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1. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals

Author

Chin, Bum Sik, Chaillon, Antoine, Mehta, Sanjay R, Wertheim, Joel O, Kim, Gayeon, Shin, Hyoung-Shik, and Smith, Davey M

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, HIV/AIDS, Genetics, Infectious Diseases, Prevention, Sexually Transmitted Infections, Infection, Adult, Age Factors, Cluster Analysis, Drug Resistance, Viral, Female, Genotype, HIV Infections, HIV-1, Heterosexuality, Homosexuality, Male, Humans, Male, Middle Aged, Molecular Epidemiology, Phylogeny, RNA, Viral, Republic of Korea, Young Adult, pol Gene Products, Human Immunodeficiency Virus, human immunodeficiency virus, molecular epidemiology, cluster analysis, phylogeny, Microbiology, Virology, Clinical sciences, Medical microbiology
Abstract

To evaluate if HIV transmission networks could be elucidated from data collected in a short time frame, 131 HIV-1 pol sequences were analyzed which were generated from treatment-naïve Korean individuals who were sequentially identified over 1 year. A transmission linkage was inferred when there was a genetic distance

Published
2016

2. Travel Pattern and Prescription Analysis at a Single Travel Clinic Specialized for Yellow Fever Vaccination in South Korea.

Author

Chin, Bum Sik, Kim, Jae Yoon, Gianella, Sara, and Lee, Myunghee

Subjects
Antibiotic prophylaxis, Malaria, Travel medicine, Vaccine, Yellow fever, Vector-Borne Diseases, Prevention, Immunization, Orphan Drug, Infectious Diseases, Rare Diseases, Vaccine Related, Infection, Antibiotic prophylaxis Malaria Travel medicine Vaccine Yellow fever
Abstract

BackgroundTravel-related risks for infectious diseases vary depending on travel patterns such as purpose, destination, and duration. In this study, we describe the patterns of travel and prescription of vaccines as well as malaria prophylaxis medication (MPM) at a travel clinic in South Korea to identify the gaps to fill for the optimization of pre-travel consultation.Materials and methodsA cohort of travel clinic visitors in 2011 was constructed and early one-third of the visitors of each month were reviewed. During the study period, 10,009 visited the travel clinic and a retrospective chart review was performed for 3,332 cases for analysis of travel patterns and prescriptions.ResultsPeople receiving yellow fever vaccine (YFV) (n = 2,933) were traveling more frequently for business and tourism and less frequently for providing non-medical service or research/education compared to the 399 people who did not receive the YFV. Overall, most people were traveling to Eastern Africa, South America, and Western Africa, while South-Eastern Asia was the most common destination for the non-YFV group. Besides YFV, the typhoid vaccine was the most commonly prescribed (54.2%), while hepatitis A presented the highest coverage (74.7%) considering the natural immunity, prior and current vaccination history. Additionally, 402 (82.5%) individuals received a prescription for MPM among the 487 individuals travelling to areas with high-risk of malaria infection. Age over 55 was independently associated with receiving MPM prescription, while purpose of providing service and travel duration over 10 days were associated with no MPM prescription, despite travelling to high-risk areas.ConclusionEastern Africa and South America were common travel destinations among the visitors to a travel clinic for YFV, and most of them were travelling for tourism and business. For the individuals who are traveling to areas with high-risk for malaria, more proactive approach might be required in case of younger age travelers, longer duration, and travel purpose of providing service to minimize the risk of malaria infection.

Published
2016

3. Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

Author

Rhee, Soo-Yon, Blanco, Jose Luis, Jordan, Michael R, Taylor, Jonathan, Lemey, Philippe, Varghese, Vici, Hamers, Raph L, Bertagnolio, Silvia, de Wit, Tobias F Rinke, Aghokeng, Avelin F, Albert, Jan, Avi, Radko, Avila-Rios, Santiago, Bessong, Pascal O, Brooks, James I, Boucher, Charles AB, Brumme, Zabrina L, Busch, Michael P, Bussmann, Hermann, Chaix, Marie-Laure, Chin, Bum Sik, D'Aquin, Toni T, De Gascun, Cillian F, Derache, Anne, Descamps, Diane, Deshpande, Alaka K, Djoko, Cyrille F, Eshleman, Susan H, Fleury, Herve, Frange, Pierre, Fujisaki, Seiichiro, Harrigan, P Richard, Hattori, Junko, Holguin, Africa, Hunt, Gillian M, Ichimura, Hiroshi, Kaleebu, Pontiano, Katzenstein, David, Kiertiburanakul, Sasisopin, Kim, Jerome H, Kim, Sung Soon, Li, Yanpeng, Lutsar, Irja, Morris, Lynn, Ndembi, Nicaise, Kee, Peng NG, Paranjape, Ramesh S, Peeters, Martine, Poljak, Mario, Price, Matt A, Ragonnet-Cronin, Manon L, Reyes-Terán, Gustavo, Rolland, Morgane, Sirivichayakul, Sunee, Smith, Davey M, Soares, Marcelo A, Soriano, Vincent V, Ssemwanga, Deogratius, Stanojevic, Maja, Stefani, Mariane A, Sugiura, Wataru, Sungkanuparph, Somnuek, Tanuri, Amilcar, Tee, Kok Keng, Truong, Hong-Ha M, van de Vijver, David AMC, Vidal, Nicole, Yang, Chunfu, Yang, Rongge, Yebra, Gonzalo, Ioannidis, John PA, Vandamme, Anne-Mieke, and Shafer, Robert W

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Good Health and Well Being, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Published
2015

4. Short Communication: Increase of HIV-1 K103N Transmitted Drug Resistance and Its Association with Efavirenz Use in South Korea

Author

Chin, Bum Sik, Shin, Hyoung-Shik, Kim, Gayeon, Wagner, Gabriel A, Gianella, Sara, and Smith, Davey M

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Sexually Transmitted Infections, Infectious Diseases, HIV/AIDS, Antimicrobial Resistance, Women's Health, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Adult, Alkynes, Anti-HIV Agents, Benzoxazines, Cluster Analysis, Cyclopropanes, Drug Resistance, Viral, Genotype, HIV Infections, HIV Reverse Transcriptase, HIV-1, Humans, Incidence, Male, Molecular Sequence Data, Mutation, Missense, Phylogeny, Republic of Korea, Sequence Analysis, DNA, Adult Anti-HIV Agents/pharmacology/*therapeutic use Benzoxazines/pharmacology/*therapeutic use Cluster Analysis *Drug Resistance, Viral Genotype HIV Infections/epidemiology/transmission/*virology HIV Reverse Transcriptase/*genetics HIV-1/*drug effects/enzymology/genetics/isolation & purification Humans Incidence Male Molecular Sequence Data *Mutation, Missense Phylogeny Republic of Korea/epidemiology Sequence Analysis, DNA, Clinical Sciences, Virology, Clinical sciences
Abstract

Previous studies reported a relatively low prevalence of transmitted drug resistance (TDR) in South Korea (

Published
2015

8. Prognostic Factors for Pulmonary Fibrosis Following Pneumonia in Patients with COVID-19: A Prospective Study

Author

Lee, Inhan, primary, Kim, Joohae, additional, Yeo, Yohwan, additional, Lee, Ji Yeon, additional, Jeong, Ina, additional, Joh, Joon-Sung, additional, Kim, Gayeon, additional, Chin, Bum Sik, additional, Kim, Yeonjae, additional, Kim, Min-Kyung, additional, Jeon, Jaehyun, additional, Yoon, Yup, additional, Jin, Sung Chan, additional, and Kim, Junghyun, additional

Published
2022
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9. Enhanced antibody responses in fully vaccinated individuals against pan-SARS-CoV-2 variants following Omicron breakthrough infection

Author

Jeong, Hye Won, primary, Kim, Se-Mi, additional, Jung, Min Kyung, additional, Noh, Ji Yun, additional, Yoo, Ji-Seung, additional, Kim, Eun-Ha, additional, Kim, Young-Il, additional, Yu, Kwangmin, additional, Jang, Seung-Gyu, additional, Gil, Juryeon, additional, Casel, Mark Anthony, additional, Rare, Rollon, additional, Choi, Jeong Ho, additional, Kim, Hee-Sung, additional, Kim, Jun Hyoung, additional, Um, Jihye, additional, Kim, Chaeyoon, additional, Kim, Yeonjae, additional, Chin, Bum Sik, additional, Jung, Sungmin, additional, Choi, Jun Yong, additional, Song, Kyoung-Ho, additional, Kim, Yong-Dae, additional, Park, Jun-Sun, additional, Song, Joon Young, additional, Shin, Eui-Cheol, additional, and Choi, Young Ki, additional

Published
2022
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16. Infection and Rapid Transmission of SARS-CoV-2 in Ferrets

Author

Kim, Young-Il, Kim, Seong-Gyu, Kim, Se-Mi, Kim, Eun-Ha, Park, Su-Jin, Yu, Kwang-Min, Chang, Jae-Hyung, Kim, Eun Ji, Lee, Seunghun, Casel, Mark Anthony B., Um, Jihye, Song, Min-Suk, Jeong, Hye Won, Lai, Van Dam, Kim, Yeonjae, Chin, Bum Sik, Park, Jun-Sun, Chung, Ki-Hyun, Foo, Suan-Sin, Poo, Haryoung, Mo, In-Pil, Lee, Ok-Jun, Webby, Richard J., Jung, Jae U., and Choi, Young Ki

Published
2020
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18. Remdesivir for Severe Coronavirus Disease 2019 (COVID-19) Versus a Cohort Receiving Standard of Care

Author

Olender, Susan Aileen, Perez, Katherine K.K., Go, Alan A.S., Balani, Bindu, Price-Haywood, Eboni E.G., Shah, Nirav N.S., Wang, Su, Walunas, Theresa T.L., Swaminathan, Shobha, Slim, Jihad, Chin, Bum Sik, De Wit, Stéphane, Ali, Shamim S.M., Soriano Viladomiu, Alex, Robinson, Philip, Gottlieb, Robert R.L., Tsang, Tak Yin Owen, Lee, Heng I.H., Hu, Hao, Haubrich, Richard, Chokkalingam, Anand A.P., Lin, Lanjia, Zhong, Lijie, Bekele, Benjamin Nebiyou, Mera-Giler, Robertino, Phulpin, Chloé, Edgar, Holly, Gallant, Joel J.E., Diaz-Cuervo, Helena, Smith, Lindsey L.E., Osinusi, Anu A.O., Brainard, Diana D.M., Bernardino, José Ignacio, Olender, Susan Aileen, Perez, Katherine K.K., Go, Alan A.S., Balani, Bindu, Price-Haywood, Eboni E.G., Shah, Nirav N.S., Wang, Su, Walunas, Theresa T.L., Swaminathan, Shobha, Slim, Jihad, Chin, Bum Sik, De Wit, Stéphane, Ali, Shamim S.M., Soriano Viladomiu, Alex, Robinson, Philip, Gottlieb, Robert R.L., Tsang, Tak Yin Owen, Lee, Heng I.H., Hu, Hao, Haubrich, Richard, Chokkalingam, Anand A.P., Lin, Lanjia, Zhong, Lijie, Bekele, Benjamin Nebiyou, Mera-Giler, Robertino, Phulpin, Chloé, Edgar, Holly, Gallant, Joel J.E., Diaz-Cuervo, Helena, Smith, Lindsey L.E., Osinusi, Anu A.O., Brainard, Diana D.M., and Bernardino, José Ignacio

Abstract

BACKGROUND: We compared the efficacy of the antiviral agent, remdesivir, versus standard-of-care treatment in adults with severe coronavirus disease 2019 (COVID-19) using data from a phase 3 remdesivir trial and a retrospective cohort of patients with severe COVID-19 treated with standard of care. METHODS: GS-US-540-5773 is an ongoing phase 3, randomized, open-label trial comparing two courses of remdesivir (remdesivir-cohort). GS-US-540-5807 is an ongoing real-world, retrospective cohort study of clinical outcomes in patients receiving standard-of-care treatment (non-remdesivir-cohort). Inclusion criteria were similar between studies: patients had confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, were hospitalized, had oxygen saturation ≤94% on room air or required supplemental oxygen, and had pulmonary infiltrates. Stabilized inverse probability of treatment weighted multivariable logistic regression was used to estimate the treatment effect of remdesivir versus standard of care. The primary endpoint was the proportion of patients with recovery on day 14, dichotomized from a 7-point clinical status ordinal scale. A key secondary endpoint was mortality. RESULTS: After the inverse probability of treatment weighting procedure, 312 and 818 patients were counted in the remdesivir- and non-remdesivir-cohorts, respectively. At day 14, 74.4% of patients in the remdesivir-cohort had recovered versus 59.0% in the non-remdesivir-cohort (adjusted odds ratio [aOR] 2.03: 95% confidence interval [CI]: 1.34-3.08, P < .001). At day 14, 7.6% of patients in the remdesivir-cohort had died versus 12.5% in the non-remdesivir-cohort (aOR 0.38, 95% CI: 22-.68, P = .001). CONCLUSIONS: In this comparative analysis, by day 14, remdesivir was associated with significantly greater recovery and 62% reduced odds of death versus standard-of-care treatment in patients with severe COVID-19. CLINICAL TRIALS REGISTRATION: NCT04292899 and EUPAS34303., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

20. Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019

Author

Lee, Jee-Soo, primary, Kim, So Yeon, additional, Kim, Taek Soo, additional, Hong, Ki Ho, additional, Ryoo, Nam-Hee, additional, Lee, Jaehyeon, additional, Park, Jae Hyeon, additional, Cho, Sung Im, additional, Kim, Man Jin, additional, Kim, Young-gon, additional, Kim, Boram, additional, Shin, Ho Seob, additional, Oh, Hyeon Sae, additional, Seo, Myoung-Seock, additional, Gwon, Tae-Rin, additional, Kim, Yeonjae, additional, Park, Jun-Sun, additional, Chin, Bum Sik, additional, Park, Wan Beom, additional, Park, Sung Sup, additional, and Seong, Moon-Woo, additional

Published
2020
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21. 73. Geographical Disparities in Clinical Outcomes of Severe COVID-19 Patients Treated with Remdesivir

Author

Diaz, George, primary, Arribas, Jose Ramon, additional, Robinson, Philip A, additional, Cattelan, Anna Maria, additional, Tashima, Karen T, additional, Tsang, Owen Tak-Yin, additional, Chen, Yao-Shen, additional, SenGupta, Devi, additional, Vendrame, Elena, additional, Blair, Christiana, additional, Chokkalingam, Anand, additional, Osinusi, Anu, additional, Brainard, Diana M, additional, Chin, Bum Sik, additional, Spinner, Christoph, additional, Criner, Gerard J, additional, Muñoz, Jose, additional, Lye, David Chien Boon, additional, and Gottlieb, Robert L, additional

Published
2020
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22. 557. Impact of Concomitant Hydroxychloroquine Use on Safety and Efficacy of Remdesivir in Moderate COVID-19 Patients

Author

Arribas, Jose Ramon, primary, Arribas, Jose Ramon, additional, Sanyal, Arun J, additional, Soriano, Alex, additional, Chin, Bum Sik, additional, Kalimuddin, Shirin, additional, Schreiber, Stefan, additional, Elboudwarej, Emon, additional, Tian, Yuan, additional, Hyland, Robert H, additional, SenGupta, Devi, additional, Chokkalingam, Anand, additional, Osinusi, Anu, additional, Brainard, Diana M, additional, Lübbert, Christoph, additional, Lye, David Chien Boon, additional, Aberg, Judith A, additional, Elorza, Enrique Navas, additional, Tashima, Karen T, additional, and McPhail, Mark, additional

Published
2020
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23. Detection and Isolation of SARS-CoV-2 in Serum, Urine, and Stool Specimens of COVID-19 Patients from the Republic of Korea

Author

Kim, Jeong-Min, primary, Kim, Heui Man, additional, Lee, Eun Jung, additional, Jo, Hye Jun, additional, Yoon, Youngsil, additional, Lee, Nam-Joo, additional, Son, Junseock, additional, Lee, Ye-Ji, additional, Kim, Mi Seon, additional, Lee, Yong-Pyo, additional, Chae, Su-Jin, additional, Park, Kye Ryeong, additional, Cho, Seung-Rye, additional, Park, Sehee, additional, Kim, Su Jin, additional, Wang, Eunbyeol, additional, Woo, SangHee, additional, Lim, Aram, additional, Park, Su-Jin, additional, Jang, JunHyeong, additional, Chung, Yoon-Seok, additional, Chin, Bum Sik, additional, Lee, Jin-Soo, additional, Lim, Duko, additional, Han, Myung-Guk, additional, and Yoo, Cheon Kwon, additional

Published
2020
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24. Leveraging a Preexisting Global Infectious Disease Network for Local Decision Making During a Pandemic.

Author

Herstein, Jocelyn J, Lowe, John J, Wolf, Timo, Vasoo, Shawn, Leo, Yee Sin, Chin, Bum Sik, Shen, Yinzhong, Hewlett, Angela L, and Lawler, James V

Subjects
PREVENTION of communicable diseases, PREVENTION of epidemics, HEALTH policy, COVID-19, EMERGENCY management, BUSINESS networks, MEDICAL protocols, DECISION making, INTERPROFESSIONAL relations
Abstract

Emerging infectious disease epidemics require a rapid response from health systems; however, evidence-based consensus guidelines are generally absent early in the course of events. Formed in 2017 by 5 high-level isolation units spanning 3 continents, the experience of the Global Infectious Disease Preparedness Network (GIDPN) early in the course of coronavirus disease 2019 (COVID-19) provides a model for accelerating best practice development and improving decision-making in health emergencies. The network served as a platform for real-time, open and transparent information-sharing during unknowns of an active outbreak by clinicians caring for patients, by researchers conducting clinical trials and transmission and infection prevention studies, and by teams advising local and national policy makers. Shared knowledge led to earlier adoption of some treatment modalities as compared to most peer institutions and to implementation of protocols prior to incorporation into national guidelines. GIDPN and similar networks are integral in enhancing preparedness for and response to future epidemics/pandemics. [ABSTRACT FROM AUTHOR]

Published
2022
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25. Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019.

Author

Lee, Jee-Soo, Kim, So Yeon, Kim, Taek Soo, Hong, Ki Ho, Ryoo, Nam-Hee, Lee, Jaehyeon, Park, Jae Hyeon, Cho, Sung Im, Kim, Man Jin, Kim, Young-gon, Kim, Boram, Shin, Ho Seob, Oh, Hyeon Sae, Seo, Myoung-Seock, Gwon, Tae-Rin, Kim, Yeonjae, Park, Jun-Sun, Chin, Bum Sik, Park, Wan Beom, and Park, Sung Sup

Subjects
SARS diagnosis, REVERSE transcriptase polymerase chain reaction, COVID-19, SEQUENCE analysis, CONVALESCENCE, REINFECTION, GENOMES, DESCRIPTIVE statistics, POLYMERASE chain reaction, DATA analysis software, DISEASE risk factors
Abstract

Background Positive results from real-time reverse-transcription polymerase chain reaction (rRT-PCR) in recovered patients raise concern that patients who recover from coronavirus disease 2019 (COVID-19) may be at risk of reinfection. Currently, however, evidence that supports reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been reported. Methods We conducted whole-genome sequencing of the viral RNA from clinical specimens at the initial infection and at the positive retest from 6 patients who recovered from COVID-19 and retested positive for SARS-CoV-2 via rRT-PCR after recovery. A total of 13 viral RNAs from the patients' respiratory specimens were consecutively obtained, which enabled us to characterize the difference in viral genomes between initial infection and positive retest. Results At the time of the positive retest, we were able to acquire a complete genome sequence from patient 1, a 21-year-old previously healthy woman. In this patient, through the phylogenetic analysis, we confirmed that the viral RNA of positive retest was clustered into a subgroup distinct from that of the initial infection, suggesting that there was a reinfection of SARS-CoV-2 with a subtype that was different from that of the primary strain. The spike protein D614G substitution that defines the clade "G" emerged in reinfection, while mutations that characterize the clade "V" (ie, nsp6 L37F and ORF3a G251V) were present at initial infection. Conclusions Reinfection with a genetically distinct SARS-CoV-2 strain may occur in an immunocompetent patient shortly after recovery from mild COVID-19. SARS-CoV-2 infection may not confer immunity against a different SARS-CoV-2 strain. [ABSTRACT FROM AUTHOR]

Published
2021
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30. Development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel SARS-CoV-2

Author

Baek, Yun Hee, primary, Um, Jihye, additional, Antigua, Khristine Joy C., additional, Park, Ji-Hyun, additional, Kim, Yeonjae, additional, Oh, Sol, additional, Kim, Young-il, additional, Choi, Won-Suk, additional, Kim, Seong Gyu, additional, Jeong, Ju Hwan, additional, Chin, Bum Sik, additional, Nicolas, Halcyon Dawn G., additional, Ahn, Ji-Young, additional, Shin, Kyeong Seob, additional, Choi, Young Ki, additional, Park, Jun-Sun, additional, and Song, Min-Suk, additional

Published
2020
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31. Use of Convalescent Plasma Therapy in Two COVID-19 Patients with Acute Respiratory Distress Syndrome in Korea

Author

Ahn, Jin Young, primary, Sohn, Yujin, additional, Lee, Su Hwan, additional, Cho, Yunsuk, additional, Hyun, Jong Hoon, additional, Baek, Yae Jee, additional, Jeong, Su Jin, additional, Kim, Jung Ho, additional, Ku, Nam Su, additional, Yeom, Joon-Sup, additional, Roh, Juhye, additional, Ahn, Mi Young, additional, Chin, Bum Sik, additional, Kim, Young Sam, additional, Lee, Hyukmin, additional, Yong, Dongeun, additional, Kim, Hyun Ok, additional, Kim, Sinyoung, additional, and Choi, Jun Yong, additional

Published
2020
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33. Correlation between Pneumonia Severity and Pulmonary Complications in Middle East Respiratory Syndrome

Author

Park, Wan Beom, primary, Jun, Kang Il, additional, Kim, Gayeon, additional, Choi, Jae-Phil, additional, Rhee, Ji-Young, additional, Cheon, Shinhyea, additional, Lee, Chang Hyun, additional, Park, Jun-Sun, additional, Kim, Yeonjae, additional, Joh, Joon-Sung, additional, Chin, Bum Sik, additional, Choe, Pyeong Gyun, additional, Bang, Ji Hwan, additional, Park, Sang-Won, additional, Kim, Nam Joong, additional, Lim, Dong-Gyun, additional, Kim, Yeon-Sook, additional, Oh, Myoung-don, additional, and Shin, Hyoung-Shik, additional

Published
2018
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35. Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance

Author

Rhee, Soo Yon, Blanco, Jose Luis, Jordan, Michael R., Taylor, Jonathan, Lemey, Philippe, Varghese, Vici, Hamers, Raph L., Bertagnolio, Silvia, de Wit, Tobias F Rinke, Aghokeng, Avelin F., Albert, Jan, Avi, Radko, Avila-Rios, Santiago, Bessong, Pascal O., Brooks, James I., Boucher, Charles A B, Brumme, Zabrina L., Busch, Michael P., Bussmann, Hermann, Chaix, Marie Laure, Chin, Bum Sik, D’Aquin, Toni T., De Gascun, Cillian F., Derache, Anne, Descamps, Diane, Deshpande, Alaka K., Djoko, Cyrille F., Eshleman, Susan H., Fleury, Herve, Frange, Pierre, Fujisaki, Seiichiro, Harrigan, P. Richard, Hattori, Junko, Holguin, Africa, Hunt, Gillian M., Ichimura, Hiroshi, Kaleebu, Pontiano, Katzenstein, David, Kiertiburanakul, Sasisopin, Kim, Jerome H., Kim, Sung Soon, Li, Yanpeng, Lutsar, Irja, Morris, Lynn, Ndembi, Nicaise, NG, Kee Peng, Paranjape, Ramesh S., Peeters, Martine, Poljak, Mario, Price, Matt A., Ragonnet-Cronin, Manon L., Reyes-Terán, Gustavo, Rolland, Morgane, Sirivichayakul, Sunee, Smith, Davey M., Soares, Marcelo A., Soriano, Vincent V., Ssemwanga, Deogratius, Stanojevic, Maja, Stefani, Mariane A., Sugiura, Wataru, Sungkanuparph, Somnuek, Tanuri, Amilcar, Tee, Kok Keng, Truong, Hong Ha M, van de Vijver, David A M C, Vidal, Nicole, Yang, Chunfu, Yang, Rongge, Yebra, Gonzalo, Ioannidis, John P A, Vandamme, Anne Mieke, Shafer, Robert W., Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), and TB, HIV and opportunistic diseases and pathogens (THOP)

Subjects
SDG 3 - Good Health and Well-being, virus diseases, Cell Biology, Biochemistry, Molecular Biology, Biotechnology
Abstract

PMID: 25849352 WOS:000354825700001 Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05–1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06–1.25), North America (OR = 1.19; 95% CI: 1.12–1.26), Europe (OR = 1.07; 95% CI: 1.01–1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12–1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92–1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling.Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen. publishersversion published

Published
2015

36. Long-term Respiratory Complication in Patients with Middle East Respiratory Syndrome: 1-year Follow-up After the 2015 Outbreak in South Korea

Author

Il Jun, Kang, primary, Park, Wan Beom, additional, Kim, Gayeon, additional, Choi, Jae-Phil, additional, Rhee, Ji-Young, additional, Cheon, Shinhye, additional, Park, Jun-Sun, additional, Kim, Yeonjae, additional, Joh, Joonsung, additional, Chin, Bum Sik, additional, Choe, Pyeong Gyun, additional, Bang, Ji Whan, additional, Park, Sang-Won, additional, Kim, Nam Joong, additional, Lim, Dong-Gyun, additional, Kim, Yeon-Sook, additional, Oh, Myoung-Don, additional, and Shin, Hyoung-Shik, additional

Published
2017
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39. Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

Author

Rhee, Soo-Yon, primary, Blanco, Jose Luis, additional, Jordan, Michael R., additional, Taylor, Jonathan, additional, Lemey, Philippe, additional, Varghese, Vici, additional, Hamers, Raph L., additional, Bertagnolio, Silvia, additional, de Wit, Tobias F. Rinke, additional, Aghokeng, Avelin F., additional, Albert, Jan, additional, Avi, Radko, additional, Avila-Rios, Santiago, additional, Bessong, Pascal O., additional, Brooks, James I., additional, Boucher, Charles A. B., additional, Brumme, Zabrina L., additional, Busch, Michael P., additional, Bussmann, Hermann, additional, Chaix, Marie-Laure, additional, Chin, Bum Sik, additional, D’Aquin, Toni T., additional, De Gascun, Cillian F., additional, Derache, Anne, additional, Descamps, Diane, additional, Deshpande, Alaka K., additional, Djoko, Cyrille F., additional, Eshleman, Susan H., additional, Fleury, Herve, additional, Frange, Pierre, additional, Fujisaki, Seiichiro, additional, Harrigan, P. Richard, additional, Hattori, Junko, additional, Holguin, Africa, additional, Hunt, Gillian M., additional, Ichimura, Hiroshi, additional, Kaleebu, Pontiano, additional, Katzenstein, David, additional, Kiertiburanakul, Sasisopin, additional, Kim, Jerome H., additional, Kim, Sung Soon, additional, Li, Yanpeng, additional, Lutsar, Irja, additional, Morris, Lynn, additional, Ndembi, Nicaise, additional, NG, Kee Peng, additional, Paranjape, Ramesh S., additional, Peeters, Martine, additional, Poljak, Mario, additional, Price, Matt A., additional, Ragonnet-Cronin, Manon L., additional, Reyes-Terán, Gustavo, additional, Rolland, Morgane, additional, Sirivichayakul, Sunee, additional, Smith, Davey M., additional, Soares, Marcelo A., additional, Soriano, Vincent V., additional, Ssemwanga, Deogratius, additional, Stanojevic, Maja, additional, Stefani, Mariane A., additional, Sugiura, Wataru, additional, Sungkanuparph, Somnuek, additional, Tanuri, Amilcar, additional, Tee, Kok Keng, additional, Truong, Hong-Ha M., additional, van de Vijver, David A. M. C., additional, Vidal, Nicole, additional, Yang, Chunfu, additional, Yang, Rongge, additional, Yebra, Gonzalo, additional, Ioannidis, John P. A., additional, Vandamme, Anne-Mieke, additional, and Shafer, Robert W., additional

Published
2015
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48. Serum Retinol-Binding Protein-4 Levels Are Increased in HIV-Infected Subjects with Metabolic Syndrome Receiving Highly Active Antiretroviral Therapy

Author

Jeong, Su Jin, primary, Chin, Bum Sik, additional, Chae, Yun Tae, additional, Jin, Sung Joon, additional, Ku, Nam Su, additional, Baek, Ji Hyeon, additional, Han, Sang Hoon, additional, Kim, Chang Oh, additional, Choi, Jun Yong, additional, Song, Young Goo, additional, Lee, Hyun Chul, additional, and Kim, June Myung, additional

Published
2012
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