HIV-Cov: The effect of HIV on SARS-CoV-2 transmission and emergence of variants of concern. Severe acute respiratory syndrome coronavirus 2

This research project aims to understand the overall impact of HIV infection on the SARS-CoV-2 viral evolution and transmission dynamics in a setting with high HIV prevalence. We will address current knowledge gaps by integrating SARS-CoV-2 genomic data, patient-level clinical data, and epidemiological data to achieve the following aims: 1) we will determine the effect of HIV infection on the transmission dynamics of COVID-19 and emergence of SARS-CoV-2 variants; and 2) we will determine the effect of HIV-associated immunosuppression on the acquisition of SARS-CoV-2 mutations. For the first Aim, advanced phylodynamic methods will be applied to determine how HIV affects the transmission and viral evolution of SARS-CoV-2 on a population scale, as well as to describe risk factors that drive individual and population-level COVID-19 transmission. For the second Aim, we will recruit and follow a cohort of COVID-19 patients with and without HIV infection to determine the effect of HIV-associated immunosuppression on the rate of emerging SARS-CoV-2 mutations. The proposed research will also utilize active case finding to minimize sampling bias. Findings from this project will inform the development of optimal public health interventions to control the pandemic by disrupting transmission chains and prevent the emergence and spread of alarming variants.

本研究项目旨在明确在人类免疫缺陷病毒（HIV）高流行地区，HIV感染对严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）的病毒演化及传播动态的整体影响。本研究将整合SARS-CoV-2基因组数据、患者个体层面的临床数据与流行病学数据，以填补当前的认知空白，并达成以下研究目标：1）明确HIV感染对新型冠状病毒肺炎（COVID-19）传播动态及SARS-CoV-2变异株出现的影响；2）明确HIV相关免疫抑制对SARS-CoV-2突变获得的影响。针对第一项研究目标，本研究将采用先进的系统发育动力学（phylodynamic）方法，明确HIV在人群层面如何影响SARS-CoV-2的传播与病毒演化，并阐明驱动个体及人群层面COVID-19传播的风险因素。针对第二项研究目标，本研究将招募伴有及不伴有HIV感染的COVID-19患者队列并进行随访，以明确HIV相关免疫抑制对SARS-CoV-2新发突变速率的影响。本研究还将采用主动病例发现策略，以最大限度降低抽样偏倚。本项目的研究结果将为优化公共卫生干预措施的制定提供依据，通过切断传播链控制疫情大流行，并防范危险变异株的出现与传播。