Progression and transmission of HIV (PATH 4.0)-A new agent-based evolving network simulation for modeling HIV transmission clusters.
Progression and transmission of HIV (PATH 4.0)-A new agent-based evolving network simulation for modeling HIV transmission clusters.
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DOI：
10.3934/mbe.2021109
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发表时间：
2021-03-03
期刊：
影响因子：
--
通讯作者：
Gopalappa C
中科院分区：
文献类型：
--
作者：
Singh S;France AM;Chen YH;Farnham PG;Oster AM;Gopalappa C
我们提出了HIV的进展和传播（PATH 4.0），这是一个用于分析聚类检测和干预策略的模拟工具。分子簇是基因相似的艾滋病毒感染群体，表明艾滋病毒传播迅速，需要艾滋病毒预防资源来改善健康结果和预防新的感染。PATH 4.0采用新开发的基于agent的进化网络建模（ABENM）技术和用于生成无标度网络的进化接触网络算法（ECNA）构建。ABENM和ECNA的开发是为了促进低流行疾病（如艾滋病毒）传播网络的模拟，这给当前的网络模拟技术带来了计算挑战。模拟传输网络是研究包括集群在内的网络动力学的必要条件。我们通过比较2010-2017年HIV诊断的模拟预测与国家HIV监测系统（NHSS）的估计来验证PATH 4.0。我们还将聚类生成算法应用于PATH 4.0来估计聚类特征，包括通过聚类状态和大小以及聚类大小分布来估计诊断为HIV感染的人的分布。模拟特征与NHSS估计吻合良好，NHSS使用分子方法检测2015-2017年诊断为HIV的人的HIV核苷酸序列中的簇。群集检测和反应是美国结束艾滋病毒流行战略的一个组成部分。虽然监测对于检测群集至关重要，但与监测相结合的模型可以使我们改进群集检测方法，了解与群集增长相关的因素，并评估干预措施，从而为有效的应对策略提供信息。由于监测数据仅可用于诊断和报告的病例，因此模型是了解聚集性病例真实规模和评估关键问题（例如聚集性病例对后续传播的相对贡献）的关键工具。我们认为，PATH 4.0是第一个可用来评估国家一级的集群检测和反应的建模工具，可以帮助为国家战略计划提供信息。
We present the Progression and Transmission of HIV (PATH 4.0), a simulation tool for analyses of cluster detection and intervention strategies. Molecular clusters are groups of HIV infections that are genetically similar, indicating rapid HIV transmission where HIV prevention resources are needed to improve health outcomes and prevent new infections. PATH 4.0 was constructed using a newly developed agent-based evolving network modeling (ABENM) technique and evolving contact network algorithm (ECNA) for generating scale-free networks. ABENM and ECNA were developed to facilitate simulation of transmission networks for low-prevalence diseases, such as HIV, which creates computational challenges for current network simulation techniques. Simulating transmission networks is essential for studying network dynamics, including clusters. We validated PATH 4.0 by comparing simulated projections of HIV diagnoses with estimates from the National HIV Surveillance System (NHSS) for 2010–2017. We also applied a cluster generation algorithm to PATH 4.0 to estimate cluster features, including the distribution of persons with diagnosed HIV infection by cluster status and size and the size distribution of clusters. Simulated features matched well with NHSS estimates, which used molecular methods to detect clusters among HIV nucleotide sequences of persons with HIV diagnosed during 2015–2017. Cluster detection and response is a component of the U.S. Ending the HIV Epidemic strategy. While surveillance is critical for detecting clusters, a model in conjunction with surveillance can allow us to refine cluster detection methods, understand factors associated with cluster growth, and assess interventions to inform effective response strategies. As surveillance data are only available for cases that are diagnosed and reported, a model is a critical tool to understand the true size of clusters and assess key questions, such as the relative contributions of clusters to onward transmissions. We believe PATH 4.0 is the first modeling tool available to assess cluster detection and response at the national-level and could help inform the national strategic plan.
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影响因子：
4.5
作者：
Fernandes RM;Cary M;Duarte G;Jesus G;Alarcão J;Torre C;Costa S;Costa J;Carneiro AV
通讯作者：
Carneiro AV
影响因子：
1.7
作者：
Buchacz, Kate;Armon, Carl;Brooks, John T.
通讯作者：
Brooks, John T.
影响因子：
56.9
作者：
Barabási, AL;Albert, R
通讯作者：
Albert, R
影响因子：
33.9
作者：
Des Jarlais, Don C.;Nugent, Ann;Holtzman, Deborah
通讯作者：
Holtzman, Deborah
DOI：
10.1056/nejmoa1108524
发表时间：
2012-08-02
期刊：
The New England journal of medicine
影响因子：
--
作者：
Baeten JM;Donnell D;Ndase P;Mugo NR;Campbell JD;Wangisi J;Tappero JW;Bukusi EA;Cohen CR;Katabira E;Ronald A;Tumwesigye E;Were E;Fife KH;Kiarie J;Farquhar C;John-Stewart G;Kakia A;Odoyo J;Mucunguzi A;Nakku-Joloba E;Twesigye R;Ngure K;Apaka C;Tamooh H;Gabona F;Mujugira A;Panteleeff D;Thomas KK;Kidoguchi L;Krows M;Revall J;Morrison S;Haugen H;Emmanuel-Ogier M;Ondrejcek L;Coombs RW;Frenkel L;Hendrix C;Bumpus NN;Bangsberg D;Haberer JE;Stevens WS;Lingappa JR;Celum C;Partners PrEP Study Team
通讯作者：
Partners PrEP Study Team