Inter-regional study of transmission, adaptation and pathogenesis of viruses with pandemic potential in Southeast Asia and West/Central Africa

对东南亚和西非/中非具有大流行潜力的病毒的传播、适应和发病机制进行区域间研究

• 批准号: 10426422
• 负责人: Anavaj SAKUNTABHAI
• 金额: $ 45.45万
• 依托单位: INSTITUT PASTEUR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-31 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10426422
• 关键词: 2019-nCoV; Acute; Africa; African; Area; Blood Circulation; Burkina Faso; COVID-19; COVID-19 patient; COVID-19 surveillance; COVID-19 vaccination; Cambodia; Cameroon; Centers for Disease Control and Prevention (U.S.); Central Africa; Cessation of life; Clinical; Communities; Coronavirus; Country; Data; Data Collection; Detection; Developed Countries; Disease; Disease Outbreaks; Disease Surveillance; Dose; Ensure; Epidemiology; Equatorial Guinea; Event; Far East; Gambia; Genetic Determinism; Genomics; Goals; Guinea; Guinea-Bissau; Health system; Incidence; Income; Ivory Coast; Knowledge; Laboratories; Laos; Madagascar; Mali; Mauritania; Medicine; Metadata; Methods; Molecular; Monitor; Niger; Patients; Population; Recording of previous events; Reporting; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2 B.1.1.7; SARS-CoV-2 B.1.351; SARS-CoV-2 B.1.617.2; Sampling; Senegal; Severities; Severity of illness; Societies; Source; Southeastern Asia; Symptoms; System; Thailand; Time; Timidity; Tunisia; Vaccinated; Vaccination; Vaccines; Variant; Vietnam; Viral Pathogenesis; Virus; base; detection method; genetic signature; genome sequencing; genomic data; molecular subtypes; pandemic disease; pathogen genomics; respiratory; response; sequencing platform; severe COVID-19; stem; tool; transmission process; variants of concern; virus genetics; whole genome

Project Summary/Abstract Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) has rapidly spread across the world. As of June, 2021, over 171 million laboratory-confirmed cases and greater than 3.68 million deaths have been reported globally. This increase in cases has been associated with emergence of new variants which have increased transmissibility and severity. While Southeast Asia kept COVID-19 cases under relative control in 2020. In 2021, SARS-CoV-2 began to spread rapidly and caused continuing outbreaks in the region. In Africa, the genomic surveillance gap, combined with very fragile health systems with limited management capacities, exposes the continent to possible new COVID-19 waves that could prove to be much more severe on the continent, where vaccination clearly remains at a very timid stage. The overall goal of the project is to increase sequencing capacity and add to the depth of sequencing knowledge available in South East Asia and African countries with 4 Specific Aims. 1)To increase sequencing numbers for samples from certain regions. We will focus on samples from land borders with Thailand and Vietnam and community transmission in Cambodia stemming from the February 20th “event.” These sequences will help to understand community transmission within Cambodia. In Africa, we will increase sequencing numbers from samples from African countries with very low sequencing coverage including Mali, Burkina Faso, Guinea, Côte d’Ivoire, Guinea-Bissau, Niger, Cabo-Verde, Mauritania, Tunisia, Madagascar, Cameroon, Equatorial Guinea and Central Africa Republic. We will confirm known variants of concern as well as detection of potential local new variants. 2)To increase sequencing numbers for samples from patients with atypical profiles. We will systematically collect data at epidemiological level for demographical data, clinical symptoms, COVID-19 vaccination status, history of COVID-19 in relation with patients. We will focus on re-infected patient samples, severe COVID-19 cases and post-vaccinated SARS-CoV-2 infected patients. 3) To monitor introduction and dissemination of known VOCs using molecular sub-typing tools. We will help participating countries building up molecular capacities to subtype known variants. 4) Identify viral genetic determinants of high transmissibility and disease severity. Sequences from severe cases will be analyzed in comparison to the sequences from the randomly selected group to identify viral genetic signatures associated to disease severity. Regarding the transmissibility, we will rely on circulation dynamics of the detected variants in each country as well as in all countries. Overall, the studies outlined in this proposal will rapidly add essential sequence data needed regarding COVID-19 cases in lower–middle income, least-developed countries. They will provide the basis for further study on inter-/intra-host variant emergence and vaccine escape in a unique population from a least-developed country in an understudied, but vitally important, region of the world.

项目概要/摘要 严重急性呼吸道冠状病毒 2 型 (SARS-CoV-2)，2019 年冠状病毒病的病原体 截至 2021 年 6 月，（COVID-19）已在全球迅速传播，已有超过 1.71 亿人经实验室确诊。 全球已报告病例数和死亡人数超过 368 万人。 与增加传播性和严重性的新变种的出现有关。 2020 年，东南亚的 COVID-19 病例得到相对控制。2021 年，SARS-CoV-2 开始传播 在非洲，基因组监测的差距导致疫情持续爆发。 卫生系统非常脆弱，管理能力有限，使非洲大陆面临可能出现的新情况 事实证明，在接种疫苗的非洲大陆，COVID-19 浪潮可能会更加严重 该项目的总体目标是提高测序能力并增加测序能力。 东南亚和非洲国家现有的测序知识的深度有 4 个具体目标。 1）为了增加来自某些地区的样本的测序数量，我们将重点关注来自某些地区的样本。 与泰国和越南的陆地边界以及柬埔寨的社区传播 2 月 20 日的“事件”。这些序列将有助于了解柬埔寨境内的社区传播。 在非洲，我们将增加来自测序率很低的非洲国家样本的测序数 覆盖范围包括马里、布基纳法索、几内亚、科特迪瓦、几内亚比绍、尼日尔、佛得角、 毛里塔尼亚、突尼斯、马达加斯加、喀麦隆、赤道几内亚和中非共和国。 关注的已知变异以及潜在的本地新变异的检测 2) 增加测序。 我们将系统地收集来自具有非典型特征的患者样本的数据。 人口统计数据、临床症状、COVID-19 疫苗接种状况、病史等流行病学水平 COVID-19 与患者的关系 我们将重点关注再次感染的患者样本、重症 COVID-19 病例。 和接种疫苗后的 SARS-CoV-2 感染患者 3) 监测病毒的引入和传播。 我们将帮助参与国建立分子分型工具。 对已知变异进行亚型分类的能力 4) 识别高传染性和高传染性的病毒遗传决定因素。 来自严重病例的序列将与来自严重病例的序列进行比较分析。 随机选择的组来识别与疾病严重程度相关的病毒遗传特征。 传播性，我们将依赖于每个国家以及所有地区检测到的变种的流通动态 总体而言，本提案中概述的研究将快速添加所需的基本序列数据。 关于中低收入、最不发达国家的 COVID-19 病例，它们将提供基础。 进一步研究宿主间/宿主内变异的出现和来自不同宿主的独特群体中的疫苗逃逸 世界上一个研究不足但极其重要的地区的最不发达国家。