Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency

Abstract

Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.

Identification of natural compounds as SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation

“…SARS-CoV-2 Delta and Lambda variants are the worldwide epidemic virus strains before the prevalence of the Omicron variant. They have named a variety of concerns (VOC) and a variety of interest (VOI), respectively ( Markarian et al, 2022 ). In this study, we constructed a protein model of the CTD of the S protein of SARS-CoV-2 Delta and Lambda variants and used molecular docking and MD simulation methods to study the infection mediated by all plant chemicals in the Chinese herbal medicine ingredient database (TCMSP) and SARS-CoV-2.…”

Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes

“…As the pandemic has proceeded, the medical and scientific communities have garnered a better understanding of the risk factors associated with severe COVID-19. 8 , 9 , 10 , 11 Male gender, older age, and a number of pre-existing conditions/comorbidities such as high body mass index (BMI), 12 cardiovascular disease, 13 asthma, 14 immunodeficiency, 15 , 16 and diabetes 17 , 18 have all been associated with more severe disease and worse patient outcomes. Social determinants of health such as access to health care, risk for exposure, and socioeconomic status have likewise been found to contribute to an individual’s disease risk.…”

Systems analysis of human innate immunity in COVID-19

“…It became obvious that the interaction between the human immune system and the virus is a major driver of viral evolution and in contrast to other coronaviruses SARS-CoV-2 is still evolving very fast [6] . Patients with immune deficiencies cannot clear the virus very efficiently, which can prolong viremia and accelerate viral evolution [7] , [8] , clearly indicating that the functional status of the immune system including its innate arm is a major determinant of disease course and severity. Furthermore, comorbidities including obesity, diabetes and cardiovascular diseases associated with chronic inflammation are major risk factors for severe courses [9] , [10] further supporting the notion that the immune system is a decisive component when it comes to disease course and severity.…”