Novel genotyping definition and molecular characteristics of canine circovirus in China.

Canine circovirus (CCV) has been detected globally, but its genotyping remains unevenly characterized. To comprehend the evolution and genotyping of CCV, 887 rectal swabs of dogs were collected during 2018-2023. According to p-distance/frequency histograms and phylogenetic trees based on complete genome sequences, the 21 newly obtained Chinese and 84 reference CCV strains were mainly divided into 7 subtypes (CCV-1a, CCV-1b, CCV-1c, CCV-1d, CCV-1e, CCV-2a, and CCV-2b). Among the 21 newly obtained CCVs, 9 strains belonged to CCV-1d, 2 strains belonged to CCV-1b, and the remaining strains belonged to CCV-1c. Recombination analysis indicated that recombination events occurred between CCV strains of different subtypes, hosts, and countries. The CCV capsid protein features 19 variable sites, with 2 sites (T58Q, P239A) displaying regional specificity and 3 (Q57T, E150Q, and T195Q) manifesting subtype specificity. Therefore, this genotyping analysis provides a reference for the molecular characteristics of CCV strains found globally.

Insecticide binding mode analysis and biological effects of acetylcholinesterase target-site resistance mutations in Spodoptera frugiperda.

It is urgent to solve insecticide resistance issues for fall armyworm (FAW), Spodoptera frugiperda. Some acetylcholinesterase-1 (Ace-1) mutations (A201S, G227A and F290V) have been identified as a cause of FAW resistance to organophosphates (OPs) and carbamates insecticides (CXs). However, the structural biological mechanisms on the relationship between the Ace-1 mutations and resistance to OPs and CXs still remain elusive. In this study, the A201S and F290V mutaions were found in eight fields populations of FAW except the G227A. Molecular docking revealed that the four Ace-1 proteins (Ace1-WT, Ace1-A201S, Ace1-G227A and Ace1-F290V) had the same binding modes and the same binding energies with acetylcholine (Ach), trichlorfon, chlorpyrifos, methomyl, carbaryl and chlorpyrifos oxide. The structural biological analysis revealed that the A201S mutations can enhance enzyme catalytic efficiency by introducing the hydroxyl group (-OH) from serine which performed the same function as the main-chain -NH and enhanced the interaction with the carboxy oxygen of acetylcholine (Ach), and the F290V mutation can effectively improve FAW resistance to insecticides by increasing the likelihood of Ach to enter the enzyme's active center for phenylalanine replaced by smaller valine under insecticide inhibition conditions. The bioassays and age-stage-specific life table analysis of FAW-SS and FAW-F290V populations revealed that F290V mutation effectively contributed to FAW resistance with a low fitness cost. This study provides a theoretical basis for future pest resistance management.

Role of MIC levels and 23S rRNA mutation sites to clarithromycin in 14-day clarithromycin bismuth quadruple therapy for Helicobacter pylori eradication: A prospective trial in Beijing.

Background: Rising clarithromycin resistance undermines Helicobacter pylori (H. pylori) treatment efficacy. We aimed to determine clarithromycin's minimum inhibitory concentration (MIC) levels and identify specific mutation sites in the 23S ribosomal subunit (23S rRNA) that predict treatment outcomes in a 14-day regimen of clarithromycin bismuth quadruple therapy (amoxicillin 1g, clarithromycin 500 mg, rabeprazole 10 mg, and colloidal bismuth pectin 200 mg). Materials and methods: We included adult H. pylori patients who hadn't previously undergone clarithromycin-based treatment, either as initial or rescue therapy. Exclusions were made for penicillin allergy, recent use of related medications, severe illnesses, or inability to cooperate. Patients underwent a 14-day clarithromycin bismuth quadruple therapy. Gastric mucosa specimens were obtained during endoscopy before eradication. MIC against amoxicillin and clarithromycin was determined using the E-test method. The receiver operating characteristic (ROC) curve helped to find the optimal clarithromycin resistance MIC breakpoint. Genetic sequences of H. pylori 23S rRNA were identified through Sanger Sequencing. (ChiCTR2200061476). Results: Out of 196 patients recruited, 92 met the inclusion criteria for the per-protocol (PP) population. The overall intention-to-treat (ITT) eradication rate was 80.00 % (84/105), while the modified intention-to-treat (MITT) and PP eradication rates were 90.32 % (84/93) and 91.30 % (84/92) respectively. No amoxicillin resistance was observed, but clarithromycin resistance rates were 36.19 % (38/105), 35.48 % (33/93), and 34.78 % (33/92) in the ITT, MITT, and PP populations respectively. Compared with the traditional clarithromycin resistance breakpoint of 0.25 µg/mL, a MIC threshold of 12 µg/mL predicted better eradication. Among 173 mutations on 152 sites in the 23S rRNA gene, only the 2143A > G mutation could predict eradication outcomes (p < 0.000). Conclusions: Interpretation of elevated MIC values is crucial in susceptibility testing, rather than a binary "susceptible" or "resistant" classification. The 2143A > G mutation has limited specificity in predicting eradication outcomes, necessitating further investigation into additional mutation sites associated with clarithromycin resistance.

Comparative analysis of clinical and immunological profiles across Omicron BA.5.2 subvariants using next-generation sequencing in a Chinese cohort.

Objective: The Omicron BA.5.2 variant of SARS-CoV-2 has undergone several evolutionary adaptations, leading to multiple subvariants. Rapid and accurate characterization of these subvariants is essential for effective treatment, particularly in critically ill patients. This study leverages Next-Generation Sequencing (NGS) to elucidate the clinical and immunological features across different Omicron BA.5.2 subvariants. Methods: We enrolled 28 patients infected with the Omicron variant, hospitalized in Zhangjiajie People's Hospital, Hunan, China, between January 20, 2023, and March 31, 2023. Throat swabs were collected upon admission for NGS-based identification of Omicron subvariants. Clinical data, including qSOFA scores and key laboratory tests, were collated. A detailed analysis of lymphocyte subsets was conducted to ascertain the extent of immune cell damage and disease severity. Results: Patients were infected with various Omicron subvariants, including BA.5.2.48, BA.5.2.49, BA.5.2.6, BF.7.14, DY.1, DY.2, DY.3, and DY.4. Despite having 43 identical mutation sites, each subvariant exhibited unique marker mutations. Critically ill patients demonstrated significant depletion in total lymphocyte count, T cells, CD4, CD8, B cells, and NK cells (P < 0.05). However, there were no significant differences in clinical and immunological markers across the subvariants. Conclusion: This study reveals that critically ill patients infected with different Omicron BA.5.2 subvariants experience similar levels of cellular immune dysfunction and inflammatory response. Four mutations - ORF1a:K3353R, ORF1a:L3667F, ORF1b:S997P, S:T883I showed correlation with immunological responses although this conclusion suffers from the small sample size. Our findings underscore the utility of NGS in the comprehensive assessment of infectious diseases, contributing to more effective clinical decision-making.

Prevalence of HIV Transmitted Drug Resistance in Nanjing from 2018 to 2021.

Background: Transmitted drug resistance (TDR) is a major challenge in the clinical management of acquired immunodeficiency syndrome (AIDS). Therefore, this study aimed to investigate the epidemic characteristics of and risk factors for human immunodeficiency virus (HIV)-1 TDR in Nanjing from 2018 to 2021 to provide support for clinical management. Methods: The HIV-1 Pol gene was amplified by nested reverse transcription polymerase chain reaction from venous blood of 1190 HIV-infected patients who did not receive antiviral therapy, and the amplified product was sequenced using an in-house sequencing method. The sequencing result was compared with the HIV drug resistance database from Stanford University to elucidate the rates of antiviral drug resistance and distribution of drug-resistant mutation sites. Factors associated with TDR were evaluated using a logistic regression model. Results: Detection of drug resistance at the gene level was successful in 1138 of 1190 HIV-1-infected patients (95.6%), and the overall 4-year drug resistance rate was 8.2% (93/1138). The drug resistance rate was higher for non-nucleoside reverse transcriptase inhibitors (NNRTIs; 6.7%) than for nucleoside reverse transcriptase inhibitors (NRTIs; 2.5%) or protease inhibitors (PIs; 0.1%) (χ 2 = 83.907, P<0.0001). The most common NNRTI-related mutation was V179D/E followed by K103N. M184V was the dominant NRTI-associated mutation, and M46L/I was the most prevalent PI-associated mutation. A CD4+ T cell count of <50 cells/µL was significantly associated with an increased risk of TDR (OR=3.62, 95% CI: 1.38-9.51, P=0.009). Conclusion: The prevalence of TDR in the city of Nanjing from 2018 to 2021 was at a moderate epidemic risk according to World Health Organization standards. Continuous monitoring of TDR can inform clinical diagnosis and treatment. Patients with advanced disease and a low CD4+ T lymphocyte count are more likely to have TDR in Nanjing.

The whole-genome sequencing of prevalent DENV-1 strains during the largest dengue virus outbreak in Xishuangbanna Dai autonomous prefecture in 2019.

In 2019, a serious dengue virus (DENV) infection broke out in the Xishuangbanna Dai Autonomous Prefecture, China. Therefore, we conducted a molecular epidemiological analysis in people that contracted DENV serotype 1 (DENV-1) during this year. We analyzed the molecular epidemiology of six DENV-1 epidemic strains in 2019 by full-length genome sequencing, amino acid mutation site analysis, evolutionary tree analysis, and recombination site comparison analysis. Through the analysis of amino acid mutation sites, it was found that DENV-1 strain (MW386867) was different from the other five epidemic DENV-1 strains in Xishuangbanna in 2019. MW386867 had unique mutation sites at six loci. The six epidemic DENV-1 strains in Xishuangbanna in 2019 were divided into two clusters. MW386867 was highly similar to the MG679800 (Myanmar 2017), MG679801 (Myanmar 2017), and KC172834 (Laos 2008), and the other five strains were highly similar to JQ045660 (Vietnam 2011), FJ176780 (GuangDong 2006). Genetic recombination analysis revealed that there was no recombination signal in the six epidemic DENV-1 strains in Xishuangbanna in 2019. We speculate that the DENV-1 epidemic in 2019 has a co-epidemic of local strains and cross-border strains.

Label-free detection of ssDNA base insertion and deletion mutations by surface-enhanced Raman spectroscopy.

Surface-enhanced Raman spectroscopy (SERS), as a label-free, highly sensitive analytical method, has become an important tool for providing substance fingerprints. In this study, silver nanoparticles containing thiosulfate ions and calcium ions (Ag@SCNPs) have been used as an enhanced substrate to eliminate the interference of impurities on DNA signals. Intrinsic structural information on single-strand DNA (ssDNA) was directly obtained through SERS. The improved enhancement system was used to explore the base-stacking rules of ssDNA in a solution environment. For the first time, single-base insertion mutations and deletion mutations, as well as their exact mutation sites, were identified, and Raman spectra with high stability, repeatability, and high signal-to-noise ratio were obtained. The method is simple, fast, and accurate, and the detection process is nondestructive. It has potential to be applied in the fields of medical diagnosis and genetics research.

Evaluation of the Outcome of Antiviral Therapy among Individuals Infected HIV-1 in Suqian District of Jiangsu Province, China.

BACKGROUND: To evaluate the condition of antiviral therapy (ART) for individuals infected HIV-1 in Suqian district of Jiangsu Province, China. METHODS: Altogether, 561 HIV-positive patients who received antiviral therapy in Suqian district in 2019 were recruited. EDTA anticoagulated blood was collected and separated to obtain the plasma samples. Viral load (VL) were tested for evaluating the outcome of ART. Then samples with VL beyond 1000IU/mL were used to conduct the molecular test in order to master the characters of HIV-1 and the prevalence of resistance strains. RESULTS: VL results showed that the virus in 91.1% of the patients who received continuous antiviral treatment for more than 6 months were effectively inhibited (VL ≤ 1000 IU / ml). Among the 50 patients who failed in the treatment, 46 HIV-1 pol gene sequences were obtained, and the positive rate was 92.0%. The most prevalent strain was CRF_ 07bc (32.6%), and new epidemic strains, such as 67_01B, 79_0107, 87_cpx, were popular in this district. Drug resistance test results showed that 56.5% of the patients failed in antiviral treatment due to drug resistance, mainly resistant to the national first-line antiviral drug 3TC. Drug-resistant strains were not found in 43.5% of the patients. CONCLUSION: ART achieved a satisfied result in Suqian district, but the main cause resulting in ART-failure was resistant, so it is very necessary to enhance the education of adherence prior to the initiation of ART.

Combined analysis of whole-exon sequencing and lncRNA sequencing in type 2 diabetes mellitus patients with obesity.

This study sought to find more exon mutation sites and lncRNA candidates associated with type 2 diabetes mellitus (T2DM) patients with obesity (O-T2DM). We used O-T2DM patients and healthy individuals to detect mutations in their peripheral blood by whole-exon sequencing. And changes in lncRNA expression caused by mutation sites were studied at the RNA level. Then, we performed GO analysis and KEGG pathway analysis. We found a total of 277 377 mutation sites between O-T2DM and healthy individuals. Then, we performed a DNA-RNA joint analysis. Based on the screening of harmful sites, 30 mutant genes shared in O-T2DM patients were screened. At the RNA level, mutations of 106 differentially expressed genes were displayed. Finally, a consensus mutation site and differential expression consensus gene screening were performed. In the current study, the results revealed significant differences in exon sites in peripheral blood between O-T2DM and healthy individuals, which may play an important role in the pathogenesis of O-T2DM by affecting the expression of the corresponding lncRNA. This study provides clues to the molecular mechanisms of metabolic disorders in O-T2DM patients at the DNA and RNA levels, as well as biomarkers of the risk of these disorders.

Methylmalonic acidemia: Current status and research priorities.

Methylmalonic acidemia (MMA) is a lethal, severe heterogeneous disorder of methylmalonate and cobalamin (cbl; vitamin B12) metabolism with poor prognosis. Two main forms of the disease have been identified, isolated methylmalonic acidurias and combined methylmalonic aciduria and homocystinuria, which is respectively caused by different gene mutations. Here, we review the improvement of pathogenesis, diagnosis and treatment in MMA. Importantly, the reported epidemiological data of MMA patients in China and the hot mutation sites in Chinese patients are listed, which will aid in improving healthcare of Chinese patients in the future. c.729_730insTT was the most common mutation in Chinese isolated MMA patients, while c.609G>A and c.658_660delAAG were in Chinese cblC type patients according to unrelated studies. The estimated newborn screening incidence was reported to be 1:26,000, 1:3,920, 1:11,160, 1:6,032 respectively in Beijing and Shanghai, Shandong province, Taian district, and Henan province of China. Alternatively, when patients with suspected inherited metabolic diseases were used as the screened sample, the relatively high incidence 0.3% and 1.32% were respectively obtained in southern China and throughout all the provinces of mainland China and Macao with the exception of five provinces (Hainan, Neimenggu, Tibet, Ningxia, and Hong Kong).

Effects of heavy-ion beam irradiation on avermectin B1a and its analogues production by Streptomyces avermitilis.

The biggest challenge in anabolism research is to improve the stability and safety of microbial metabolite production on an industrial scale. One class of metabolites, avermectins, are produced by Streptomyces avermitilis. In this study, an avermectin B1a-high-producing mutant was produced using heavy ion mutagenesis and selected based on LTQ-MS and HPLC-UV method. The mutants ZJAV-Y-147 and ZJAV-Y-HS, obtained after subjecting the spores of S. avermitilis to 70 Gy of 12C6+ heavy ion irradiation, were found to best improve the avermectin B1a production (4822.23 µg/mL and 4632.17 µg/mL, respectively). These two mutants' yielded of avermectin B1a were 2-fold high than the original strains. The DNA of the original and mutant strains were analyzed by RAPD technique with four random primers after irradiated with ion beam irradiation. The results show that different high-titer S. avermitilis strains contain different genetic modifications. In addition, the mutation position, mutation type and sequence context of all mutations of aveC, aveD, aveI, aveR gene in two mutants S.avermitilis were researched, and the production of avermectin B1a and its analogues of wild-type and mutants were analyzed by fermenting 240 h, which was suggested that the partial base deletion of aveI gene may be the key sites for increasing avermectin B1a production after the 12C6+-ion irradiation. All these modifications promote increased avermectin biosynthesis, leading to multiple high-titer S. avermitilis strains. The results demonstrate that this is an effective approach to engineer S. avermitilis as a host for the biological production of commercial analogs.

Visceral pathology of acute systemic injury in newborn mice on the onset of Coxsackie virus infection.

Coxsackievirus B (CVB) is a significant pathogen of neonatal diseases with severe systemic involvement and high mortality. Hence, it is essential to develop a CVB-induced acute systemic disease model on newborn mouse and study the injury at the onset phase. In this work, a clinical strain of CVB3, Nancy, and its variant strain, Macocy, were adopted in 24 hour old neonates by oral infection. The pathological changes in the heart, liver and lung tissues were analyzed by pathology assays. In situ end labeling assay for programmed cell death was carried out for liver tissues. The data on fatality and infection rates and pathology scores were analyzed statistically. The genomic sequences of the two strains were aligned. The model represented the manifest clinical syndromes of hepatitis, pneumonia and myocardial injury at the onset phase, in which massive numbers of hepatocytes had undergone programmed cell death. Statistical and pathological analysis indicated that the myocardial injury was mild, whereas the liver and lung were more severe. The fatality rate, infection and pathology of the two CVB strains were the same. Therefore, two nucleotide mutations in the 5' UTR and four amino acid mutations in polyprotein, which did not alter virulence, were shown. By peroral CVB infection of neonatal mice, we developed an acute systemic disease model for studying visceral pathology and systemic disease. At the onset of acute neonatal systemic disease, the hepatitis and pneumonia may be the dominant reason of death, as the injury of liver and lung is more severe than that of heart.