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2. The receptor binding domain of SARS-CoV-2 Omicron subvariants targets Siglec-9 to decrease its immunogenicity by preventing macrophage phagocytosis

Author

He, Xin, Zhang, Xiantao, Wu, Bolin, Deng, Jieyi, Zhang, Yongli, Zhu, Airu, Yuan, Yaochang, Lin, Yingtong, Chen, Achun, Feng, Jinzhu, Wang, Xiumei, Wu, Shijian, Liu, Yingying, Liu, Jie, Wang, Yalin, Li, Rong, Liang, Chaofeng, Yuan, Quyu, Liang, Yu, Fang, Qiannan, Xi, Zhihui, Li, Wenjie, Liang, Liting, Zhang, Zhenglai, Tang, Hui, Peng, Yi, Ke, Changwen, Ma, Xiancai, Cai, Weibin, Pan, Ting, Liu, Bingfeng, Deng, Kai, Chen, Jun, Zhao, Jincun, Wei, Xuepeng, Chen, Ran, Zhang, Yiwen, and Zhang, Hui

Published
2024
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3. Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants

Author

Yu, Haisheng, Liu, Banghui, Zhang, Yudi, Gao, Xijie, Wang, Qian, Xiang, Haitao, Peng, Xiaofang, Xie, Caixia, Wang, Yaping, Hu, Peiyu, Shi, Jingrong, Shi, Quan, Zheng, Pingqian, Feng, Chengqian, Tang, Guofang, Liu, Xiaopan, Guo, Liliangzi, Lin, Xiumei, Li, Jiaojiao, Liu, Chuanyu, Huang, Yaling, Yang, Naibo, Chen, Qiuluan, Li, Zimu, Su, Mengzhen, Yan, Qihong, Pei, Rongjuan, Chen, Xinwen, Liu, Longqi, Hu, Fengyu, Liang, Dan, Ke, Bixia, Ke, Changwen, Li, Feng, He, Jun, Wang, Meiniang, Chen, Ling, Xiong, Xiaoli, and Tang, Xiaoping

Published
2023
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6. Iron Deficiency: Global Trends and Projections from 1990 to 2050.

Author

Wang, Li, Liang, Dan, Huangfu, Hengqian, Shi, Xinfu, Liu, Shuang, Zhong, Panpan, Luo, Zhen, Ke, Changwen, and Lai, Yingsi

Abstract

Background: Iron deficiency (ID) remains the leading cause of anemia, affects a vast number of persons globally, and continues to be a significant global health burden. Comprehending the patterns of ID burden is essential for developing targeted public health policies. Methods: Using data from the Global Burden of Disease (GBD) 2021 study for the years 1990–2021, the XGBoost model was constructed to predict prevalence and disability-adjusted life years (DALYs) for the period 2022–2050, based on key demographic variables. Shapley Additive exPlanations (SHAP) values were applied to interpret the contributions of each variable to the model's predictions. Additionally, the Age–Period–Cohort (APC) model was used to evaluate the effects of age, period, and birth cohort on both prevalence and DALYs. The relationship between the Socio-Demographic Index (SDI) and ID's age-standardized prevalence rate (ASPR) as well as the age-standardized DALYs rate (ASDR) was also analyzed to assess the influence of socioeconomic development on disease burden. Results: The global prevalent cases of ID grew from 984.61 million in 1990 to 1270.64 million in 2021 and are projected to reach 1439.99 million by 2050. Similarly, global DALYs from ID increased from 28.41 million in 1990 to 32.32 million in 2021, with a projected rise to 36.13 million by 2050. The ASPR declined from 18,204/100,000 in 1990 to 16,433/100,000 in 2021, with an estimated annual percentage change (EAPC) of −0.36% over this period. It is expected to decrease further to 15,922 by 2050, with an EAPC of −0.09% between 2021 and 2050. The ASDR was 518/100,000 in 1990 and 424/100,000 in 2021, with an EAPC of −0.68% from 1990 to 2021. It is expected to remain relatively stable at 419/100,000 by 2050, with an EAPC of −0.02% between 2021 and 2050. In 2021, the highest ASPRs were recorded in Senegal (34,421/100,000), Mali (34,233/100,000), and Pakistan (33,942/100,000). By 2050, Mali (35,070/100,000), Senegal (34,132/100,000), and Zambia (33,149/100,000) are projected to lead. For ASDR, Yemen (1405/100,000), Mozambique (1149/100,000), and Mali (1093/100,000) had the highest rates in 2021. By 2050, Yemen (1388/100,000), Mali (1181/100,000), and Mozambique (1177/100,000) are expected to remain the highest. SHAP values demonstrated that gender was the leading predictor of ID, with age and year showing negative contributions. Females aged 10 to 60 consistently showed higher prevalence and DALYs rates compared to males, with the under-5 age group having the highest rates for both. Additionally, men aged 80 and above exhibited a rapid increase in prevalence. Furthermore, the ASPR and ASDR were significantly higher in regions with a lower SDI, highlighting the greater burden of ID in less developed regions. Conclusions: ID remains a significant global health concern, with its burden projected to persist through 2050, particularly in lower-SDI regions. Despite declines in ASPR and ASDR, total cases and DALYs are expected to rise. SHAP analysis revealed that gender had the greatest influence on the model's predictions, while both age and year showed overall negative contributions to ID risk. Children under 5, women under 60, and elderly men aged 80+ were the most vulnerable groups. These findings underscore the need for targeted interventions, such as improved nutrition, early screening, and addressing socioeconomic drivers through iron supplementation programs in low-SDI regions. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Single-dose rAAV5-based vaccine provides long-term protective immunity against SARS-CoV-2 and its variants

Author

Liao, Guochao, Lau, Hungyan, Liu, Zhongqiu, Li, Chinyu, Xu, Zeping, Qi, Xiaoxiao, Zhang, Yu, Feng, Qian, Li, Runze, Deng, Xinyu, Li, Yebo, Zhu, Qing, Zhu, Sisi, Zhou, Hua, Pan, Hudan, Fan, Xingxing, Li, Yongchao, Li, Dan, Chen, Liqing, Ke, Bixia, Cong, Zhe, Lv, Qi, Liu, Jiangning, Liang, Dan, Li, An’an, Hong, Wenshan, Bao, Linlin, Zhou, Feng, Gao, Hongbin, Liang, Shi, Huang, Bihong, Wu, Miaoli, Qin, Chuan, Ke, Changwen, and Liu, Liang

Published
2022
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10. Global Incidence of Diarrheal Diseases—An Update Using an Interpretable Predictive Model Based on XGBoost and SHAP: A Systematic Analysis.

Author

Liang, Dan, Wang, Li, Liu, Shuang, Li, Shanglin, Zhou, Xing, Xiao, Yun, Zhong, Panpan, Chen, Yanxi, Wang, Changyi, Xu, Shan, Su, Juan, Luo, Zhen, Ke, Changwen, and Lai, Yingsi

Abstract

Background: Diarrheal disease remains a significant public health issue, particularly affecting young children and older adults. Despite efforts to control and prevent these diseases, their incidence continues to be a global concern. Understanding the trends in diarrhea incidence and the factors influencing these trends is crucial for developing effective public health strategies. Objective: This study aimed to explore the temporal trends in diarrhea incidence and associated factors from 1990 to 2019 and to project the incidence for the period 2020–2040 at global, regional, and national levels. We aimed to identify key factors influencing these trends to inform future prevention and control strategies. Methods: The eXtreme Gradient Boosting (XGBoost) model was used to predict the incidence from 2020 to 2040 based on demographic, meteorological, water sanitation, and sanitation and hygiene indicators. SHapley Additive exPlanations (SHAP) value was performed to explain the impact of variables in the model on the incidence. Estimated annual percentage change (EAPC) was calculated to assess the temporal trends of age-standardized incidence rates (ASIRs) from 1990 to 2019 and from 2020 to 2040. Results: Globally, both incident cases and ASIRs of diarrhea increased between 2010 and 2019. The incident cases are expected to rise from 2020 to 2040, while the ASIRs and incidence rates are predicted to slightly decrease. During the observed (1990–2019) and predicted (2020–2040) periods, adults aged 60 years and above exhibited an upward trend in incidence rate as age increased, while children aged < 5 years consistently had the highest incident cases. The SHAP framework was applied to explain the model predictions. We identified several risk factors associated with an increased incidence of diarrhea, including age over 60 years, yearly precipitation exceeding 3000 mm, temperature above 20 °C for both maximum and minimum values, and vapor pressure deficit over 1500 Pa. A decreased incidence rate was associated with relative humidity over 60%, wind speed over 4 m/s, and populations with above 80% using safely managed drinking water services and over 40% using safely managed sanitation services. Conclusions: Diarrheal diseases are still serious public health concerns, with predicted increases in the incident cases despite decreasing ASIRs globally. Children aged < 5 years remain highly susceptible to diarrheal diseases, yet the incidence rate in the older adults aged 60 plus years still warrants additional attention. Additionally, more targeted efforts to improve access to safe drinking water and sanitation services are crucial for reducing the incidence of diarrheal diseases globally. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Author

Lu, Jing, du Plessis, Louis, Liu, Zhe, Hill, Verity, Kang, Min, Lin, Huifang, Sun, Jiufeng, François, Sarah, Kraemer, Moritz U.G., Faria, Nuno R., McCrone, John T., Peng, Jinju, Xiong, Qianling, Yuan, Runyu, Zeng, Lilian, Zhou, Pingping, Liang, Chumin, Yi, Lina, Liu, Jun, Xiao, Jianpeng, Hu, Jianxiong, Liu, Tao, Ma, Wenjun, Li, Wei, Su, Juan, Zheng, Huanying, Peng, Bo, Fang, Shisong, Su, Wenzhe, Li, Kuibiao, Sun, Ruilin, Bai, Ru, Tang, Xi, Liang, Minfeng, Quick, Josh, Song, Tie, Rambaut, Andrew, Loman, Nick, Raghwani, Jayna, Pybus, Oliver G., and Ke, Changwen

Published
2020
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15. Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids

Author

Sun, Jiufeng, Xiao, Jianpeng, Sun, Ruilin, Tang, Xi, Liang, Chumin, Lin, Huifang, Zeng, Lilian, Hu, Jianxiong, Yuan, Runyu, Zhou, Pingping, Peng, Jinju, Xiong, Qianlin, Cui, Fengfu, Liu, Zhe, Lu, Jing, Tian, Junzhang, Ma, Wenjun, and Ke, Changwen

Subjects
Severe acute respiratory syndrome -- Forecasts and trends -- Health aspects, Coronaviruses -- Forecasts and trends -- Health aspects, Medical research -- Forecasts and trends -- Health aspects, COVID-19 -- Health aspects -- Forecasts and trends, RNA -- Forecasts and trends -- Health aspects, Market trend/market analysis, Health
Abstract

In December 2019, coronavirus disease (COVID-19) caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, China (1,2). As of April 1, 2020, the virus [...]

Published
2020
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16. A compromised specific humoral immune response against the SARS-CoV-2 receptor-binding domain is related to viral persistence and periodic shedding in the gastrointestinal tract

Author

Hu, Fengyu, Chen, Fengjuan, Ou, Zhihua, Fan, Qinghong, Tan, Xinghua, Wang, Yaping, Pan, Yuejun, Ke, Bixia, Li, Linghua, Guan, Yujuan, Mo, Xiaoneng, Wang, Jian, Wang, Jinlin, Luo, Chun, Wen, Xueliang, Li, Min, Ren, Peidi, Ke, Changwen, Li, Junhua, Lei, Chunliang, Tang, Xiaoping, and Li, Feng

Published
2020
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27. An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques

Author

Feng, Liqiang, Wang, Qian, Shan, Chao, Yang, Chenchen, Feng, Ying, Wu, Jia, Liu, Xiaolin, Zhou, Yiwu, Jiang, Rendi, Hu, Peiyu, Liu, Xinglong, Zhang, Fan, Li, Pingchao, Niu, Xuefeng, Liu, Yichu, Zheng, Xuehua, Luo, Jia, Sun, Jing, Gu, Yingying, Liu, Bo, Xu, Yongcun, Li, Chufang, Pan, Weiqi, Zhao, Jincun, Ke, Changwen, Chen, Xinwen, Xu, Tao, Zhong, Nanshan, Guan, Suhua, Yuan, Zhiming, and Chen, Ling

Published
2020
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28. Comparison of nonhuman primates identified the suitable model for COVID-19

Author

Lu, Shuaiyao, Zhao, Yuan, Yu, Wenhai, Yang, Yun, Gao, Jiahong, Wang, Junbin, Kuang, Dexuan, Yang, Mengli, Yang, Jing, Ma, Chunxia, Xu, Jingwen, Qian, Xingli, Li, Haiyan, Zhao, Siwen, Li, Jingmei, Wang, Haixuan, Long, Haiting, Zhou, Jingxian, Luo, Fangyu, Ding, Kaiyun, Wu, Daoju, Zhang, Yong, Dong, Yinliang, Liu, Yuqin, Zheng, Yinqiu, Lin, Xiaochen, Jiao, Li, Zheng, Huanying, Dai, Qing, Sun, Qiangming, Hu, Yunzhang, Ke, Changwen, Liu, Hongqi, and Peng, Xiaozhong

Published
2020
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29. Molecular Evolution, Diversity, and Adaptation of Influenza A(H7N9) Viruses in China

Author

Lu, Jing, Raghwani, Jayna, Pryce, Rhys, Bowden, Thomas A., Theze, Julien, Huang, Shanqian, Song, Yingchao, Zou, Lirong, Liang, Lijun, Bai, Ru, Jing, Yi, Zhou, Pingping, Kang, Min, Yi, Lina, Wu, Jie, Pybus, Oliver G., and Ke, Changwen

Subjects
Influenza -- Analysis, Amino acids -- Analysis, Phylogeny -- Analysis, Health
Abstract

Since its first detection in March 2013, avian influenza A(H7N9) virus has caused 1,534 human infections that, as of November 30, 2017, had resulted in 608 deaths. Recurrent waves of [...]

Published
2018
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32. The Evolution and Transmission of Epidemic GII.17 Noroviruses

Author

Lu, Jing, Fang, Lin, Zheng, Huanying, Lao, Jiaqian, Yang, Fen, Sun, Limei, Xiao, Jianpeng, Lin, Jinyan, Song, Tie, Ni, Tao, Raghwani, Jayna, Ke, Changwen, Faria, Nuno R., Bowden, Thomas A., Pybus, Oliver G., and Li, Hui

Published
2016

34. Influenza H5/H7 Virus Vaccination in Poultry and Reduction of Zoonotic Infections, Guangdong Province, China, 2017-18

Author

Wu, Jie, Ke, Changwen, Lau, Eric H.Y., Song, Yingchao, Cheng, Kit Ling, Zou, Lirong, Kang, Min, Song, Tie, Peiris, Malik, and Yen, Hui-Ling

Subjects
Influenza vaccines -- Health aspects, Poultry industry -- Health aspects, Infection -- Health aspects, Avian influenza -- Health aspects, Zoonoses -- Health aspects, Vaccination -- Health aspects, Farms, Influenza, Health
Abstract

Human infections with avian influenza A(H7N9) virus have been documented in China since 2013 (1). Among 1,220 confirmed H7N9 case-patients during 2013-2017, a total of 73% reported poultry exposure, and [...]

Published
2019
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38. Monitoring Avian Influenza Viruses from Chicken Carcasses Sold at Markets, China, 2016

Author

Mao, Xiaoxiao, Wu, Jie, Lau, Eric H.Y., Cheng, Kit Ling, Zhong, Zhifeng, Song, Yinchao, Ji, Xunmin, Zhou, Lirong, Ke, Changwen, Peiris, Joseph Sriyal Malik, Wang, Hong, and Yen, Hui-Ling

Subjects
Avian influenza, Supermarkets -- International economic relations, Food contamination, Avian influenza viruses, Business logistics, Health
Abstract

Live poultry markets (LPMs) are hot spots for avian influenza virus (AIV) amplification among poultry and dissemination to humans (1). Direct contact with live poultry is a major route of [...]

Published
2017
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39. Human infection with highly pathogenic avian influenza A(H7N9) virus, China

Author

Ke, Changwen, Mok, Chris Ka Pun, Zhu, Wenfei, Zhou, Haibo, He, Jianfeng, Guan, Wenda, Wu, Jie, Song, Wenjun, Wang, Dayan, Liu, Jiexiong, Lin, Qinhan, Chu, Daniel Ka Wing, Yang, Lei, Zhong, Nanshan, Yang, Zifeng, Shu, Yuelong, and Peiris, Joseph Sriyal Malik

Subjects
Influenza -- Research, Avian influenza viruses -- Risk factors -- Research, Health
Abstract

Avian influenza A(H7N9) viruses with zoonotic potential emerged in East China in early 2013. From February 2013 through February 20, 2017, a total of 1,222 patients with A(H7N9) disease had [...]

Published
2017
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41. Emergence of epidemic variants of SARS-CoV-2 by acquiring combinations of new highly mutable nucleotides in its genome

Author

Wang, Hui, Liu, Yuqi, Li, Peng, Liu, Chaowu, Li, Kuibiao, Cao, Lan, Zhang, Ying, Cheng, Zichun, Huang, Kailing, Zheng, Zhouxia, Xin, Xiaoqian, Liu, Yifeng, Peng, Xiaofang, Liang, Dan, Ke, Bixia, Wang, Tao, Chen, Qingpei, Luo, Weihua, Qin, Chaolang, Sun, Lihong, Chen, Guobing, Luo, Oscar Junhong, Li, Jixi, Zhang, Qiao, Di, Biao, Zhang, Zhoubin, Ke, Changwen, Jia, Hongling, and Gao, Feng

Published
2023
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42. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Author

Munk, Patrick, Brinch, Christian, Møller, Frederik Duus, Petersen, Thomas N., Hendriksen, Rene S., Seyfarth, Anne Mette, Kjeldgaard, Jette S., Svendsen, Christina Aaby, van Bunnik, Bram, Berglund, Fanny, Bego, Artan, Power, Pablo, Rees, Catherine, Lambrinidis, Dionisia, Neilson, Elizabeth Heather Jakobsen, Gibb, Karen, Coventry, Kris, Collignon, Peter, Cassar, Susan, Allerberger, Franz, Begum, Anowara, Hossain, Zenat Zebin, Worrell, Carlon, Vandenberg, Olivier, Pieters, Ilse, Victorien, Dougnon Tamègnon, Gutierrez, Angela Daniela Salazar, Soria, Freddy, Grujić, Vesna Rudić, Mazalica, Nataša, Rahube, Teddie O., Tagliati, Carlos Alberto, Rodrigues, Dalia, Oliveira, Guilherme, de Souza, Larissa Camila Ribeiro, Ivanov, Ivan, Juste, Bonkoungou Isidore, Oumar, Traoré, Sopheak, Thet, Vuthy, Yith, Ngandijo, Antoinette, Nzouankeu, Ariane, Olivier, Ziem A. Abah Jacques, Yost, Christopher K., Kumar, Pratik, Brar, Satinder Kaur, Tabo, Djim-Adjim, Adell, Aiko D., Paredes-Osses, Esteban, Martinez, Maria Cristina, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Lau, Lok Ting, Chung, Teresa, Jiao, Xiaoyang, Yu, Yongjie, JiaYong, Zhao, Morales, Johan F. Bernal, Valencia, Maria Fernanda, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Deogratias, Zozo Nyarukweba, Elsborg, Bodil, Hansen, Lisbeth Truelstrup, Jensen, Pernille Erland, Abouelnaga, Mohamed, Salem, Mohamed Fathy, Koolmeister, Marliin, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Le Guyader, Soizick, Schaeffer, Julien, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Schubert, Sara, Hesse, Sina, Berendonk, Thomas U., Saba, Courage Kosi Setsoafia, Mohammed, Jibril, Feglo, Patrick Kwame, Banu, Regina Ama, Kotzamanidis, Charalampos, Lytras, Efthymios, Lickes, Sergio A., Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Ballal, Mamatha, Bangera, Sohan Rodney, Fani, Fereshteh, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Diaconu, Elena Lavinia, Corno, Gianluca, Di Cesare, Andrea, Alba, Patricia, Hisatsune, Junzo, Yu, Liansheng, Kuroda, Makoto, Sugai, Motoyuki, Kayama, Shizuo, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Jamil, Kazi, Fakhraldeen, Saja Adel, Alaati, Tareq, Bērziņš, Aivars, Avsejenko, Jeļena, Kokina, Kristina, Streikisa, Madara, Bartkevics, Vadims, Matar, Ghassan M., Daoud, Ziad, Pereckienė, Asta, Butrimaite-Ambrozeviciene, Ceslova, Penny, Christian, Bastaraud, Alexandra, Rasolofoarison, Tiavina, Collard, Jean-Marc, Samison, Luc Hervé, Andrianarivelo, Mala Rakoto, Banda, Daniel Lawadi, Amin, Arshana, Rajandas, Heraa, Parimannan, Sivachandran, Spiteri, David, Haber, Malcolm Vella, Santchurn, Sunita J., Vujacic, Aleksandar, Djurovic, Dijana, Bouchrif, Brahim, Karraouan, Bouchra, Vubil, Delfino Carlos, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, Jeunen, Gert-Jan, Gemmell, Neil, Chambers, Stephen T., Mendoza, Fania Perez, Huete-Pιrez, Jorge, Vilchez, Samuel, Ahmed, Akeem Olayiwola, Adisa, Ibrahim Raufu, Odetokun, Ismail Ayoade, Fashae, Kayode, Sørgaard, Anne-Marie, Wester, Astrid Louise, Ryrfors, Pia, Holmstad, Rune, Mohsin, Mashkoor, Hasan, Rumina, Shakoor, Sadia, Gustafson, Natalie Weiler, Schill, Claudia Huber, Rojas, Maria Luz Zamudio, Velasquez, Jorge Echevarria, Magtibay, Bonifacio B., Catangcatang, Kris, Sibulo, Ruby, Yauce, Felipe Campos, Wasyl, Dariusz, Manaia, Celia, Rocha, Jaqueline, Martins, Jose, Álvaro, Pedro, Di Yoong Wen, Doris, Shin, Hanseob, Hur, Hor-Gil, Yoon, Sukhwan, Bosevska, Golubinka, Kochubovski, Mihail, Cojocaru, Radu, Burduniuc, Olga, Hong, Pei-Ying, Perry, Meghan Rose, Gassama, Amy, Radosavljevic, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Pastuchová, Katarína, Truska, Peter, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Song, Min Joon, Quintela-Baluja, Marcos, Lopez, Mariano Gomez, Cerdà-Cuéllar, Marta, Perera, R.R.D.P., Bandara, N.K.B.K.R.G.W., Premasiri, H.I., Pathirage, Sujatha, Charlemagne, Kareem, Rutgersson, Carolin, Norrgren, Leif, Örn, Stefan, Boss, Renate, Van der Heijden, Tanja, Hong, Yu-Ping, Kumburu, Happiness Houka, Mdegela, Robinson Hammerthon, Hounmanou, Yaovi Mahuton Gildas, Chonsin, Kaknokrat, Suthienkul, Orasa, Thamlikitkul, Visanu, de Roda Husman, Ana Maria, Bidjada, Bawimodom, Njanpop-Lafourcade, Berthe-Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Kurekci, Cemil, Ejobi, Francis, Kalule, John Bosco, Thomsen, Jens, Obaidi, Ouidiane, Jassim, Laila Mohamed, Moore, Andrew, Leonard, Anne, Graham, David W., Bunce, Joshua T., Zhang, Lihong, Gaze, William H., Lefor, Brett, Capone, Drew, Sozzi, Emanuele, Brown, Joe, Meschke, John Scott, Sobsey, Mark D., Davis, Michael, Beck, Nicola Koren, Sukapanpatharam, Pardi, Truong, Phuong, Lilienthal, Ronald, Kang, Sanghoon, Wittum, Thomas E., Rigamonti, Natalia, Baklayan, Patricia, Van, Chinh Dang, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Larsson, D. G. Joakim, Koopmans, Marion, Woolhouse, Mark, Aarestrup, Frank M., Virology, Producció Animal, and Sanitat Animal

Subjects
genomic analysis, sewage, antimicrobial resistance, Multidisciplinary, Sewage, Drug Resistance, Bacterial, Metagenome, General Physics and Astronomy, Drug Resistance, Bacterial/genetics, Genomics, General Chemistry, General Biochemistry, Genetics and Molecular Biology, Anti-Bacterial Agents/pharmacology, Anti-Bacterial Agents
Abstract

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention. Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Published
2022
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45. Effect of live poultry market interventions on influenza A(H7N9) virus, Guangdong, China

Author

Wu, Jie, Lu, Jing, Faria, Nuno R., Zeng, Xianqiao, Song, Yingchao, Zou, Lirong, Yi, Lina, Liang, Lijun, Ni, Hanzhong, Kang, Min, Zhang, Xin, Huang, Guofeng, Zhong, Haojie, Bowden, Thomas A., Raghwani, Jayna, He, Jianfeng, He, Xiang, Lin, Jinyan, Koopmans, Marion, Pybus, Oliver G., and Ke, Changwen

Subjects
Avian influenza -- Health aspects, Epidemics -- Health aspects, Genomics -- Health aspects, Earthquakes -- Health aspects, Cladistic analysis -- Health aspects, Poultry industry -- International economic relations -- Health aspects, Infection -- Health aspects, Phylogeny -- Health aspects, Health
Abstract

Since its first notification on March 30, 2013 (1), avian influenza A(H7N9) virus caused 3 complete epidemic waves of human infection in China, comprising 670 laboratory-confirmed clinical cases and 274 [...]

Published
2016
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