hepatitis B virus (HBV), polio virus, respiratory syncytial virus (RSV), are discussed. Also, the most probable applications and properties of AgNPs that can help prepare it as an antiviral agent are discussed. Results: The use of AgNPs against various viruses, including the coronavirus family, is found to be effective;therefore, it can be considered for the development of antiviral agents, disinfectants, antiviral coated mask, and their therapeutic use against the treatment of novel coronavirus with minimum side effect and great efficiency. Conclusion: AgNPs were successfully used for the treatment of various viral diseases of the coronavirus family such as H1N1, H3N2, influenza, even for SARS and MERS coronaviruses. AgNPs coated masks, disinfectants, fabrics, wipes, and inhalation systems are effective for the inhibition of SARS-CoV-2 infection. Since sanitizers have a temporary effect, the development of some other potential alternatives having low toxicity, ease of use, long lasting efficiency, health cautiousness, minimum side effect, sustainable fabrics is required.
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The purpose of this research was to develop formulations of chewing candies (CCs) in a sustainable manner by using berry by-products in combination with antimicrobial lactic acid bacteria (LAB) strains. To implement this aim, the optimal quantities of by-products from lyophilised raspberry (Rasp) and blackcurrant (Bcur) from the juice production industry were selected. Prior to use, Lactiplantibacillus plantarum LUHS135, Liquorilactobacillus uvarum LUHS245, Lacticaseibacillus paracasei LUHS244, and Pediococcus acidilactici LUHS29 strains were multiplied in a dairy industry by-product—milk permeate (MP). The antimicrobial activity of the selected ingredients (berry by-products and LAB) was evaluated. Two texture-forming agents were tested for the CC formulations: gelatin (Gl) and agar (Ag). In addition, sugar was replaced with xylitol. The most appropriate formulation of the developed CCs according to the product’s texture, colour, total phenolic compound (TPC) content, antioxidant activity, viable LAB count during storage, overall acceptability (OA), and emotions (EMs) induced in consumers was selected. It was established that the tested LAB inhibited three pathogens out of the 11 tested, while the blackcurrant by-products inhibited all 11 tested pathogens. The highest OA was shown for the CC prepared with gelatin in addition to 5 g of Rasp and 5 g of Bcur by-products. The Rasp and LUHS135 formulation showed the highest TPC content (147.16 mg 100 g−1 d.m.), antioxidant activity (88.2%), and LAB count after 24 days of storage (6.79 log10 CFU g−1). Finally, it was concluded that Gl, Rasp and Bcur by-products, and L. plantarum LUHS135 multiplied in MP are promising ingredients for preparing CCs in a sustainable manner;the best CC formula consisted of Gl, Rasp by-products, and LUHS135 and showed the highest OA (score 9.52) and induced the highest intensity of the EM ‘happy’ (0.231).
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The water and soils pollution due to mercury emissions from mining industries represents a serious environmental problem and continuous risk to human health. Although many strategies have been designed for the recovery or elimination of this metal from environmental sources, microbial bioremediation has proven to be the most effective and environmentally friendly strategy and thus control heavy metal contamination. The main objective of this work, using native bacterial strains obtained from contaminated soils of the Peruvian region of Secocha, was to identify which of these strains would have growth capacity on mercury substrates to evaluate their adsorption behavior and mercury removal capacity. Through a DNA analysis (99.78% similarity) and atomic absorption spectrometry, the Gram-positive bacterium Zhihengliuella alba sp. T2.2 was identified as the strain with the highest mercury removal capacity from culture solutions with an initial mercury concentration of 162 mg·L−1. The removal capacity reached values close to 39.5% in a period of incubation time of 45 days, with maximum elimination efficiency in the first 48 h. These results are encouraging and show that this native strain may be the key to the bioremediation of water and soils contaminated with mercury.