Genetic variation characteristics of HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019 / 中国基层医药

Objective:To analyze the genetic variation characteristics of the HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019. Methods:Twenty strains of influenza A virus (H3N2) were randomly selected from 10 network laboratories in Guizhou province for RNA extraction. Reverse transcriptase-polymerase chain reaction and sequencing were performed. The products were analyzed using bioinformatics software.Results:The nucleotide homology of the HA gene of the 20 strains was 97.7%-100%, which was highly homologous to the vaccine strains A/Hong-Kong/4801/2014 recommended by WHO in 2017 and A/Singapore-INFIMH/16-0019/2016 recommended by WHO in 2018, but they were significantly different from the vaccine strain A/Kansas/14/2017 recommended by WHO in 2019. Genetic analysis showed that the 20 strains were divided into two branches, and the strains that were prevalent in 2019 were located in different branches, with marked genetic differences. Key site analysis showed mutations in antigenic determinants A, B, C, and E and mutations in the anterior and posterior walls of receptor binding sites. Key site analysis also showed that there was an increase in the number of glycosylation sites compared with the vaccine strains prevalent in the same year. Genetic distance, antigen sites, and glycosylation sites were slightly different between virus strains prevalent in 2017-2018 and virus strains prevalent in 2019. Conclusion:The HA gene of the influenza A virus subtype H3N2 in Guizhou province from 2017 to 2019 showed heterogeneity and gene mutation, especially in 2019. Therefore, close monitoring of the genetic evolution of the influenza A virus subtype H3N2 is necessary.

Expression level of serum HBV RNA in HBeAg-positive chronic hepatitis B patients at different periods and its value of measurement / 临床肝胆病杂志

Objective To investigate the expression level and potential clinical value of serum HBV RNA in HBeAg-positive chronic hepatitis B (CHB) patients at different periods. Methods A total of 61 CHB patients who attended the outpatient and inpatient services of Department of Hepatology, Hangzhou Xixi Hospital, from August 2019 to December 2020 were enrolled, and according to the antiviral therapy for HBeAg-positive CHB patients, they can be divided into group A with untreated HBeAg-positive CHB (HBeAg+ and HBV DNA+) patients, group B with treatment-experienced patients before HBeAg seroconversion (HBeAg+ and HBV DNA-), and group C with treatment-experienced patients after HBeAg seroconversion (HBeAg- and HBV DNA-). Peripheral blood HBV RNA load was measured at different periods, and its correlation with HBsAg and HBV DNA was analyzed. The t -test was used for comparison of normally distributed continuous data between groups, and the Mann-Whitney U test was used for comparison of non-normally distributed continuous data between two groups; the chi-square test was used for comparison of categorical data between groups; a Pearson or Spearman correlation analysis was used to describe the correlation between two variables. Results The positive rates of HBV RNA in these three groups were 100% (22/22), 88.2% (15/17), and 22.7% (6/22), respectively. In group A, HBV RNA was positively correlated with HBsAg and HBV DNA ( r =0.612 and 0.922, both P < 0.01), while in groups B and C, there was no correlation between HBV RNA and HBsAg. Group B had significantly higher levels of HBV RNA and HBsAg than group C ( Z =-4.44 and -2.41, both P < 0.05). The HBV DNA-positive group had a significantly higher level of HBV RNA than the HBV DNA-negative group ( Z =-6.16, P < 0.01). Conclusion After HBV DNA clearance achieved by antiviral therapy with nucleos(t)ide analogues in CHB patients, serum HBV RNA can still be detected in some of these patients. Since HBV RNA only comes from cccDNA in the liver, it can better reflect viral replication activity in the liver than HBV DNA and thus has a certain clinical value in the management of CHB patients.

Proposal for detection of 2019-nCoV nucleic acid in clinical laboratories / 中华检验医学杂志

In December, the outbreak of a novel coronavirus (2019-nCoV) in Wuhan, China, has attracted extensive global attention. On January 20, 2020,the Chinese health authorities upgraded the coronavirus to a Class B infectious disease in the Law of the People's Republic of China on the Prevention and Treatment of Infectious Diseases, and considered it as Class A infectious diseases in disease control and prevention. On January 22, 2020, the 2019-nCoV nucleic acid detection test was listed as the diagnostic criteria in the "guidelines for diagnosis and treatment of pneumonia due to 2019-nCoV (Trial Version 2)" . Therefore, standardizing the operation process of the 2019-nCoV nucleic acid detection in clinical laboratories has become a top priority. It is of paramount importance to establish standard protocols for detection of the 2019-nCoV nucleic acids in clinical laboratories to improve the reliability of the results and ensure the biosafety of laboratory personnel.

Correlation between CD4 Count and HIV-1 Viral Load among ART Naive Patients Attending ICTC, SMS Medical College, Jaipur

Objectives: To study the correlation between CD4 count &HIV-1 viral load among ART Naive patients attending ICTCSMS Medical College, Jaipur.Material and Methods: This study was conducted on 250 HIVserologically confirmed, ART Naive cases from ICTC, SMSJaipur. RNA extraction was done from plasma samples byQiagen Viral RNA Mini Kit then HIV-1 Viral load wasdetermined by Qiagen HIV-1 viral load kit on ABI 7500 Fast dxReal Time PCR, while CD4 count was done on FACSCALIBUR flowcytometer (BD Biosciences). SPSS ver. 21.0was used to determine correlation between CD4 count & HIV-1viral load.Results: Out of 250, 216 (86.4%) cases were found in whichviral RNA was detected. These samples were correlated withtheir CD4 Count. The mean of viral load was 194746.2791 ±550442.61805 IU/ml while CD4 count was 282.7674 ±217.56456 cells/ul. Females were having Avg. Viral load228506.7273 & CD4 count 337.21 and males were found tohave Avg. Viral load 179791.9866 & CD4 count 258.65Conclusion: This study concluded a negativecorrelation between HIV-1 RNA viral load and CD4 count inHIV-seropositive ART naïve patients of this part of the country.Our study confirmed that HIV-1 RNA viral load levels aresignificantly higher in women than in men, but no suchsignificant gender difference in the CD4 count was found.

The application of serum HBV RNA detection in anti-HBV treatment / 中华检验医学杂志

The persistence of covalently closed circular DNA (cccDNA) in the nucleus of liver cells is a key factor that hinders the cure of chronic hepatitis B. However,it is difficult to eliminate cccDNA with existing anti-HBV therapy. Recent studies have found that serum HBV RNA may be a new indicator reflecting the activity of cccDNA in hepatocytes and evaluating the clinical efficacy of CHB patients . This article reviews recent advances in the properties,detection methods,and clinical significance of HBV RNA, particularly the application of antiviral therapy in CHB patients.

The clinical significance of HCV antibody S/CO values in the diagnosis of active HCV infection in cancer patients / 中华检验医学杂志

Objective To investigate the clinical significance of HCV antibody S /CO values in active HCV infection diagnosis in cancer patients .Methods 390 cancer patients were enrolled from Cancer Hospital Chinese Academy of Medical Sciences between January 2013 and April 2015.All of the cancer patients had pathological diagnosis , including 240 males and 150 females, aged from 25 to 83 years old. HCV antibody and HCV RNA levels were detected using the Abbott i 2000 immunity analyzer and Roche LC480 real-time fluorescent quantitative PCR machine , respectively.The relationship between HCV antibody S/CO value and RNA level was analyzed in the group of HCC and non-HCC patients.Results There were obvious statistical differences in age (P＝0.004), gender (P＜0.001) and HCV antibody levels (P＜0.001) between the group of HCC and non-HCC patients.There was no statistical difference in distribution of RNA positive rate between the two groups (P＝0.528).Using ROC curve analysis, the best cut-off value to diagnose active HCV infection in cancer patients is 10.0 with sensitivity 97.6%and specificity 81.3%. According to the results of the ROC curve , the cut-off was 11.4 and 10.4 in HCC and non-HCC patients respectively.Conclusion The best cut-off value to diagnose active HCV infection in cancer patients is 10.0, either in HCC or in non-HCC.

Clinical value of serum HBV RNA / 临床肝胆病杂志

Although there are various indicators for evaluating the effect of anti-HBV therapy,they have low accuracy and sensitivity.New indicators are still needed to guide clinical practice.Recent studies have found that HBV RNA might be a new potential indicator for clinical detection.This article reviews the basic concepts of HBV RNA,related detection methods,and the value of HBV RNA in clinical diagnosis.

Correlation between HCV genotype and anti-HCV antibody level in hepatitis C patients / 中华检验医学杂志

Objective To investigate the relationship between anti-HCV antibody level and hepatitis C virus genotype in the patients.Methods Total of 603 anti-HCV positive serum samples were collected during 2013 to 2014 by retrospective research method.HCV RNA were detected in anti-HCV positive samples by repeat test and the genotype were detected in HCV RNA positive samples.The distribution of anti-HCV level in different hepatitis C genotype patients was analyzed and the body's response to viral antibodies and viral genotype correlation with anti-HCV concentration interquartile range was explored.Rates among genotype groups were compared using chi-square test.Results Totally 412 of 603 (68.33％) samples were anti-HCV positive by double reagent screening.174(42.3％) samples were detected as HCV RNA positive.The distributions of different anti-HCV level in different genotype patients were 1a(n =8) 1/8,1/8,4/8,2/8;1b(n =112)25.9％ (29/112),17.0％ (19/112),25.9％ (29/112),31.3％ (35/112);2a(n =14)3/14,4/14,5/14,2/14;3a(n =11)3/11,6/11,2/11,0/11;3b(n =16)4/16,11/16,1/16,0/16;6a(n =8)2/8,2/8,1/8,3/8 with anti-HCV concentration interquartile range respectively.The anti-HCV concentration distribution was different in patients with different HCV genotypes.The anti-HCV concentration distribution in patients of 1 b,2a and 6a genotypes were evently,while anti-HCV level was relatively high in 1a (13.65) and relatively low in 3b (8.77).There were differences in different genotypes of antibody concentrations (x2 =35.2,P ＜ 0.05).Conclusions There was correlation between anti-HCV level and HCV genotype.Because there were fewer cases in some genotypes,it was necessary to investigate more samples to corfirm the above results.

Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data

BACKGROUND: New sequencing technologies have opened the way to the discovery and the characterization of pathogenic viruses in clinical samples. However, the use of these new methods can require an amplification of viral RNA prior to the sequencing. Among all the available methods, the procedure based on the use of Phi29 polymerase produces a huge amount of amplified DNA. However, its major disadvantage is to generate a large number of chimeric sequences which can affect the assembly step. The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes. FINDINGS: Three different assembly softwares (ABySS, Ray and SPAdes) were tested for their ability to correctly assemble the full-length of viral genomes. Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig. CONCLUSIONS: The proposed pipeline is able to overcome drawbacks due to the generation of chimeric reads during the amplification of viral RNA which considerably improves the assembling of full-length viral genomes.

Factors Associated with a Low CD4 Count among HIV-1 Infected Patients at Enrolment into HAART in Jos, Nigeria.

Aim: To determine the factors associated with a low CD4 count among HIV-1 positive patients. Study Design: Cross-sectional study. Place and Duration of Study: Adult HIV clinic at the Jos University Teaching Hospital, Jos, between October 2010 and April 2011. Methodology: Data on demographic, clinical and laboratory variables for 218 HIV-1 infected patients aged 20 years and older were analysed. A low CD4 cell count was defined as CD4 cell count <200 cells/ml based on the WHO criteria for severe immune suppression. A multivariate logistic regression modeling was fitted to determine the variables that were independently associated with a low CD4 count. Results: Of the 218 HIV-1 infected patients, 119 (54.6%) had a low CD4 count at enrolment. The odds of having a low CD4 count was: 7 times higher in patients with WHO clinical stage 3 or 4 compared to those with stage 1 or 2 (P<.001) and 4 times higher in those with HIV RNA viral load ≥4.6 log10 copies/ml compared to those with less (P<.001); but the odds of having a low CD4 count was reduced by 63% in those patients that were resident in Plateau State compared to those resident outside the state (P=.01). Conclusion: Our study patients were more likely to have a CD4 count <200 cells/ml which would suggest late presentation/ late HIV diagnosis and thus a delayed opportunity for timely access to HIV care and initiation of antiretroviral therapy. There is the need to intensify efforts in early routine HIV counseling and testing not only in health facilities in the cities but also in smaller towns and rural communities, so as to reduce the frequency of late HIV diagnosis with its potential implications.