Dynamics of HIV-1 infected population acquired via different sexual contacts route: a case study of Turkey

This paper aims to study the transmission dynamics of HIV/AIDS in heterosexual, men having sex with men (MSM)/bisexuals and others in Turkey. Four equilibrium points were obtained which include disease free and endemic equilibrium points. The global stability analysis of the equilibria was carried out using the Lyapunov function which happens to depend on the basic reproduction number R0. If R0 1, the endemic equilibrium point is stable and epidemics will occur. We use raw data obtained from Kocaeli University, PCR Unit, Turkey to analyze and predict the trend of HIV/AIDS among heterosexuals, MSM/bisexual, and others. The basic reproduction number for heterosexuals, MSM/bisexuals, and others was found to be 1.08, 0.6719, and 0.050, respectively. This shows that the threat posed by HIV/AIDS among heterosexuals is greater than followed by MSM/bisexuals, and than the others. So, the relevant authorities should put priorities in containing the disease in order of their threat

Modelling the effect of horizontal and vertical transmissions of HIV infection with efficient control strategies

In this paper a mathematical model is developed to study the transmission dynamics of HIV infection and the effect of horizontal and vertical transmission in Turkey is analyzed. Model is fitted with the use of confirmed HIV cases of both vertical and horizontal transmission from 2011 to 2018. Using the next generation operator the basic reproduction number of the model is obtained, which shows whether the disease persists or dies out in time. Further analysis shows that the model is locally asymptotically stable when the basic reproduction number R0 1. The most sensitive parameters efficient for the control of the infection are obtained using forward normalized sensitivity index. Lastly, the results are obtained with the aid of mesh and contour plots, which show that decreasing the values of transmission rate diseases induced mortality rates and progression rates play a significant role in controlling the spread of HIV transmission

Transmission dynamics and control strategies of COVID-19: a modelling study

In this paper a mathematical model is proposed, which incorporates quarantine and hospitalization to assess the community impact of social distancing and face mask among the susceptible population. The model parameters are estimated and fitted to the model with the use of laboratory confirmed COVID-19 cases in Turkey from March 11 to October 10, 2020. The partial rank correlation coefficient is employed to perform sensitivity analysis of the model, with basic reproduction number and infection attack rate as response functions. Results from the sensitivity analysis reveal that the most essential parameters for effective control of COVID-19 infection are recovery rate from quarantine individuals (δ1), recovery rate from hospitalized individuals (δ4), and transmission rate (β). Some simulation results are obtained with the aid of mesh plots with respect to the basic reproductive number as a function of two different biological parameters randomly chosen from the model. Finally, numerical simulations on the dynamics of the model highlighted that infections from the compartments of each state variables decreases with time which causes an increase in susceptible individuals. This implies that avoiding contact with infected individuals by means of adequate awareness of social distancing and wearing face mask are vital to prevent or reduce the spread of COVID-19 infection

MIKROBIYOLOJI BULTENI

The duration of hepatitis C virus (HCV) infection and the response to the standard therapy is strongly related to the HCV genotypes. In addition, the geographical distribution of HCV genotypes is important for the epidemiological studies in terms of distribution and possible risk groups. The aim of this retrospective study was to investigate the distribution of HCV genotypes in Manisa region (located at the Aegean part of Turkey). A total of 100 anti-HCV (microparticle EIA; Abbott Laboratories, USA) and HCV-RNA (real time RT-PCR; Applied Biosystems, USA) positive patients (53 female, 47 male; mean age: 44.4 +/- 10.4 years), who were admitted to Celal Bayar University Medical School Hospital between 2002-2005, were included to the study. Quantitative HCV-RNA levels of the patients were between 10(4)-10(8) copies/ml. Complementary DNAs obtained from HCV-RNAs isolated by Invitek RTP DNA/RNA Virus Mini Kit were used for genotyping with selected primers [primer 11 (5'-AGG TCT CTG AGA CCG TGC ACC ATG AGC AC-3') and primer 13 (5'-CTG TGA GGA ACT ACT GTC TT-3') for the first PCR; primer 12 (5'-ACT GCC TGA TAG GGT GCT TGC GAG TG-3') and primer 14 (5'-CAC GCA GAA AGC GTC TAG-3') for the second PCR]. The RT-PCR products were purified with Invisorb Spin PCRapid Kit and sequenced by BigDye Terminator v3.1 Cycle Sequencing Kit in ABI Prism 310 Genetic Analyzer. Genotype I was found in 92% of the patients (92%) and genotypes 2 and 4 were found in 7% of the patients, while HCV genotype could not be identified in one patient (1%). When evaluating the subtypes, genotype 1b was determined in 90 patients (90%), genotype 4a in five patients (5%), genotype 1 a in two patients (2%) and genotype 2a in two patients (2%). In conclusion, 1b was found to be the most common HCV genotype in Manisa region in concordance with the previous data obtained in Turkey, followed by genotype 4a, although a rare one. The data of this study is noteworthy especially for the arrangement of treatment and follow-up of HCV infected patients

MIKROBIYOLOJI BULTENI

Direct-acting antiviral agents (DAA) such as NS3 protease inhibitors is the first class of drugs used for chronic hepatitis C (CHC) treatment. NS3 inhibitors (PI) with low genetic barrier have been approved to be used in the CHC genotype 1 infections, and in the treatment of compensated liver disease including cirrhosis together with pegile interferon and ribavirin. Consequently, the development of drug resistance during DAA treatment of CHC is a major problem. NS3 resistant variants can be detected before treatment as they can occurnaturally. The aim of this study was to investigate new and old generation NS3 inhibitors resistance mutations before DAA treatment in hepatitis C virus (HCV) that were isolated from CHC. The present study was conducted in 2015 and included 97 naive DAA patients infected with HCV genotype 1, who were diagnosed in Manisa and Kocaeli cities of Turkey. Magnetic particle based HCV RNA extraction and than RNA detection and quantification were performed using commercial real-time PCR assay QIASypmhony + Rotorgene Q/ArtusHCV QS-RGQ and COBAS Ampliprep/COBAS TaqMan HCV Tests. HCV NS3 viral protease genome region was amplified with PCR and mutation analysis was performed by Sanger dideoxy sequencing technique of NS3 protease codons (codon 32-185). HCV NS3 protease inhibitors; asunaprevir, boceprevir, faldaprevir, grazoprevir, pariteprevir, simeprevir and telaprevir were analysed for resistant mutations by Geno2pheno-HCV resistance tool. HCV was genotyped in all patients and 88 patients (n= 88/97, 91%) had genotype 1. Eight (n= 8/97, 8.2%) and 80 (n= 80/97, 82.4%) HCC patients were subgenotyped as 1a and 1b, respectively. Many aminoacid substitutions and resistance mutations were determined in 39/88 (44%) patients in the study group. Q80L, S122C/N, S138W were defined as potential substitutions (6/88 patients; 7%); R109K, R117C, S122G, I132V, I170V, N174S were described as potential resistance (34/88 patients; 39%); V36L, T54S, V55A, Q80H were characterized as resistance (7/88 patients; 8%) and Q80K, A156S were defined as high resistance (3/88 patients; 3%) mutations. Based on resistance and high resistance mutations, clinically significant mutations were defined in 10/88 (11%) of the patients. Our study shows that it is essential to analyse HCV NS3 protease inhibitors drug resistance before DAA treatment of CHC patients. On the other hand, our results pointed out that analysis of NS5A and NS5B genome region mutations may also be required in the near future

MIKROBIYOLOJI BULTENI

Detection of borderline and/or low positive anti-HCV results by enzyme immunoassay (EIA) leads to severe problems in routine laboratories and needs confirmation with nucleic acid amplification tests which can increase the cost. In EIA tests, if the ratio of sample to cut-off (S/Co) is >= 1, the sample is accepted as positive according to the manufacturers' instructions. Although over the last decade the application of S/Co values have also applied to HCV-RNA readings, the current study aims to determine whether the S/Co value is adequate and applicable for the anti-HCV EIA test, and to determine whether a correlation exists between HCV-RNA and HCV infections. A total of 658 cases (402 female, 256 male; mean age: 49.4 +/- 17.0 years) who were found anti-HCV positive between January 2011-July 2013 were included in the study. Anti-HCV tests were performed by chemiluminescent EIA (Architect i2000SR, Abbott, USA and LiaisonXL Murex, DiaSorin, Italy) and HCV-RNA by real-time PCR (Cobas Ampliprep/Cobas TaqMan HCV, Roche, USA). The mean S/Co value of the cases was 7.3 +/- 4.8 (range: 1.00-17.59) and mean HCV-RNA value was 2.3x10(5) +/- 2.1x10(6) copies/ml. When the anti-HCV S/Co value of varying ranges was compared with HCV-RNA readings a particular trend was noted. In the anti-HCV S/Co values of 1.0-4.0; 4.1-7.0; 7.1-10.0; 10.1-13.0; 13.1-16.0 and (3)16.1, HCV-RNA positivity rates were detected as 1.9%, 24.7%, 37.1%, 46.7%, 56.4% and 75%, respectively. Statistical analysis indicated an intermediate positive correlation (r=0.454) between anti-HCV ve HCV-RNA readings (p=0.000). An adequate S/Co value was accepted as 5.0 based on the ROC analysis, and this value gave a performance confidence level of 95.6% when determining whether a patient is HCV positive. Based on the data of this study it became evident that further EIA testing is not required if the S/Co value is >= 5.0, however if the S/Co value is less than 5.0, then further clinical analysis and revaluation of the patient is required

JOURNAL OF VIROLOGICAL METHODS

Quantitation of hepatitis B virus (HBV) DNA is often performed in specimens that have been frozen and thawed more than once. It is important to establish whether viral load measurements are affected by repeated freeze-thaw cycles. The effect of multiple freeze-thaw cycles on HBV DNA quantitation was carried out by testing serum specimens subjected to I (baseline) to 10 cycles with the appropriate Digene Hybrid Capture System. Five HBV DNA-positive samples were selected at random from sera with concentrations ranging from 7 pg/ml to 3529 pg/ml and they were frozen and thawed up to 10 cycles and then tested for changes in HBV DNA levels. Negative control and positive standards were tested in triplicate; and all specimens were tested in duplicate. The stability of HBV DNA in serum was evaluated by scattergrarn analysis by determining the number of samples showing a greater than or equal to20% change in HBV DNA levels after freeze-thaw cycles. With the exception of one sample (7 pg/ml) 10 cycles of freezing and thawing did not change significantly the HBV DNA quantity in any of the samples tested. The results showed that the quantity of HBV DNA in four of five serum specimens subjected up to 10 freeze-thaw cycles was stable. (C) 2004 Elsevier B.V. All rights reserved

FUTURE VIROLOGY

Aim: We aimed to investigate the adipogenic effects of adenovirus (Ad) serotypes 5, 36 and 8 in a Colo-320 cell line using histochemical, immunohistochemical and electron microscopic methods. Materials & methods: Ad serotypes were inoculated in a Colo-320 cell line and were cultured for 14 days. They were then collected and fixed with 4% paraformaldehyde to analyze their adipogenic effects using histochemistry, immunohistochemistry and electron microscopic methods. Intracellular lipid droplets were detected in the Colo-320 cells inoculated with Ad36 and Ad5 by electron microscopic analyses. Results: After Oil Red O staining, the pink-orange staining was positive intracellularly in Colo-320 cells infected with Ad36 and Ad5. In addition, the leptin immunoreactivity was also positive in these cells. Conclusion: Our results suggested that intracellular lipid accumulation occured after infection with Ad36 and Ad5. The positive staining of Oil Red O and leptin also supported the electron microscopic results; therefore, we conclude that this accumulation occurred due to adipogenic effects of Ad36 and Ad5