Drug Resistance Sites Research Articles

The Global Trend of Drug Resistant Sites in Influenza A Virus Neuraminidase Protein from 2011 to 2020.

Influenza A virus (IAV) causes highly contagious respiratory disease worldwide, so prevention and control of IAV is extremely important. However, overuse of neuraminidase inhibitor (NAI) drugs leads to drug resistance. To explore the up-to-date geographical distribution and evolution of drug-resistant mutations (DRMs) in the NA protein of IAV, 81,492 near full-length NA sequences downloaded from NCBI and GISAID databases, including 34,481 H1N1 and 46,622 H3N2, were processed and analyzed. Our results showed the annual number of NA sequences from 2011 to 2019 continuously increased. Meanwhile, almost 85% of sequences were from developed countries in North America, Europe and Asia. Clustering analysis demonstrated H3N2 varied more than H1N1. Notably, H3N2 exhibited a higher frequency of DRMs than H1N1, with prevailing DRMs mainly located at non-active sites within the NA protein. Phylogenetic analyses showed NA harboring DRMs collected in the same year and from the same location clustered together, which may be related to the local economic level, clinical monitoring of DRMs and research level. Consequently, it is imperative to enhance global surveillance targeting drug resistance in IAV infections which can mitigate the transmission of drug-resistant strains. In summary, our research provides valuable insights for clinical medication while establishing a robust scientific basis for IAV prevention and treatment strategies to improve overall efficacy.

Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance

BackgroundHuman Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis. MethodsWe implemented dWGS and performed parallel pol Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis. ResultsOptimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of pol sequence alone. ConclusionsThese findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional pol sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.

Metagenomic next-generation sequencing-based retrospective investigation of the drug resistance sites of Mycoplasma pneumoniae in children

Objective: To analyze the drug-resistant gene loci of Mycoplasma pneumoniae (MP) using metagenomic next-generation sequencing (mNGS). Methods: From November 2022 to October 2023, 697 clinical samples (including sputum, alveolar lavage fluid and blood) of 686 children with Mycoplasma pneumoniae positive detected by mNGS were retrospectively analyzed. Samples were divided into intensive care unit (ICU) group and non-ICU group, Chi-square test was used to compare groups, and Mann-Kendall trend test was used to analyze the change trend of the detection rate of drug resistance gene loci over time. Results: Of the 697 samples, 164 were from the ICU group and 533 were from the non-ICU group. The detection rate of Mycoplasma pneumoniae resistance gene was 44.3% (309/697), and all detected drug-resistant gene loci of MP were A2063G. The detection rate of Mycoplasma pneumoniae in ICU group was 50.0% (82/164), and the detection rates of Mycoplasma pneumoniae resistance gene loci in sputum, alveolus lavage fluid and blood samples were 75.0% (18/24) and 48.4% (62/128), respectively. The detection rate in sputum was higher than alveolus lavage fluid samples (χ2=5.72,P=0.017). The detection rate of Mycoplasma pneumoniae in non-ICU group was 42.6% (227/533), the detection rate of Mycoplasma pneumoniae resistance gene loci in sputum and alveolar lavage fluid was 40.0% (16/40), 44.3% (201/454), and no detection rate in blood samples (0/12). There was no significant difference in the detection rate of alveolar lavage fluid and sputum (χ2=0.27, P=0.602). From November 2022 to October 2023, the detection rate of submitted samples showed an increasing trend month by month (overall: Z=3.99, ICU inspection group: Z=2.93, non-ICU group: Z=3.01, all P<0.01). Among the bacteria commonly detected with Mycoplasma pneumoniae, Streptococcus pneumoniae accounted for the highest proportion, the detection rate was 15.5% (108/697), and Epstein-Barr virus accounted for the highest proportion of 17.6% (123/697). Conclusions: From November 2022 to October 2023, the detection rate of Mycoplasma pneumoniae drug resistance gene loci showed an increasing trend. The detection rate of drug resistance gene loci in sputum samples of ICU group was higher than alveolus lavage fluid. No new drug resistance site were detected.

The global epidemic trend analysis of influenza type B drug resistance sites from 2006 to 2018.

Influenza is a severe respiratory viral infection that causes significant morbidity and mortality, due to annual epidemics and unpredictable pandemics. With the extensive use of neuraminidase inhibitor (NAI) drugs, the influenza B virus has carried different drug-resistant mutations. Thus, this study aimed to analyze the prevalence of drug-resistant mutations of the influenza B virus. Near full-length sequences of the neuraminidase (NA) region of all influenza B viruses from January 1, 2006, to December 31, 2018, were downloaded from public databases GISAID and NCBI. Multiple sequence alignments were performed using Clustal Omega 1.2.4 software. Subsequently, phylogenetic trees were constructed by FastTree 2.1.11 and clustered by ClusterPickergui_1.2.3.JAR. Then, the major drug resistance sites and surrounding auxiliary sites were analyzed by Mega-X and Weblogo tools. Among the amino acid sequences of NA from 2006 to 2018, only Clust04 in 2018 carried a D197N mutation of the NA active site, while other drug resistance sites were conserved without mutation. According to the Weblogo analysis, a large number of N198, S295, K373, and K375 mutations were found in the amino acid residues at the auxiliary sites surrounding D197, N294, and R374. We found the D197N mutation in Clust04 of the 2018 influenza B virus, with a large number of N198, S295, K373, and K375 mutations in the helper sites around N197, N294, and R374 from 2006 to 2018. NA inhibitors are currently the only kind of specific antiviral agent for the influenza B virus, although these mutations cause mild NAIs resistance.

Phylogenetic and epidemiological characteristics of H9N2 avian influenza viruses in Shandong Province, China from 2019 to 2021

H9N2 avian influenza virus (AIV) has widely circulated in poultry worldwide and sporadic infections in humans and mammals. During our surveillance of chicken from 2019 to 2021 in Shandong Province, China, we isolated 11 H9N2 AIVs. Phylogenetic analyses showed that the 8 gene segments of the 11 isolates were closely related to several sublineages of Eurasian lineage: BJ/94-like clades (HA and NA genes), G1-like clades (PB2 and M genes), and SH/F/98-like clades (PB1, PA, NP and NS genes). The isolates showed mutation sites that preferentially bind to human-like receptors (HA) and mammalian fitness sites (PB2, PB1 and PA), as well as mutations in antigen and drug resistance sites. Moreover, studies with mice revealed 4 isolates with varying levels of pathogenicity. The average antibody titer of the H9N2 AIVs was 8.60 log2. Based on our results, the epidemiological surveillance of H9N2 AIVs should be strengthened.

TMIC-28. COMBINING INDUCED NEURAL STEM CELL THERAPY AND IMMUNOMODULATION IN GLIOBLASTOMA

Abstract Glioblastoma (GBM) is an aggressive malignant adult brain tumor and is characterized by poor prognosis and survival outcome. Insufficient drug accumulation to the tumor site and development of monotherapy drug resistance are critical challenges to overcome in combating GBM. Human induced neural stem cells (hiNSC) therapy is promising due to the stem cells’ innate capability to migrate to the tumors and deliver therapeutics. We previously have developed spheroidal iNSCs and engineered them to constitutively secrete pro-apoptotic protein TRAIL—hiNeuroS-TRAIL. However, investigating a combination therapy along with hiNeuroS-TRAIL therapy is needed to potentially avoid monotherapy resistance and enhance overall treatment durability. One of the GBM hallmarks is its immunosuppressed tumor microenvironment (TME). GBM-associated macrophages and microglia (GAMs) display pro-tumoral phenotypes in TME—inhibiting their ability to target the tumor cells or recruit other immune cells. In humans, higher glioma grade is associated with higher expression of Mer Tyrosine Kinase Receptor (MerTK) in both GBM cells and GAMs. Activation of MerTK in GAMs and GBM cells exacerbates immunosuppression and tumor progression respectively. Inhibiting MerTK activation via a small molecule drug, MRX-2843 and combining with hiNeuroS-TRAIL demonstrated robust synergistic tumor killing effects in vitro (CDI=0.22) and ex vivo (CDI=0.18). Additionally, the preliminary data for in vivo pilot study revealed that the median survival for the combination therapy treated group of mice extended over 24 days whereas the median survival for control, MRX-2843, and hiNeuroS-TRAIL treated groups of mice were 16, 18, and 21 days respectively. We think that combining these two therapies could significantly extend the survival in our murine model of GBM. Therefore, we will be optimizing dose concentration and cell counts for single agent therapies, and we will then repeat in vivo y synergy study with optimized therapies and a larger sample size to fully uncover the potential of this combination therapy.

Characterization of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China

BackgroundSichuan province is one of the highest AIDS epidemic provinces in China, with a large number of floating population. The annual number of cases of HIV/AIDS reported in Sichuan has been the highest province in China for several successive years. There is a lack of widespread and representative data on the distribution of HIV genotypes in Sichuan. We aim to investigate the characteristics of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China.MethodArchived plasma samples (n = 1524) from HIV-1 newly-diagnosed individuals in April 2019 were selected by cross-sectional investigation from all 21 cities in Sichuan province. Phylogenetic relationship, transmission cluster, and genotypic drug resistance analyses were performed using HIV-1 polymerase (pol) gene sequences. We also analysed the association of demographic and virological factors with transmitted drug-resistance (TDR) and transmission clusters.ResultsPartial pol gene sequences were obtained from 1297 cases. HIV-1 epidemic strains in Sichuan province: the majority of genotypes were circulating recombinant form (CRF) 07_BC (675, 52.04%), CRF01_AE (343, 26.45%), CRF08_BC (115, 8.87%), CRF85_BC (67, 5.17%), subtype B (33, 2.54%), the other genotypes only accounted for 4.93%, and unique recombinant forms (URFs) (23, 1.77%) were observed in the study, and the difference of age, ethnicity, education, occupation, region and transmission pathway of different genotypes were statistically significant. According to WHO HIVDR surveillance threshold, the level of TDR has reached a medium level, with 72 of 1297 (5.55%) cases carrying drug-resistance mutation sites, TDR mutation frequency to nonnucleoside reverse transcriptase inhibitors (NNRTIs, 3.85%) was much higher than nucleoside reverse transcriptase inhibitors (NRTIs, 0.31%) and protease inhibitors (PIs, 1.70%), and CRF08_BC was a risk factor for TDR (odds ratio, 8.32; 95% CI 4.38–15.80 for CRF07_BC, P < 0.05). The most common drug resistance HIV-1 mutation pattern for NNRTI was V106 (1.31%, 17/1297) and E138 (1.16%, 15/1297), and for PI was M46 (0.69%, 9/1297). A total of 205 (15.8%) pol sequences were involved in the genetic transmission network clusters, CRF01_AE (odds ratio, 2.369; 95% CI 1.659–3.382; P < 0.05), subtype B (odds ratio, 13.723; 95% CI 6.338–29.71; P < 0.05), drug resistance (odds ratio, 0.306; 95% CI 0.106–0.881; P < 0.05) and different levels of education (P < 0.05) were significantly associated to be in clusters.ConclusionThe distribution of HIV-1 genotypes in Sichuan is more diverse and complex, and the Men who have sex with men (MSM) is underrated, arguing for behavior scaling up intervention in this specific population besides the elderly people with heterosexual transmission risk groups. The risk of TDR mutation frequency increased in newly diagnosed patients highlights the significance of genotypic drug resistance monitoring and molecular surveillance of pretreatment HIV-1 drug resistance. The regimen composed of TDF, 3TC and EFV was still currently the preferred solution used free first-line therapy.

Transmission and Drug Resistance Characteristics of Human Immunodeficiency Virus-1 Strain Using Medical Information Data Retrieval System.

This study was aimed at exploring the transmission and drug resistance characteristics of acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus-1 (HIV-1). The query expansion algorithm based on Candecomp Parafac (CP) decomposition was adopted to construct a data information retrieval system for semantic web and tensor decomposition. In the latent variable model based on tensor decomposition, the three elements in the triples generated feature vectors to calculate the training samples. The HIV patient data set was selected to evaluate the performance of the system, and then, the HIV gene resistance of 213 patients was retrospectively analyzed based on the electronic medical records. 43 cases showed failure of ribonucleic acid drug resistance, the ART virological failure rate was 24.43% (43/213), and one case was not reported. There was 1 case of RNA hemolysis that could not be detected. There were 50 resistant cases of nonnucleotide reverse transcriptase inhibitors (NNRTI), accounting for 29.94% (50/167), and there were 17 resistant cases of nucleotide reverse transcriptase inhibitors (NRTI), accounting for 10.18% (17/167) of all mutation cases. Among the HIV-1 strains, 19 cases failed the detection of drug resistance sites in the integrase region, and mutations in the integrase region were significantly more than those in the protease region. There were 12 types of HIV-1 strains with drug-resistant mutations. The fusion technical scheme constructed in this study showed excellent performance in medical information retrieval. In this study, the characteristics of HIV-1 of AIDS patients were analyzed from different directions, and effective treatment was performed for patients, so as to provide reference for clinical diagnosis of AIDS patients.

Ten-Year Molecular Surveillance of Drug-Resistant Plasmodium spp. Isolated From the China-Myanmar Border.

Antimalarial drug resistance has emerged as a major threat to global malaria control efforts, particularly in the Greater Mekong Subregion (GMS). In this study, we analyzed the polymorphism and prevalence of molecular markers associated with resistance to first-line antimalarial drugs, such as artemisinin, chloroquine, and pyrimethamine, using blood samples collected from malaria patients in the China–Myanmar border region of the GMS from 2008 to 2017, including 225 cases of Plasmodium falciparum and 194 cases of Plasmodium vivax. In artemisinin resistance, only the C580Y mutation with low frequency was detected in pfk13, and no highly frequent stable mutation was found in pvk12. In chloroquine resistance, the frequency of K76T mutation in pfcrt was always high, and the frequency of double mutations in pvmdr1 of P. vivax has been steadily increasing every year. In pyrimidine resistance, pfdhfr and pvdhfr had relatively more complex mutant types associated with drug resistance sites, and the overall mutation rate was still high. Therefore, artemisinin-based combination therapies are still suitable for use as the first choice of antimalarial strategy in the China–Myanmar border region in the future.

Risk Factors Associated with Lost to Follow up Among Multidrug Resistance Tuberculosis Patients Registered for Treatment in Programmatic Management of Drug Resistant Tuberculosis Sites of Punjab, Pakistan

Introduction: Pakistan, a country with a 27 high burden countries of multidrug resistance tuberculosis. To predict the associated risk factors and proportion of loss to follow up among MDR-TB patients treated at PMDT sites of Punjab from 2017 to 2019. Methodology: This case control study based on the standardized reporting and recording case record forms called as Electronic Nominal Review System (ENRS) of National TB Control Program, Pakistan. A logistic regression model was used to assess risk factors of lost to follow up MDR-TB patients. Results: A total of 539 patients with MDR-TB were included in the final analysis. Among them, 207 patients (7.5%) had lost to follow up outcome at the end of the study. MDR-TB lost to follow up patients were more likely to report older age (AOR: 1.40, CI: 1.14-1.71, p=0.000), history of lost to follow up from first line drugs treatment (AOR: 0.39, CI: 0.28-0.56, p=0.000), co-morbid (AOR:1.54, CI: 1.24-1.91, p=0.000), adverse reaction of second line drugs (AOR: 0.45, CI: 0.37-0.56, p=0.000), long distance between patient’s home and PMDT site (AOR: 0.68, CI: 0.52-0.89, p=0.001). Conclusion: The history of lost to follow up from first line drugs treatment, co-morbid, older age and long distance were independent risk factors of MDR-TB. Proper training for PMDT sites staff, friendly follow up services and psychological counseling may help to reduce lost to follow up.

Molecular evolution and characterization of hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 viruses isolated in Beijing, China, during the 2017-2018 and 2018-2019 influenza seasons.

We investigated and analysed the molecular evolution of hemagglutinin (HA) and neuraminidase (NA) of influenza A(H1N1)pdm09 virus during the 2017-2018 and 2018-2019 influenza seasons in Beijing, China. We collected and extracted RNA from influenza A(H1N1)pdm09 strains from Peking University People's Hospital and analyzed their HA and NA genes by RT-PCR and sequencing. Phylogenetic analysis of HA and NA sequences was used to compare the amino acid sequences of 51 strains with those of reference strains. All strains belonged to subclade 6B.1, with S162N and I216T substitutions (H1 numbering). Our strains differed from strain A/Michigan/45/2015, with the substitutions S91R, S181T and I312V in the HA antigenic epitope. An E189G mutation was detected in the 190 helix of the receptor binding region of HA. A new potential glycosylation site, 179 (NQT), which was not detected before the 2015 influenza season, was identified. Two strains were mutated at I223, the NA inhibitor resistance site. During 2012-2019, amino acids of HA and NA mutated over time. Co-occurrence mutations N146D, S200P, S202I and A273T in HA appeared along with Q51K, F74S and D416N in NA in six strains during two influenza seasons. Our work reveals the molecular changes and phylogenetic characteristics of influenza A(H1N1)pdm09 virus and suggests that a vaccine probably provides suboptimal protection. The biological characteristics of the new glycosylation and drug-resistance sites detected in this work need to be studied further. The co-occurrence of mutations in HA and NA might affect the characteristics of the virus and need to be given more attention.

KinaseMD: kinase mutations and drug response database.

Mutations in kinases are abundant and critical to study signaling pathways and regulatory roles in human disease, especially in cancer. Somatic mutations in kinase genes can affect drug treatment, both sensitivity and resistance, to clinically used kinase inhibitors. Here, we present a newly constructed database, KinaseMD (kinase mutations and drug response), to structurally and functionally annotate kinase mutations. KinaseMD integrates 679 374 somatic mutations, 251 522 network-rewiring events, and 390 460 drug response records curated from various sources for 547 kinases. We uniquely annotate the mutations and kinase inhibitor response in four types of protein substructures (gatekeeper, A-loop, G-loop and αC-helix) that are linked to kinase inhibitor resistance in literature. In addition, we annotate functional mutations that may rewire kinase regulatory network and report four phosphorylation signals (gain, loss, up-regulation and down-regulation). Overall, KinaseMD provides the most updated information on mutations, unique annotations of drug response especially drug resistance and functional sites of kinases. KinaseMD is accessible at https://bioinfo.uth.edu/kmd/, having functions for searching, browsing and downloading data. To our knowledge, there has been no systematic annotation of these structural mutations linking to kinase inhibitor response. In summary, KinaseMD is a centralized database for kinase mutations and drug response.

Niosomes from Preparation to Application in Drug Delivery

Introduction: In recent years, the treatment strategy for infectious and autoimmune diseases has significantly changed. Up to now, cancer treatment has been conducted on the basis of clinical and pathological methods. The most common cancer treatments is limited to chemotherapy, radiation therapy and surgery. However, cancer treatment is still not optimal. Common challenges for treatment of certain disease, e.g. cancer, are: systematic and non-specific distribution of drug agents, intolerable toxicity, insufficient drug concentration at the site of treatment and drug resistance. In recent years, the development and application of nanotechnology has been considered revolutionary in the field of cancer treatment. This technology offers a unique way to early detection and treatment of cancer. Designing and developing o new drug delivery systems not only increases the drug activity in the target tissue, but also reduces the drug toxicity and leaves it in a controlled manner. Newcomer vesicles consist of non-ionic surfactants that are biodegradable, non-toxic, stable, and inexpensive and can be used for targeted drug delivery. The niosomal vesicles are composed of nonionic surfactants that are biodegradable, non-toxic, stable and lower cost; and it can be used for targeted drug delivery. The major advantages of niosomes can be mentioned: the greater chemical stability, high purity, the availability of various types of non-ionic surfactants, proper storage of drug and cheapness.

Analysis of drug-resistance-associated mutations and genetic barriers in hepatitis C virus NS5B sequences in China.

The hepatitis C virus (HCV) NS5Bprotein is an RNA-dependent RNA polymerase that is required for viral genome replication and constitutes themost important target region for drugs being developed as direct-acting antivirals (DAAs) against HCV genotype 1. However, the extreme genetic variability leading to drug resistance mutations and genetic barriers has dramatically compromised the effectiveness of DAA therapy. The purpose of this study was to analyze the genetic variability of NS5B polymerase in HCV patients from different provinces of China to identify the impact of these resistance sites on genetic barriers. We analyzed 3489 NS5B sequences of HCV strains circulating in different regions of China, obtained from the GenBank database, 153 of which were from three cities in Sichuan Province (Yibin, Zigong and Zhangzhou). Sequence alignment was conducted using MEGA 6.0, the genetic information was translated into amino acids, and the percentage of polymorphic amino acid sites was calculated. The Vijver method was used to evaluate the occurrence of genetic barriers in HCV NS5B sequences. Blood samples were collected from 153 HCV patients from Sichuan for NS5B sequence analysis using real-time PCR and the Sanger method. Of the 17 antiviral drug resistance sites summarized from the published literature, nine were found in Chinese NS5B sequences, and C316Y was identified as the dominant mutation. Analysis of genetic barriers revealed that the probability of mutation to a drug-resistance-associated amino acid, in response to selective pressure from antiviral drugs was 100% at site 96 and 99.7% at site 282. Our study is the first to analyze the drug resistance sites and to evaluate genetic barriers in NS5B sequences that could affect the responsiveness of Chinese HCV patients to DAA therapy. The results provide a valuable basis for drug development and introduction of foreign-origin antiviral drugs in China that targeting the HCV NS5B region.

An overview of the new rifampicin-resistant tuberculosis regimens available at decentralised drug-resistant tuberculosis sites for persons older than six years.

No abstract available.

The prevalence clinically significant virus mutations among patients with chronic viral hepatitis B.

The prevalence of clinically significant virus mutations in patients with chronic viral hepatitis B from the Kyrgyz Republic was analyzed. Blood plasma samples of 64 patients with verified chronic viral hepatitis B obtained from Kyrgyzstan indigenous people were used in the work. Asymmetric PCR was carried out with extended oligonucleotides and the first reaction amplification product was further used in a new PCR with one of the nested pairs overlapping primers that flanked the entire HBV genome together, followed by sequencing. Based on the phylogenetic analysis of 64 HBV isolates obtained from patients from the Kyrgyz Republic, it was shown that only the genotype D virus was present in the examined group, the HBV subgenotype D1 (68.75%) prevailed compared with the HBV subgenotype D2 (18.75%) and subgenotype D3 (12.5%). For all subgenotypes, several independent infection sources are obvious, subclusters that include isolates from Kyrgyzstan, Kazakhstan and Uzbekistan are distinguished, as well as subclusters that include isolates only from Kyrgyzstan, which are less similar to isolates previously deposited in the international database, which probably indicates an independent HBV homologous evolution in the region. Clinically significant mutations were identified in 26.5% of patients. Including 12.5% with escape mutations that prevent the virus detection and / or allow the virus to replicate despite the vaccine (122K, 128V, 133I, 134N). Another 12.5% of the isolates are characterized by mutations that are independently associated with the liver cirrhosis and hepatocellular carcinoma development, including 21, 24, 27 nucleotides deletions in the Pre-S2 region and the S11F mutation in the PreCore region. In one case, unusual 236S and 250P mutations were found in the positions described as drug resistance sites of the P region associated with the resistance development to adefovir, tenofovir, and entecavir. The hepatitis B virus genetic structure analysis, early virus mutations detection in patients with chronic hepatitis B virus can help to choose the right vaccination strategy, antiviral and immunosuppressive therapy, as well as predict the clinical course and disease progression.

Spread and evolution of influenza A (H1N1) pdm09 virus in Hubei, 2015–2019

ObjectiveTo understand spread, phylogenetic characteristics, epitope and drug-resistance site of influenza A (H1N1) pdm09 virus in Hubei province during 2015–2019. MethodsThe spread period of the virus were divided according to the positive rate of influenza virus nucleic acid detection downloaded from influenza surveillance information system in China. Sequencing of 39 strains of influenza A (H1N1) pdm09 virus isolated from the positive samples in real-time fluorescence PCR in Hubei during 2015–2019 was conducted and 13 sequences of the strains isolated from Hubei were downloaded from global influenza database to analyze the distribution of phylogenetic clade, epitope and drug-resistant mutation sites by using bioinformatics software and simulate the structure of mutation sites by 3D modeling. ResultsThe annual spread of influenza A (H1N1) pdm09 virus lasted for 11–14 weeks in Hubei from 2015 to 2019, and the spread intensity increased year by year. Multiple branches of 6B.1A to 6B.1A7 evolved from 6B clade in phylogenetic tree of the HA and NA genes. Twelve epitope substitutions of HA and two drug-resistance sites of NA were detected, and there were obvious differences in D222G substitution virulence identifying marker and drug-resistance site I223V on homology in 3D modeling structure. ConclusionThe spread intensity and phylogenetic clade number of influenza A (H1N1) pdm09 virus increased In Hubei during 2015–2019. Sporadic virulence marker and drug-resistance site were detected for influenza A (H1N1) pdm09 virus. The results of this analysis can be used to improve the epidemiological research and genetic evolution surveillance of influenza virus in Hubei.

HIV-1 drug resistance and influencing factors among people living with HIV/AIDS before antiretroviral therapy in Liangshan Yi Autonomous Prefecture

Objective: To explore HIV-1 drug resistance and influencing factors among people living with HIV/AIDS before antiretroviral therapy in Liangshan Yi Autonomous Prefecture (Liangshan). Methods: Between January 1 and June 30, in both 2017 and 2018, a cross-sectional survey was conducted in Liangshan HIV-1 pol sequences were gathered and analyzed according to WHO Guidelines on HIV drug resistance surveillance of 2014. Both HyPhy 2.2.4 and Cytoscape 3.6.1 software were used to analyze the drug resistant strains of HIV-1 transmission network. Results: A total of 464 people living with HIV/AIDS was recruited. The proportion of HIV-1 CRF07_BC subtype was 88.6% (411/464), with HIV-1 drug resistance rate was 9.9% (46/464). The HIV-1 drug resistance rates of non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors(NRTI) and protease inhibitors (PI) were 6.7% (31/464), 1.9% (9/464) and 0.4% (2/464) respectively. New recombinant strains of HIV-1 URF_01BC subtype was independently clustered according to the drug resistant mutation sites. Results from the multivariate logistic analysis showed that injected drug users group had higher risk on HIV-1 drug resistance (aOR=3.03, 95%CI:1.40-6.54) than heterosexual group among people living with HIV/AIDS. Conclusions: HIV-1 drug resistance rate had already been in a high level before antiretroviral therapy was in place. The newly identified recombinant strains of HIV-1 URF_01BC subtype were independently clustered according to the drug resistant mutation sites. It was necessary to strengthen the prevention of the HIV-1 drug resistant strains transmission.

Analysis of hepatitis B virus (HBV) drug resistance variations in HBV carriers of Chinese blood donors

Background: To analyze hepatitis B virus (HBV) mutations of nucleoside drug resistance in blood donors of Shantou Central Blood Station. Methods: A total of 22,539 blood donors in Shantou City in 2014 were recruited in the study. Two hundred and one blood samples were detected positive by two types of enzyme-linked immunosorbent assay (ELISA) and 99 cases of HBV positive samples were detected by fluorescence quantitative polymerase chain reaction (PCR). Among them, 45 cases with viral loads greater than 1,000 IU/mL were sequenced by PCR sequencing method. Drug resistance mutation sites of sample DNA sequences were analyzed. Results: All known 10 drug resistant sites of HBV were not detected from these 45 cases of HBV blood donor carriers. Conclusions: The prevalence of HBV strains from blood donors in Shantou were wild-type.

Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

BackgroundIt is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the pathogen carries specific mutations at drug-resistance sites. This advancement has led to the collation of TB databases such as PATRIC and ReSeqTB that possess both whole genome sequences and drug resistance phenotypes of infecting Mtb isolates. Bioinformatics tools have also been developed to predict drug resistance from whole genome sequencing (WGS) data.Here, we evaluate the performance of four popular tools (TBProfiler, MyKrobe, KvarQ, PhyResSE) with 6746 isolates compiled from publicly available databases, and subsequently identify highly probable phenotyping errors in the databases by genetically predicting the drug phenotypes using all four software.ResultsOur results show that these bioinformatics tools generally perform well in predicting the resistance status for two key first-line agents (isoniazid, rifampicin), but the accuracy is lower for second-line injectables and fluoroquinolones. The error rates in the databases are also non-trivial, reaching as high as 31.1% for prothionamide, and that phenotypes from ReSeqTB are more susceptible to errors.ConclusionsThe good performance of the automated software for drug resistance prediction from TB WGS data shown in this study further substantiates the usefulness and promise of utilising genetic data to accurately profile TB drug resistance, thereby reducing misdiagnoses arising from error-prone culture-based drug susceptibility testing.