Genotype 1 Research Articles

Efficacy and safety of direct-acting antiviral regimen for patients with hepatitis C virus genotype 2: a systematic review and meta-analysis.

Direct-acting antivirals (DAAs) show high cure rates in treating chronic hepatitis C virus (HCV). However, the effect of DAAs on patients infected with genotype 2 (GT2) is difficult to determine despite the availability of several DAA regimens. A systematic search of six databases (PubMed, Embase, Cochrane Library, Web of Science, CNKI, and Clinicaltrial.gov) was conducted through April 20, 2022. We considered the sustained virological response 12 weeks after treatment (SVR12) as the efficacy outcome, and adverse events (AEs) as the safety outcome. By calculating the mean SVR12 and the proportion of AEs among patients, we considered the intervention effect for each DAA regimen. The random effect model was then used in all meta-analyses. This systematic review and meta-analysis aimed to summarize the evidence on efficacy and safety of DAAs in patients infected with HCV GT2. The Bayesian Markov Chain Monte Carlo (MCMC) network metanalysis was used to indirectly compare regimen in GT2 patients. Among 31 articles included (2,968 participants), consisting of 1,387 treatment-naive patients and 354 patients with cirrhosis. The overall pooled SVR12 rate was 94.62% (95% CI: 92.43-96.52%) among the participants who received all doses of treatment. Meta-analysis results of AEs revealed that fatigue was the most common AE (14.0%, 95% CI: 6.4-21.6%), followed by headache (13.1%, 95% CI: 9.2-17.1%), whereas death and serious adverse events were uncommon. We compared DAA-based treatments indirectly using meta-analysis and found the combination of Sofosbuvir plus Velpatasvir and Glecaprevir plus Pibrentasvir, each administered over a 12-week period, were identified as the most effective and relatively safe in managing chronic hepatitis C virus genotype 2 (HCV GT2) infection. Both treatments achieved a SVR12 of 100% (95% CI 99-100%).

Pharmacophore-Assisted Covalent Docking Identifies a Potential Covalent Inhibitor for Drug-Resistant Genotype 3 Variants of Hepatitis C Viral NS3/4A Serine Protease.

The emergence of drug-resistance-inducing mutations in Hepatitis C virus (HCV) coupled with genotypic heterogeneity has made targeting NS3/4A serine protease difficult. In this work, we investigated the mutagenic variations in the binding pocket of Genotype 3 (G3) HCV NS3/4A and evaluated ligands for efficacious inhibition. We report mutations at 14 positions within the ligand-binding residues of HCV NS3/4A, including H57R and S139P within the catalytic triad. We then modelled each mutational variant for pharmacophore-based virtual screening (PBVS) followed by covalent docking towards identifying a potential covalent inhibitor, i.e., cpd-217. The binding stability of cpd-217 was then supported by molecular dynamic simulation followed by MM/GBSA binding free energy calculation. The free energy decomposition analysis indicated that the resistant mutants alter the HCV NS3/4A-ligand interaction, resulting in unbalanced energy distribution within the binding site, leading to drug resistance. Cpd-217 was identified as interacting with all NS3/4A G3 variants with significant covalent docking scores. In conclusion, cpd-217 emerges as a potential inhibitor of HCV NS3/4A G3 variants that warrants further in vitro and in vivo studies. This study provides a theoretical foundation for drug design and development targeting HCV G3 NS3/4A.

Efficacy and Safety of Ombitasvir/Paritaprevir/Ritonavir Plus Dasabuvir in Treating HCV Genotypes 1 and 4 in Patients with Advanced Chronic Kidney Disease

ABSTRACT This study assessed the efficacy and safety of ombitasvir/paritaprevir/ritonavir (OBV/PTV/r) combined with dasabuvir (DSV) for treating hepatitis C genotype 4 (GT4) and genotype 1 (GT1) in patients with stage 4 or 5 chronic kidney disease (CKD). Among 88 patients, including treatment-naïve and Peginterferon/Ribavirin (RBV)-experienced, treated with OBV/PTV/r±RBV (dosed between 200 mg per week to daily) and additional DSV for GT1, 94.3% achieved sustained virologic response at 12 weeks (SVR12), demonstrating high efficacy. RBV was used at the discretion of the treating physician. The treatment was well-tolerated, with two non-treatment-related deaths reported. The findings suggest that a 12-week regimen of OBV/PTV/r±DSV is highly effective and safe for GT1 and GT4 patients with advanced CKD, regardless of baseline characteristics.

Performance of HCV core antigen and PCR testing in a predominantly genotype 3 population.

Hepatitis C core antigen (HCVcAg) is becoming increasingly recognized as an alternative to molecular testing for the confirmation of chronic hepatitis C. However, there are limited data on the performance of this assay in a genotype 3 (GT3) predominant country like Pakistan. We conducted a study to evaluate the diagnostic performance of HCVcAg against the HCV polymerase chain reaction (PCR) molecular test. HCV antibody-positive patients requiring confirmatory testing were recruited from August to October 2018 at the Pakistan Kidney and Liver Institute and Research Center (PKLI&RC), Lahore, Pakistan. Patients with previously known diagnoses or treatment histories were excluded. The Abbott HCV Ag assay was used for HCVcAg testing. Results ≥3.00 fmol/L were considered positive for HCVcAg. The Abbott RealTime HCV assay was used for PCR testing with a lower detection limit of ≥12 IU/mL. We computed the sensitivity, specificity and correlation of HCVcAg against HCV PCR. A total of 394 patients were recruited. The median age of the patients was 42 years. Most participants were females (51.5%, n = 203), 30.7% (n = 121) had HTN, 10.4% DM (n = 41) and 5% had APRI ≥2. The overall sensitivity was 98.0% and the specificity was 98.6%. The lowest detection limit of cAg was an HCV RNA value of 4657 IU/mL. The levels of cAg were highly correlated with those of HCV RNA by Spearman's rank correlation test (r = 0.935, p < .001). HCVcAg represents a suitable alternative with high sensitivity and specificity compared with HCV PCR in the GT3-predominant population and can be incorporated into algorithms to improve linkage to care.

Up-to-date Epidemiology of Chronic Hepatitis C Virus Infection among Bulgarian Patients: a Single Centre Experience

Epidemiological data about chronic infection with Hepatitis C virus (HCV) are limited in Bulgaria. The aim of this study was to determine the Viremic Rate and the distribution of HCV genotypes in one centre for diagnosis and treatment of chronic liver diseases. Geographic patterns of genotype distribution and associations of genotype with viral load, gender and age were investigated. Serum samples from 1731 individuals with a positive HCV Antibody Test, collected between 2016 and 2019, were analysed. HCV RNA levels were determined by HCV quantitative RNA real time polymerase chain reaction. Individuals with detectable HCV RNA further underwent HCV genotyping analysis using the Versant HCV Genotype Assay (LiPA) 2.0. The mean age of all patients was 52.9±15.3 (17–87). Among those, 54.1% were men and 45.9% women. Most patients came from the south-western region of Bulgaria (21.7%). Viral load was proven in 1385 out of 1731 individuals (VR=80%). Genotype 1 (G1) was the predominant genotype (89.8%), followed by G3 (8.5%), G2 (0.9%), G4 (0.6%) and G5 (0.1%). Among individuals with G1, infection with subtype 1b was seen in 77.4% and with subtype 1a in 22.6%. Viral load was not found to be dependent on age or gender. Viral load was higher in patients with G1 compared to G3 ($$p=0.001$$). Finally, patients with G1b were significantly older than patients with G1a ($$p&lt;0.001$$) and G3 ($$p&lt;0.001$$). VR in the studied population (80%) appears to be higher than the VR reported for Central Europe (73.3%). In Bulgaria, the most prevalent genotype is G1 (89.8%). This is a higher rate in comparison to the observed G1 rate in Central Europe (70%). The second most prevalent genotype is G3 (8.5%), with fewer cases identified than in Central Europe (21%).

Hepatitis E outbreak in the health district of Bocaranga-Koui, Central African Republic, 2018–2019

BackgroundHepatitis E virus (HEV) is a major public health disease causing large outbreaks and sporadic cases of acute hepatitis. We investigated an outbreak of HEV infection that occurred in September 2018 in the health district (HD) of Bocaranga-Koui, located in the northwestern part of Central African Republic (CAR).MethodsBlood samples were collected from 352 patients aged 0–85 years suspected to be infected with yellow fever (YF), according to the World Health Organization YF case definition. The notification forms from recorded cases were used. Water consumed in the HD were also collected. Human samples found negative for anti-YF IgM were then tested by ELISA for anti-HEV IgM and IgG antibodies. Positive anti-HEV (IgM and/or IgG) samples and collected water were then subjected to molecular biology tests using a real time RT-PCR assay, followed by a nested RT-PCR assay for sequencing and phylogenetic analysis.ResultsOf the 352 icterus patients included, anti-HEV IgM was found in 142 people (40.3%) and anti-HEV IgG in 175 (49.7%). Although HEV infection was detected in all age groups, there was a significant difference between the 0–10 age groups and others age groups (P = 0.001). Elevated levels of serum aminotransferase were observed in anti-HEV IgM-positive subjects. Phylogenetic analysis showed HEV genotype 1e in infected patients as well as in the contaminated water.ConclusionThis epidemic showed that CAR remains an HEV-endemic area. The genotype 1e strain was responsible for the HEV outbreak in Bocaranga-Koui HD. It is necessary to implement basic conditions of hygiene and sanitation to prevent further outbreaks of a HEV epidemics, to facilitate access to clean drinking water for the population, to launch intensive health education for basic hygiene measures, to sett up targeted hygiene promotion activities and, finally, to ensure that formal health care is available.

Molecular analysis of the env, LTR, and pX regions of bovine leukemia virus in dairy cattle of Türkiye.

Bovine leukemia virus is a retrovirus that causes enzootic bovine leukosis and is associated with global economic losses in the livestock industry. The aim of this study was to investigate the genotype determination of BLVs from cattle housed in 6 different farms in Türkiye and the characterization of their LTR and pX (tax, rex, R3, and G4 gene) regions. For this purpose, blood samples from 48 cattle infected with BLV were used. The phylogenetic analysis based on the env gene sequences revealed that all BLVs were clustered in genotype 1 (G1), and the sequences of the LTR (n = 48) and the pX region (n = 33) of BLVs were obtained. Also, analysis of these nucleic acid and amino acid sequences allowed assessments similar to those reported in earlier studies to be relevant to transactivation and pathogenesis. This study reports the molecular analysis of the LTR and pX region of BLVs in Türkiye for the first time.

Elucidating the biological characteristics and pathogenicity of the highly virulent G2a porcine epidemic diarrhea virus.

Since the large-scale outbreak of porcine epidemic diarrhoea (PED) in 2010, caused by the genotype 2 (G2) variant of the porcine epidemic diarrhoea virus (PEDV), pig farms in China, even those vaccinated with the G2b vaccine, have experienced infections from the G2a variant, leading to significant economic losses. This study successfully isolated the G2a strain DY2020 from positive small intestine contents (SICs) by blind passage on Vero cells for four generations. The SICs were taken from Daye, Hubei Province, China. The biological characteristics were identified by indirect immunofluorescence assay (IFA) and transmission electron microscopy (TEM). The growth kinetics of the strain on Vero cells were detected by TCID50, and the virus titre could reach 107.35 TCID50 ml-1 (SD: 5.07×106). The pathogenicity towards colostrum-deprived piglets was conducted by assessing faecal viral shedding, morphometric analysis of intestinal lesions, and immunohistochemical staining. The results showed that DY2020 was highly virulent to colostrum-deprived piglets, with severe watery diarrhoea and other clinical symptoms appeared at 6 h post-infection (h p.i.), and all died within 30 h. Pathological tissue examination results showed that the lesions mainly occurred in the intestines of piglets, causing pathological changes such as shortening of intestinal villi. In summary, the discovery of the G2a strain DY2020 in this study is of great significance for understanding Hubei PEDV and provides an important theoretical basis for the development of new efficient PEDV vaccines.

Computational medicinal chemistry applications to target Asian-prevalent strain of hepatitis C virus.

Hepatitis C Virus (HCV), affecting millions of people worldwide, is the leading cause of liver disorder, cirrhosis, and hepatocellular carcinoma. HCV is genetically diverse having eight genotypes and several subtypes predominant in different regions of the globe. The HCV NS3/4A protease is a primary therapeutic target for HCV with various FDA-approved antivirals and several clinical developments. However, available protease inhibitors (PIs) have lower potency against HCV genotype 3 (GT3), prevalent in South Asia. In this study, the incumbent computational tools were utilized to understand and explore interactions of the HCV GT3 receptor with the potential inhibitors after the virtual screening of one million compounds retrieved from the ZINC database. The molecular dynamics, pharmacological studies, and experimental studies uncovered the potential PIs as ZINC000224449889, ZINC000224374291, and ZINC000224374456 and the derivative of ZINC000224374456 from the ZINC library. The study revealed that these top-hit compounds exhibited good binding and better pharmacokinetics properties that might be considered the most promising compound against HCV GT3 protease. Viability test, on primary healthy Human Gingival Fibroblasts (HGFs) and cancerous AGS cell line, was also carried out to assess their safety profile after administration. In addition, Surface Plasmon Resonance (SPR) was also performed for the determination of affinity and kinetics of synthesized compounds with target proteins.

Evidence for the circulation of genotype 4 Eurasian avian-like lineage swine H1N1 influenza A viruses on Korean swine farms, obtained using a newly developed one-step multiplex RT-qPCR assay.

Genotype 4 (G4) Eurasian avian-like lineage swine H1N1 influenza A viruses, which are reassortants containing sequences from the pandemic 2009 H1N1 virus lineage, triple-reassortant-lineage internal genes, and EA-lineage external genes, have been reported in China since 2013. These have been predominant in pig populations since 2016 and have exhibited pandemic potential. In this study, we developed a one-step multiplex RT-qPCR assay targeting the M, HA1, and PB2 genes to detect G4 and related EA H1N1 viruses, with detection limits of 1.5 × 101 copies/μL and 1.15 × 10-2 ng/μL for the purified PCR products and RNA templates, respectively. The specificity of the detection method was confirmed using various influenza virus subtypes. When the one-step multiplex RT-qPCR assay was applied to swine respiratory samples collected between 2020 and 2022 in Korea, a virus related to G4 EA H1N1 strains was detected. Phylogenetic analysis based on portions of all eight genome segments showed that the positive sample contained HA, NA, PB2, NS, and NP genes closely related to those of G4 EA H1N1 viruses, confirming the ability of our assay to accurately detect G4 EA H1N1 viruses in the field.

Rubella virus genotype 2B endemicity and related utility of serum-based molecular characterization in Uganda

There are 13 globally recognized rubella virus genotypes of which only 2 (1E and 2B) have been detected recently. The largest percentage of all reported rubella virus sequences come from China and Japan with Africa reporting limited data. In a bid to address the lack of rubella genotype data in Uganda and the World Health Organization Africa region, we sought to characterize rubella viruses retrospectively using sera collected from suspected measles patients that turned out rubella IgM positive.Seven sequences belonging to genotype 2B sub-lineage 2B-L2c were obtained. These sequences clustered with other genotype 2B sequences previously reported from Uganda. None of the other genotypes (1E and 1G) reported from Uganda in the earlier years were detected. In addition, none of the sequences were obtained after the introduction of the measles-rubella containing vaccine. The above highlight the need for continuous rubella virological surveillance to confirm interruption of endemic rubella genotype circulation.

DYNAMICS OF LEAD TOLERANCE IN TOBACCO (NICOTIANA TABACUM L.) GENOTYPES

Lead nitrate has reports of significantly inhibiting plant growth. Early exploration of the genotypic difference for lead nitrate stress in tobacco has started. The presented study had eight tobacco genotypes subjected to 200 μM lead nitrate (Pb [NO3]2) stress in a hydroponic culture. Lead stress treatment to plants for 14 days had data recording at three times intervals of stressed plants. Assessing photosynthetic and antioxidant enzymes’ activities was in a time series order of one day, seven days, and 14 days. One-day, seven-day, and fourteen-day-old seedlings gained treatment of 200 μM lead nitrate stress and control. Soil Plant Analysis Development (SPAD) values for most genotypes decreased, while oxidant and anti-oxidant enzymes increased activity. Chlorophyll-a, chlorophyll-b, and total chlorophyll evaluated after lead nitrate toxicity showed reduced activity in studied tobacco genotypes compared with control as time passed. All chlorophyll contents, i.e., chlorophyll a, b, and total chlorophyll, declined with a longer span in lead nitrate solution. Genotype QVA-20 could benefit lead-salt tolerance and susceptible genotype ‘long chang’ cigarette based on chlorophyll content and SPAD values. Chlorophyll a capacity decreased as lead exposure to plants increased, but chlorophyll b increased in all genotypes on the 15th day. The MDA (malondialdehyde) content increased in all tobacco genotypes with increased lead nitrate exposure. Meanwhile, SOD (superoxide dismutase) contents decreased in genotypes RG-8, E1, and X6 with increased time, but POD (peroxidase) contents increased in all genotypes on the 14th day. Genotypes RG-8, E1, and X6 proved considerably tolerant of lead toxicity at 200 µM.

Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan.

The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92-102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes.

Evaluation of a Quantitative Dual-Target EBV DNA Test on a Fully Automated Molecular Testing System.

The measurement of Epstein-Barr virus (EBV) deoxyribonucleic acid (DNA) is key to diagnosing and managing EBV-associated complications in transplant recipients. The performance of the new Conformité Européenne (CE) and Food and Drug Administration (FDA)-cleared quantitative Roche cobas EBV real-time PCR assay was determined by using EDTA-plasma dilution panels and clinical samples that were spiked with either the World Health Organization's EBV international standard or high-titer EBV lambda stock. Correlation with the Abbott Realtime EBV assay was assessed in clinical specimens and conducted at two independent laboratories. An in silico analysis revealed that the dual-target test (EBNA1 and BMRF2) was 100% inclusive for the known diversity of EBV. The overall limit of detection (LoD) was 16.6 IU/mL for genotype 1 (GT1). GT2 LoD was verified at 18.8 IU/mL. The linear ranges were from 1.40 × 101 to 2.30 × 108 IU/mL and from 2.97 × 101 to 9.90 × 107 IU/mL for GT1 and GT2, respectively. Accuracy was confirmed across the linear range (mean difference not exceeding ±0.18 log10). Precision was not influenced by the factors analyzed (standard deviation of 0.02 to 0.17 log10), including the presence of potentially interfering endogenous or exogenous substances. Plasma samples were stable under several conditions (variable time points, storage, and freeze/thaw cycles). In clinical EBV DNA-positive samples, correlation between the cobas EBV test and the comparator was high (n = 126 valid results; R2 = 0.96) with a 0.1 mean log10 titer difference. The cobas EBV test is an accurate, sensitive, specific, and reproducible assay for the detection of EBV DNAemia in plasma. In general, high levels of automation and calibration to the international standard will lead to improvements in the harmonization of quantitative EBV DNA test results across laboratories.

Newly emerged genotypes of highly pathogenic H5N8 avian influenza viruses in Kagoshima prefecture, Japan during winter 2020/21.

During the 2020/21 winter season, 29 and 10 H5N8 high pathogenicity avian influenza viruses (HPAIVs) were isolated from environmental water and wild birds, respectively, in Kagoshima prefecture, Japan. Furthermore, seven subtypes of low pathogenicity avian influenza viruses (LPAIVs) were also isolated; H1N1, H2N9, H3N2, H3N6, H3N8, H4N6, and H6N6 subtypes. While the H5 hemagglutinin (HA) genes of the G1 cluster were isolated throughout the winter season, those of the G2 cluster were also detected in late winter, suggesting that H5 HPAIVs possessing H5 HA genes from the two different clusters were individually introduced into Kagoshima prefecture. Intriguingly, genetic constellations revealed that the H5N8 HPAIVs could be classified into six genotypes, including four previously reported genotypes (E1, E2, E3, and E7), and two new genotypes (tentatively named E8 and E9). The PB1 and PA gene segments of genotypes E8 and E9 shared high similarity with those of LPAIVs, whereas the remaining gene segments were close to those of genotype E1. Furthermore, LPAIVs whose PA gene segment was close to that of genotype E9 were isolated from the environmental water. Overall, we revealed that various HPAIV genotypes circulated in Kagoshima prefecture during the 2020/21 winter season. This study highlights the importance of monitoring both HPAIV and LPAIV to better understand AIV ecology in migratory waterfowl populations.

Determining of the effects of paclobutrazol treatments on seedling height control of wild Gypsophila bicolor (Freyn &amp; Sint.) Grossh

Within the scope of this study, seeds were collected from Gypsophila bicolor (Freyn&amp;Sint.) Grossh plants in their natural environment and two different locations (Turkey). The research was carried out to determine the effects of paclobutrazol applied at different concentrations (0.6, 0.9, 1.2, 1.5- and 2.0-ml L-1) on the seedling height control in the cotyledon leaf stage of G. bicolor. As a result of the study, it was determined that the decrease in the number of leaves per plant was determined at a dose of 1.2 mg L-1 paclobutrazol. The effect of paclobutrazol treatments on the seedling height control of G. bicolor changed according to the genotype as well as the dose. As the dose of paclobutrazol applied increased, the number of side branches decreased. It was determined that the seedling stem thickness increased in 47.71% with the dose of 2.0 mg L-1 when compared to the control treatment. The application in which the highest chlorophyll (SPAD) value was obtained from the application with a dose of 1.5 mg L-1. The chlorophyll value of G2 (Genotype 2 (ERZ) (G2)) was higher than that of G1 (Genotype 1 (VAN)). Seedling biomass of G1 increased in 15.87% in 1.2 mg L-1 treatment when compared to control. In the present study, darker green leaves were obtained from the highest dose of paclobutrazol, 2.0 mg L-1. As a general result, it was concluded that 1.5 mg L-1 dose of paclobutrazol was sufficient for both genotypes for plant height control in the seedling period.

Biological Characteristics and Pathogenicity Analysis of a Low Virulence G2a Porcine Epidemic Diarrhea Virus.

Since the outbreak caused by a porcine epidemic diarrhea virus (PEDV) variant in 2010, the current epidemic of PEDV genotype 2 (G2) has caused huge economic losses to the pig industry in China. In order to better understand the biological characteristics and pathogenicity of the current PEDV field strains, 12 PEDV isolates were collected and plaque purified during 2017 to 2018 in Guangxi, China. The neutralizing epitopes of the spike proteins and the ORF3 proteins were analyzed to evaluate genetic variations, and they were compared with the reported G2a and G2b strains. Phylogenetic analysis of the S protein showed that the 12 isolates were clustered into the G2 subgroup (with 5 and 7 strains in G2a and G2b, respectively) and that they shared 97.4 to 99.9% amino acid identities. Among them, one of the G2a strains, CH/GXNN-1/2018, which had a titer of 106.15 PFU/mL, was selected for pathogenicity analysis. Although piglets infected with the CH/GXNN-1/2018 strain exhibited severe clinical signs and the highest level of virus shedding within 24 h postinfection (hpi), recovery and decreased virus shedding were seen after 48 hpi, and no piglets died during the whole process. Thus, the CH/GXNN-1/2018 strain had low virulence in suckling piglets. Virus neutralizing antibody analysis showed that the CH/GXNN-1/2018 strain induced cross-protection against both homologous G2a and heterologous G2b PEDV strains as early as 72 hpi. These results are of great significance for understanding PEDV in Guangxi, China, and they provide a promising naturally occurring low-virulent vaccine candidate for further study. IMPORTANCE The current epidemic of porcine epidemic diarrhea virus (PEDV) G2 has caused huge economic losses to the pig industry. Evaluation for low virulence of the PEDV strains of subgroup G2a would be useful for the future development of effective vaccines. In this study, 12 field strains of PEDV were obtained successfully, and they were characterized from Guangxi, China. The neutralizing epitopes of the spike proteins and the ORF3 proteins were analyzed to evaluate antigenic variations. One of the G2a strains, CH/GXNN-1/2018, was selected for pathogenicity analysis, and it showed that the CH/GXNN-1/2018 strain had low virulence in suckling piglets. These results provide a promising naturally occurring low-virulent vaccine candidate for further study.

Sub-genotypes of hepatitis C virus in the Middle East and North Africa: Patterns of distribution and temporal changes.

Infection with the hepatitis C virus (HCV) remains a considerable public health concern in the Middle East and North Africa (MENA). The objectives of this study were to analyze the HCV genotype (GT) and sub-genotype (SGT) distribution in the MENA region and to assess the temporal change in the number of sequences within the MENA region. All HCV molecular sequences collected in the MENA region had been retrieved from GenBank as of 1 August 2022. The number of HCV sequences retrieved was 6740 representing sequences from a total of 17 MENA countries with a majority from Iran (n=1969, 29.2%), Egypt (n=1591, 23.6%), Tunisia (n=1305, 19.4%) and Saudi Arabia (n=1085, 16.1%). The determination of GT/SGT was based on the NCBI genotyping and Blast tool. Genotype 1 (GT1) dominated infections in the MENA (n=2777, 41.2%), followed by GT4 (n=2566, 39.0%). Additionally, SGT4a (1515/6393, 23.7%) was the most common SGT in the MENA, and SGT4a was dominant in Egypt and Saudi Arabia, followed by SGT1b (n=1308, 20.5%), which was dominant in Morocco and Tunisia, while SGT1a (n=1275, 19.9%) was common in Iran, Iraq and Palestine. Furthermore, significant temporal increase in the number of HCV MENA sequences was observed. On the SGT level, specific patterns of HCV genetic diversity were seen in the MENA region, with the most common SGT being 4a, in addition to increasing the availability of HCV sequences in the MENA region.

Construction and immunogenicity of a trypsin-independent porcine epidemic diarrhea virus variant.

Porcine epidemic diarrhea virus (PEDV) is a re-emerging enteropathogenic coronavirus that causes high mortality in neonatal piglets. The addition of trypsin plays a crucial role in the propagation of PEDV, but also increases the complexity of vaccine production and increases its cost. Previous studies have suggested that the S2' site and Y976/977 of the PEDV spike (S) protein might be the determinants of PEDV trypsin independence. In this study, to achieve a recombinant trypsin-independent PEDV strain, we used trypsin-dependent genotype 2 (G2) PEDV variant AJ1102 to generate three recombinant PEDVs with mutations in S (S2' site R894G and/or Y976H). The three recombinant PEDVs were still trypsin dependent, suggesting that the S2' site R894 and Y976 of AJ1102 S are not key sites for PEDV trypsin dependence. Therefore, we used AJ1102 and the classical trypsin-independent genotype 1 (G1) PEDV strain JS2008 to generate a recombinant PEDV carrying a chimeric S protein, and successfully obtained trypsin-independent PEDV strain rAJ1102-S2'JS2008, in which the S2 (amino acids 894-1386) domain was replaced with the corresponding JS2008 sequence. Importantly, immunization with rAJ1102-S2'JS2008 induced neutralizing antibodies against both AJ1102 and JS2008. Collectively, these results suggest that rAJ1102-S2'JS2008 is a novel vaccine candidate with significant advantages, including no trypsin requirement for viral propagation to high titers and the potential provision of protection for pigs against G1 and G2 PEDV infections.

Global Dynamics of Porcine Enteric Coronavirus PEDV Epidemiology, Evolution, and Transmission.

With a possible origin from bats, the alphacoronavirus Porcine epidemic diarrhea virus (PEDV) causes significant hazards and widespread epidemics in the swine population. However, the ecology, evolution, and spread of PEDV are still unclear. Here, from 149,869 fecal and intestinal tissue samples of pigs collected in an 11-year survey, we identified PEDV as the most dominant virus in diarrheal animals. Global whole genomic and evolutionary analyses of 672 PEDV strains revealed the fast-evolving PEDV genotype 2 (G2) strains as the main epidemic viruses worldwide, which seems to correlate with the use of G2-targeting vaccines. The evolving pattern of the G2 viruses presents geographic bias as they evolve tachytely in South Korea but undergo the highest recombination in China. Therefore, we clustered six PEDV haplotypes in China, whereas South Korea held five haplotypes, including a unique haplotype G. In addition, an assessment of the spatiotemporal spread route of PEDV indicates Germany and Japan as the primary hubs for PEDV dissemination in Europe and Asia, respectively. Overall, our findings provide novel insights into the epidemiology, evolution, and transmission of PEDV, and thus may lay a foundation for the prevention and control of PEDV and other coronaviruses.