Safety and immunogenicity of CoronaVac and ChAdOx1 heterologous prime-boost vaccines in an overweight population in Chiang Mai, Thailand.

Background: In early 2021, the Ministry of Public Health of Thailand announced heterologous regimens for COVID-19 vaccines using CoronaVac as the first dose followed by ChAdOx1 nCoV-19 at 3 weeks apart. Priority was given to individuals above 60 years old and those who had seven underlying conditions, including obesity. The vaccine regimen was evaluated for safety and immunogenicity in overweight populations in Chiang Mai, Thailand. Methods: Participants who had a COVID-19 vaccination appointment for the heterologous prime-boost regimen were enrolled. Before each immunization and on day 28 following the second dosage, blood samples were taken, and were examined for anti-spike and neutralizing antibodies by using an indirect ELISA and virus neutralization assays. Safety profile of the vaccine regimen was assessed via a self-recorded diary of adverse events after each vaccination. Results: No serious adverse events related to vaccination were reported during study period and the majority of adverse reactions were fatigue and pain at the injection site. The levels of anti-spike IgG were 26.3, 56.4 and 1752.1 BAU/mL at baseline, 21 days after first dose and 28 days after second dose, respectively. At 4 weeks after complete vaccination, the median inhibition rates of neutralizing antibody determined by surrogate neutralization assay against wild type, Delta and Omicron variants were 95.2, 85.0 and 3.8, respectively. Moreover, the NT50 level against wild type and Delta variants determined by pseudotyped virus neutralization assay were 133.3 and 41.7, respectively. The neutralizing activity against Omicron variant was almost lower than cutoff level for detection. Conclusions: The heterologous CoronaVac-ChAdOx1vaccination was safe, well-tolerated and able to induce humoral immunity against wild-type and Delta variants but not against the Omicron variant in overweight population.

Effects of quercetin and extracts from Phyllanthus emblica, Morus alba, and Ginkgo biloba on platelet recovery in a rat model of chemotherapy-induced thrombocytopenia.

Background: Chemotherapy-induced thrombocytopenia (CIT) is a major reason for chemotherapy delays, dose reduction, or even treatment discontinuation, which may impact oncologic outcomes. We investigated the effects of quercetin and extracts of Phyllanthus emblica fruit (PEE), Morus alba leaf (MAE), and Ginkgo biloba leaf (GBE) on platelet recovery in a rat model of chemotherapy-induced thrombocytopenia. Methods: The total phenolic content (TPC), total flavonoid content (TFC), quercetin content, and antioxidant activities of all the extracts were determined. Sixty male Sprague Dawley rats were categorized into healthy controls and CIT groups. The CIT groups was administered a cyclophosphamide solution, while the control group received a saline solution. Each group was then subdivided into five subgroups of six animals which were administered with PEE, MAE, GBE, quercetin, or a vehicle for 15 days. Results: The highest quercetin content was found in PEE, followed by MAE and GBE, which correlated with their antioxidant properties. Administration of these extracts and quercetin did not significantly change the platelet counts in healthy rats. Thrombocytopenic rats treated with PEE, MAE, and GBE also were not associated with significant changes in platelet counts. However, more rapid platelet count recovery was observed in all groups receiving extracts. On day 11, platelet counts in the PEE, MAE, and GBE groups returned to near baseline levels with a mean of 4.29 %, -40.77 %, and -14.24 %, respectively, compared to -71 % in the CIT group. In thrombocytopenic rats treated with quercetin, there was a significant increase in platelet counts on days 9 and 11, with a mean decrease of 5.41 % from baseline on day 11. Conclusion: Quercetin improved platelet recovery in the animal model of CIT. This finding merits for further investigation to better elucidate the health benefits of quercetin and quercetin-rich plants and potential pharmacokinetics underpinning their activity in thrombocytopenia.

Isolation and Identification of Microorganisms and Antibiotic Resistance Microorganisms from Beehives Located in Palm, Corn and Longan Plantations, Thailand.

This study aims to determine the prevalence of microorganisms and antibiotic-resistant microorganisms in beehives located on different plantations in Thailand. Seventeen swabs immersed in transport media were utilized for samples from different zones within beehives. Traditional microbial culture-based methods, biochemical tests, MALDI-TOF MS (VITEK® MS, bioMerieux, Marcy-l'Étoile, France), and antibiotic drug susceptibility (disk-diffusion) tests were used to detect microorganism and antimicrobial resistance bacteria. The results from 16 beehive swabs found Gram-positive bacteria at 59.5%, Gram-negative bacteria at 35.1%, and fungi (yeast) at 5.4%. These organisms are classified as 11, 11, and 2 types of Gram-positive bacteria, Gram-negative bacteria, and fungi (yeast), respectively. Furthermore, no organism showed resistance to vancomycin or cefoxitin for antibiotic drug susceptibility testing. In contrast, all Acinetobacter spp. were susceptible to ciprofloxacin, levofloxacin, ceftazidime, cefotaxime, imipenem, and meropenem, except for Acinetobacter schindleri, which was resistant to ceftazidime and cefotaxime. For other organisms, due to the limitations of tests to identify some environmental microbial species, the antimicrobial susceptibility test results cannot be interpreted as resistant or susceptible to the drug for these organisms. The study's findings will support prevention, healthcare services, and public health systems.

Prevalence and Genotypic Diversity of Human Papillomavirus Infection Among Male and Female Sex Workers in Thailand.

BACKGROUND: Human papillomavirus (HPV) is associated with cancer. Female sex workers (FSWs) are known to be at risk for HPV, but little is known about male sex workers (MSWs). METHODS: We examined HPV prevalence and associated risk factors in both populations. During 2022, HPV testing using vaginal or penile samples, HIV testing, and interviews were performed among 100 MSWs and 100 FSWs in Chiang Mai, Thailand. RESULTS: The prevalence of all HPV types was 63.5% (66% in MSW, 61% in FSW), HPV-16 prevalence was 14%, HPV-52 was 13%, and HPV-18 was 4%. There was no difference between MSW and FSW for these subtypes. The prevalence of HPV-16 or HPV-18 was 17%, and for HPV-16, HPV-18, or HPV-52, it was 26%. HIV-positive participants had a higher prevalence of all HPV types (94% vs. 60%, P = 0.004), HPV-16 or HPV-18 (39% vs. 15%, P = 0.018), and HPV-16, HPV-18, or HPV-52 (50% vs. 23%, P = 0.017). CONCLUSIONS: We demonstrated an equally high HPV prevalence across the sexes. Further studies are needed to determine if this indicates an equal risk for cancer. Increased HPV awareness, screening, and vaccination should be considered, regardless of gender.

A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA.

Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop--mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed tube. Nasopharyngeal and throat swabs collected from at-risk individuals testing for SARS-CoV-2 were used to assess the sensitivity and specificity of a new RT-LAMP assay against a commercial qRT-PCR assay. Total RNA extracts were submitted to the RT-LAMP reaction under optimal conditions and amplified at 65 °C for 30 min using three sets of specific primers targeting the nucleocapsid gene. The reaction was detected using two different indicator dyes, hydroxynaphthol blue (HNB) and cresol red. A total of 82 samples were used for detection with HNB and 94 samples with cresol red, and results were compared with the qRT-PCR assay. The sensitivity of the RT-LAMP-based HNB assay was 92.1% and the specificity was 93.2%. The sensitivity of the RT-LAMP-based cresol red assay was 80.3%, and the specificity was 97%. This colorimetric feature makes this assay highly accessible, low-cost, and user-friendly, which can be deployed for massive scale-up and rapid diagnosis of SARS-CoV-2 infection, particularly in low-resource settings.

Comparison of antibody responses following natural infection with Severe Acute Respiratory Syndrome Coronavirus 2 or receipt of CoronaVac or ChAdOx1 (AZD1222) vaccination in Chiang Mai, Thailand.

Background: In Thailand, early vaccination initiatives for SARS-CoV-2 relied on CoronaVac (Sinovac Life Sciences) and ChAdOx1 (Oxford-AstraZeneca) vaccines. However, the data of immunogenicity of these two vaccines in Thai populations is limited. This real time, head-to-head comparative study was conducted to investigate antibody (Ab) responses to SARS-CoV-2 following infection or receipt of either CoronaVac or ChAdOx1 vaccination in Chiang Mai, Thailand. Methods: Sera was collected within two months from participants having a history of documented SARS-CoV-2 infection or at one month after the second dose of CoronaVac vaccine. Sera from participants with a history of receiving one dose of ChAdOx1 vaccination was collected twice, at one month following each vaccine dose. Neutralizing antibodies (NAbs) were assessed using the surrogate neutralization test and anti-spike protein antibodies were assessed using an in-house enzyme-linked immunosorbent assay. Results: The prevalence of NAbs against SARS-CoV-2 was 92.1 %, 95.7 %, 64.1 % and 100 % in the infection group, CoronaVac group, ChAdOx1 group after 1st dose, and ChAdOx1 group after 2nd dose, respectively. The inhibition rate in individuals receiving two doses of ChAdOx1 vaccine (90.8%) was significantly higher than individuals who had recovered from natural infection (71.7%) or individuals who had received two doses of CoronaVac vaccine (66.7%). The prevalence of anti-spike Abs was 97.4 %, 97.8 %, 97.4 % and 100 % in the infection group, CoronaVac group, ChAdOx1 group after 1st dose, and ChAdOx1 group after 2nd dose, respectively. Significantly higher levels of anti-spike Abs were observed in the ChAdOx1 group after two doses of vaccination (1975 AU/mL) compared to those who had recovered from natural infection (468.5 AU/mL) and individuals who had received CoronaVac (554.4 AU/mL). Neutralizing activity had a statistically significant positive correlation with levels of anti-spike Abs. Conclusions: ChAdOx1 vaccine may provide superior immunogenicity than CoronaVac and natural infection.

A preliminary study on the effectiveness of maternal to neonatal transfer of antibodies against SARS-CoV-2 in the women vaccinated with heterologous CoronaVac-ChAdOx1.

The objective is to evaluate the effectiveness of placental transfer of maternally derived SARS-CoV-2 IgG antibodies after the vaccination of pregnant women with heterologous CoronaVac-ChAdOx1. Thirty pregnant women were vaccinated with CoronaVac as the first dose, followed by ChAdOx1 3 weeks later. The antibody levels in the maternal blood and in the umbilical cord blood at the time of delivery were determined. The results showed that the vaccination effectively increased antibody levels in both mothers and newborns. The antibody levels in the mothers were strongly correlated with those in the newborns (P < .001). The high levels of passive immunity in the newborns were achieved when the first and second doses of vaccination were given more than 40 and 20 d before delivery, respectively. After 1 month of the second dose, the immune levels seemed to decline in the mothers but increase in the newborns. The antibody levels in the newborns appear to be higher than those in the mothers in cases of delivery after 20 d of the second dose (1419 ± 699 vs 1222 ± 593 BAU/L; p < .05). In conclusion, heterologous CoronaVac-ChAdOx1-S schedule can increase antibody levels in a short time during pregnancy. Also, the regimen effectively increases immunity in the newborns. The antibody levels in the newborns appear to be higher than that in the mothers in most cases, if receiving the second dose more than 3 weeks before delivery. Therefore, the regimen should be considered as an effective regimen for pregnant women, especially in settings where mRNA vaccine is not available.

Highly Specific and Rapid Detection of Hepatitis C Virus Using RT-LAMP-Coupled CRISPR-Cas12 Assay.

Hepatitis C virus (HCV) infection can be cured with pan-genotypic direct-acting antiviral agents. However, identifying individuals with current hepatitis C remains a major challenge, especially in resource-limited settings where access to or availability of molecular tests is still limited. The goal of this study was to develop and validate a molecular assay for the rapid detection of HCV RNA in resource-limited settings. It is based on a combination of reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 12a (CRISPR-Cas12a) cleavage assay that allows the recognition of specific HCV nucleic acid sequences. Amplified products after the cleavage reactions can be visualized on lateral flow strips or measured with a fluorescence detector. When tested on clinical samples from individuals infected with HCV, HIV, or HBV, or from healthy donors, the RT-LAMP-coupled CRISPR-Cas12 assay yielded 96% sensitivity, 100% specificity, and 97% agreement as compared to the reference method (Roche COBAS AmpliPrep/COBAS TaqMan HCV Test). This assay could detect HCV RNA concentrations as low as 10 ng/µL (an estimated 2.38 Log10 IU/mL). Therefore, this sensitive and specific assay may represent an affordable and reliable point-of-care test for the identification of individuals with active hepatitis C in low-resource settings.

Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma.

Nucleic acid extraction from biological samples is an important step for hepatitis C virus (HCV) diagnosis. However, such extractions are mostly based on silica-based column methodologies, which may limit their application for on-site diagnosis. A simple, rapid, and field-deployable method for RNA extraction is still needed. In this study, we evaluated the efficacy of four simple RNA extraction methods for the detection of HCV in plasma samples: a silica-membrane-based method, a magnetic-beads-based method, boiling with diethyl pyrocarbonate (DEPC)-treated distilled water, and using a commercial lysis buffer. HCV RNA was detected using both real-time reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Using real-time RT-PCR, extracted RNA from the silica-membrane-based and magnetic-beads-based methods had a 100% detection rate for RNA extraction from plasma. Using RT-LAMP, extracted RNA from the silica-membrane-based method showed a 66% detection rate, while the magnetic-beads-based method had a 62% detection rate. In summary, magnetic-beads-based extraction can be used as an alternative RNA extraction method for on-site HCV detection. Boiling with DEPC-treated distilled water was not appropriate for low HCV load samples, and boiling with a lysis buffer was not recommended.

Prevalences of SARS-CoV-2 RNA and anti-SARS-CoV-2 among at-risk populations in Chiang Mai and Lamphun provinces, Thailand, during November 2020-January 2021.

Non-healthcare workers with a high potential for exposure to severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) may contribute to the virus spreading. Data among asymptomatic and high exposure risk populations is still scarce, in particular Chiang Mai and Lamphun provinces, Thailand. We conducted a cross-sectional observational study aiming to assess the prevalence of SARS-CoV-2 RNA positivity, anti-SARS-CoV-2 IgM/IgG, and potential associated factors among asymptomatic/mild symptomatic individuals with a high exposure risk in Chiang Mai and Lamphun provinces, during the second wave of outbreak in Thailand (November 2020-January 2021). Socio-demographic data was collected through an on-line questionnaire prior to collection of nasopharyngeal/throat swab samples and blood samples tested for SARS-CoV-2 RNA (DaAn Gene, China) and anti-SARS-CoV-2 IgM/IgG antibodies (commercial lateral flow immunoassays), respectively. Univariable and multivariable logistic regression analysis were used to analyze associated factors. None of 1,651 participants were found positive for SARS-CoV-2 RNA (0%, 95% confidence intervals, CI: 0-0.2). Fourteen were positive for anti-SARS-CoV-2 IgM/IgG antibodies (0.9%, 95% CI: 0.5-1.4), including 7 positives for IgM and 7 positives for IgG (0.4%, 95% CI: 0.2-0.9). Being over 50 years old was independently associated with virus exposure (OR: 5.8, 95% CI: 1.0-32.1%, p = 0.045). Despite high exposure risk, no current infection was found, and a very high proportion was still susceptible to SARS-CoV-2 infection and would clearly benefit from vaccination. Continuing active surveillance, rolling out of vaccination and monitoring response to vaccine will help better control the COVID-19 spread.

Antibody response to rabies pre-exposure vaccination among village health volunteers in a northern region of Thailand.

BACKGROUND: Rabies is a lethal, however the disease is preventable through vaccination either before or immediately after an exposure. This study aimed to provide a pre-exposure prophylaxis rabies immunization to village health volunteers (VHV) who provide rabies vaccination for pets and free-roaming dogs in their villages and evaluate the antibody level and adverse effects after vaccination. We also assessed the knowledge related to rabies of these VHVs before field trip for pet vaccination. METHODS: This study was conducted at Mae Kha sub district, San Pa Tong district, Chiangmai, Thailand between January and March 2020. Consenting participants were interviewed using a questionnaire, received an intradermal two-dose, seven-day pre-exposure rabies vaccination, and sera were tested for anti-rabies antibody levels with the cost effective easy competitive enzyme-linked immunosorbent assay (CEE-cELISA) before and after vaccination. RESULTS: A total of 27 VHVs were recruited from 14 villages in Mae Kha sub district. All of them were male and had a median age of 61.5 years (interquartile range: 55-64). After vaccination, seroconversion rate was 92 % (23/25) with a median of 12.4 EU/mL (interquartile range: 8.9-20.1). Two participants who had rabies vaccination one year previously still had adequate levels before receiving a booster dose. All participants did not show any serious adverse reactions after vaccination. CONCLUSION: A regimen of two-dose, seven-day vaccination series in high-risk health volunteers using an intradermal administration provides a high seroconversion rate, efficacy and safe for pre-exposure vaccination schedule. In addition, rabies-related knowledge should be provided to village health volunteers before their fieldwork.

Rapid visual detection of hepatitis C virus using a reverse transcription loop-mediated isothermal amplification assay.

OBJECTIVES: The aim was to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of hepatitis C virus (HCV) in a single closed tube. METHODS: Plasma samples were collected from 200 HCV-infected patients. HCV-RNA was detected by one-step RT-LAMP processed at 65 °C for 60 min. The amplified products were detected by hydroxynaphthol blue (HNB)-dependent visual method and gel electrophoresis. Specificity was tested against other viruses. Sensitivity was determined using serial dilutions of extracted RNA. RESULTS: The RT-LAMP assay detected 97.5% of HCV-RNA genotype 1, 91.1% of genotype 3, and 100% of genotype 6. The color change was evidenced with the naked eye. The assay demonstrated a clinical sensitivity of 95.5% and specificity of 100%, as well as no cross-reactivity with other viruses (i.e., hepatitis B virus, HIV). The limit of detection was as low as 10 ng per reaction for HCV genotypes 1a and 6, while it was 100 ng for genotype 3a. The assay showed a 100% detection threshold at a viral load of 5.00 log10 IU/mL in the clinical samples tested. CONCLUSIONS: This study demonstrated the use of an RT-LAMP assay for the detection of HCV in a simple, rapid, and cost-effective manner, which will be useful in resource-limited settings to allow the identification of individuals in need of HCV treatment.

Prevalence and factors associated with hepatitis B and D virus infections among migrant sex workers in Chiangmai, Thailand: A cross-sectional study in 2019.

OBJECTIVES: To determine the prevalence of hepatitis B surface antigen (HBsAg) and antibody to hepatitis delta virus (anti-HDV) and associated factors among migrant sex workers in Chiangmai, Thailand. METHODS: This cross-sectional study was conducted at various sexual entertainment venues in Chiangmai, Thailand, in 2019. Consenting participants were interviewed using a questionnaire, and plasma was tested for hepatitis B virus (HBV) markers (DiaSorin, Italy) and anti-HDV antibody (DIA.PRO Diagnostic Bioprobes, Italy), if HBsAg-positive. Associations between HBsAg positivity or HDV antibody and potential factors were examined using univariable and multivariable logistic regression analysis. RESULTS: A total of 396 migrant sex workers, half of them female, were recruited between February and September 2019. Their median age was 25 years (interquartile range 22-30 years) and 95% were Burmese. Overall, HBsAg prevalence was 11.4%; 8.1% in females and 14.7% in males (Chi-square, p = 0.040). One-third were still susceptible to HBV. No HBsAg-positive participants had anti-HDV antibodies. HBsAg positivity was associated with being male (adjusted odds ratio (aOR) 3.01, 95% confidence interval (CI) 1.25-7.68, p = 0.014), having attended school (aOR 4.50, 95% CI 1.26-15.98, p = 0.020), being separated/divorced/widowed (aOR 5.77, 95% CI 1.48-22.52, p = 0.012), and having unprotected sex (aOR 3.38, 95% CI 1.31-8.71, p = 0.012). CONCLUSIONS: In this young population, higher HBsAg prevalence in males may be related to sexual transmission, indicating the need for HBV screening programs linked with HBV prevention and care.

HIV RNA measurement in dried blood spots of HIV-infected patients in Thailand using Abbott m2000 system.

World Health Organization recommends using dried blood spots (DBS) for HIV RNA viral load (VL) measurement whenever plasma processing is not convenient or feasible. DBS collected from 80 treatment-naïve HIV-infected patients presenting in three hospitals of two different regions of Thailand were shipped to a central laboratory along with corresponding plasma specimens. Viral load was measured in both DBS and plasma using the Abbott m2000 system. HIV RNA levels were strongly correlated (r = 0.94) with a mean of differences of 0.23 log10 copies/mL. Using the 1,000 copies/mL cut-off, the sensitivity of DBS was 97% (95%CI, 91-100%) and specificity was 75% (95%CI, 19-99%). DBS are useful to scale-up HIV RNA VL testing in settings with limited access to VL testing.

HIVCoR: A sequence-based tool for predicting HIV-1 CRF01_AE coreceptor usage.

Determination of HIV-1 coreceptor usage is strongly recommended before starting the coreceptor-specific inhibitors for HIV treatment. Currently, the genotypic assays are the most interesting tools due to they are more feasible than phenotypic assays. However, most of prediction models were developed and validated by data set of HIV-1 subtype B and C. The present study aims to develop a powerful and reliable model to accurately predict HIV-1 coreceptor usage for CRF01_AE subtype called HIVCoR. HIVCoR utilized random forest and support vector machine as the prediction model, together with amino acid compositions, pseudo amino acid compositions and relative synonymous codon usage frequencies as the input feature. The overall success rate of 93.79% was achieved from the external validation test on the objective benchmark dataset. Comparison results indicated that HIVCoR was superior to other bioinformatics tools and genotypic predictors. For the convenience of experimental scientists, a user-friendly webserver has been established at http://codes.bio/hivcor/.

Serologic characteristics of hepatitis B virus among hill-tribe children in Omkoi district, Chiangmai province, Thailand.

INTRODUCTION: Thailand has integrated hepatitis B (HB) vaccination of newborns into the national Expanded Program on Immunization (EPI) in 1992. This has led to a dramatic decrease of HBsAg prevalence in children. However, HB vaccine coverage in remote areas is not well-known. This study aimed to investigate serologic characteristics of hepatitis B virus (HBV) among hill-tribe children in Omkoi District, Chiangmai Province, Thailand. METHODOLOGY: This cross-sectional study was conducted on stored samples collected from hill-tribe children attending the primary/secondary school in Omkoi District in December 2014. Sera were tested for HBsAg, anti-HBs and anti-HBc using enzyme immunoassays (MUREX, DiaSorin, Italy). Samples with anti-HBc positive were further assessed for HBV DNA using an in-house HBV DNA semi-nested polymerase chain reaction (PCR) assay. RESULTS: Of 210 children evaluated, 4 (1.9%:95% CI 0.5-4.8) were HBsAg-positive. Of the 206 children HBsAg negative, 17 were anti-HBc and anti-HBs positive, 15 anti-HBc positive only, 26 anti-HBs positive only and 148 negative for both anti-HBc and anti-HBs. None of the children with anti-HBc were positive for HBV DNA. CONCLUSIONS: A high percentage of children had no markers of HBV protection suggesting that HB vaccine coverage was not optimal in this area. Our results warrant HBV serologic investigations in other remote areas to assess whether HB vaccine coverage needs to be improved and to identify children who should be vaccinated.

Effect of Amino Acid Substitutions Within the V3 Region of HIV-1 CRF01_AE on Interaction with CCR5-Coreceptor.

Specific amino acids within the V3 loop of HIV-1 CRF01_AE envelope glycoprotein that are involved in the interaction with CCR5/CXCR4 coreceptors, are not well characterized. We generated V3 mutants using polymerase chain reaction (PCR)-based site-directed mutagenesis of HIV-1 CRF01_AE R5-env plasmids at specific positions. Mutant viruses were produced by env-pseudotyped virus assay, tested for coreceptor usage using U373.R5 and U373.X4 cells, and viral entry was assessed with luciferase activity measurement. All viruses, harboring either single or double mutations, used the CCR5 coreceptor. However, those containing a single substitution at positions 7, 11, 18, and 32 and those with mutations at positions 5/32 and 18/32 had reduced infectivity. Only virus with arginine substitution at position 11 seemed to be involved in CXCR4 coreceptor usage. Our results suggest that some V3 positions may be necessary for the binding to coreceptor, but not for the switch of coreceptor usage.

HIV-1 coreceptor usage in perinatally infected Thai children.

HIV-1 coreceptor usage in children who were born to HIV-1 infected mothers in Thailand is not well characterized. Here, the prevalence of coreceptor usage and genotype among HIV-1 infected children in Thailand were observed. Proviral DNA from 284 HIV-1 infected children who received HIV-1 early infant diagnosis between 2007 and 2013 under the National AIDS Program were studied. Genotypic tropism testing was performed based on amplification of the V3 region in a triplicate nested-PCR following by DNA sequencing. HIV-1 coreceptor usage was determined using Geno2pheno[coreceptor] with a false positive rate of 10%. Samples from 267 children were successfully amplified and coreceptor usage could be determined. Two hundred and thirty-seven (89%) children were infected with CRF01_AE, 29 (11%) were subtype B and 1 was subtype C. CCR5-using variants were found in 148 (55%) children and CXCR4-using variants were observed in 119 (45%) children. No significant differences in coreceptor usage and age, gender, signs of HIV infection, children's or maternal ARV receiving were observed. The only significant difference was found in N-linked glycosylation characteristic. This evidence showed that X4 viruses can be highly observed at an early age of children which has important clinical implications and may limit usage of CCR5 antagonist family.

HIV-1 CRF01_AE coreceptor usage prediction using kernel methods based logistic model trees.

The determination of HIV-1 coreceptor usage plays a major role in HIV treatment. Since Maraviroc has been used in a treatment for patients those exclusively harbor R5-tropic strains, the efficient performance of classifying HIV-1 coreceptor usage can help choose the most advantaged HIV treatment. In general, HIV-1 variants are classified as R5-tropic and X4-tropic or dual/mixed tropic based on their coreceptor usages. The classification of the coreceptor usage has been developed by using the various computational methods or genotypic algorithms based on V3 amino acid sequences. Most genotypic tools have been designed based on a data set of the HIV-1 subtype B that seemed to be reliable only for this subtype. However, the performance of these tools decreases in non-B subtypes. In this study, the support vector machine (SVM) method has been used to classify the HIV-1 coreceptor. To develop an efficient SVM classifier, we present a feature selector using the logistic model tree (LMT) method to select the most relevant positions from the V3 amino acid sequences. Our approach achieves as high as 97.8% accuracy, 97.7% specificity, and 97.9% sensitivity measured by ten-fold cross-validation on 273 sequences.