Utilizing microbiome approaches to assist source tracking, treatment and pre‐ vention of COVID-19: Review and Assessment

COVID-19 has been one of the most serious infectious diseases since the end of 2019. However, the original source, as well as the treatment and prevention of causative agent of COVID-19 (namely SARS-CoV-2) are still unclear nearly a year after its publicly report. The microbiome approach, which has emerged in recent years focusing on human-related microbes, has become one of the promising avenues for source tracking, treatment, and prevention of varieties of infectious diseases including COVID-19. In this review, we summarized the microbiome approach as a supplementary approach for source tracking, treatment, and prevention of SARS-CoV-2 infection. We first provided background information on SARS-CoV-2 and microbiome approaches. Then we illustrated current strategies of microbiome methods to assist three aspects of SARS-CoV-2 research, namely source tracking, treatment, and prevention, respectively. Finally, we summarized the microbiome approaches and provided perspectives for future studies on faster and more effective SARS-CoV-2 epidemiology and pathogenesis based on microbiome approaches. 1. Background In December 2019, COVID-19 (or 2019-nCoV) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been one of the most urgent infectious diseases on the globe. Owing to the high fatality rate, long incubation period, and character of human-to-human transmission of SARS-CoV-2, it has now been reported to infect individuals with all ages and slight predominant in men [1]. The World Health Organization (WHO) has declared COVID-19 a pandemic on March 11, 2020. At the end of August 2020, it has infected more than 24 million people and accounted for more than 820,000 deaths globally, and these numbers continue to increase sharply [2]. The initial mortality rate of COVOD-19 was around 2% on Wednesday, January 29, 2020, and the updated mortality rate was 3.4% on August 28, 2020, estimated by WHO [3]. As to different counties, the actual fatality rate of populations with different age groups are different [4], [5]. Several studies have indicated that the high mortality rate in COVID-19 patients with older age and co-morbid diseases, including hypertension, obesity, type 2 diabetes, and other basic metabolic diseases [1], [6]. It’s well-known that the human microbiome is a hub linking with almost all organs, and the gut microbiome is associated with many diseases, such as inflammatory bowel diseases (IBD), hypertension, and type 2 diabetes, etc. [7]. The alterations of gut microbiota lead to the dysbiosis of the human gut microbiome and the disorder of gut homeostasis, which affects the phenotype of the host [8], [9]. Several studies have reported the clinical symptoms of COVID-19 patients and these results indicated that gastrointestinal symptoms were common in COVID-19 patients [10], [11], [12]. Among the gastrointestinal symptoms, such as diarrhea, abdominal pain, or vomiting, caused by SARS-CoV-2 during the early phases of the COVID-19 [13]. Of course, it should be noted that diarrhea is not common in COVID-19 patients (2%-20%) [14], [15]. However, the COVID-19 patients with gastrointestinal symptoms is dangerous. And gastrointestinal symptoms might be one of the important factors for the high mortality rate of COVID-19 patients [16], especially the patients with older age and basic metabolic diseases, including hypertension and type 2 diabetes, etc. Thus, we proposed that microbiome approaches might be used to assist the treatment and prevention of COVID-19. At present, physicians and scientists from various countries have devoted efforts to the treatment of COVID-19 patients and tackle key problems in urgent scientific research, including the development of diagnosis and treatment plans, the discovery of specific drugs, the development of SARS-CoV-2 vaccines, etc [17]. Among these issues, the source tracking of SARS-CoV-2 pathogen, treatment and prevention of infection by the pathogen have drawn great interests [18]. As to the source tracking of SARS-CoV-2, the transmissions of SARS-CoV-2 from animals to humans and humans to humans in a population were introduced in this review. Such as, by using microbiome approaches, several studies have shown that the host of SARS-CoV-2 might be pangolins [19], [20], [21] or directly from bat [16]. Obviously, the microbiome approaches, coupled with artificial intelligence (AI) technologies, is also a very effective method for tracking the source of SARS-CoV-2 [22]. Therefore, we proposed that utilizing microbiome approaches to assist SARS-CoV-2 source tracking, treatment and prevention of COVID-19. Secondly, it has already found that maintaining a healthy human gut microbiota is important to the treatment and prevention of COVID-19 [23], [24]. However, despite these advancements in utilizing microbiome approaches for better source tracking, treatment, and prevention of COVID-19, there is still a lack of systematic review on how these tasks could be done for solving the emergent COVID-19 crisis based on microbiome approaches. Therefore, in this review, we provided a holistic view on how microbiome approaches could assist in SARS-CoV-2 source tracking, treatment and prevention of COVID-19 (Figure 1). We first provided background information on SARS-CoV-2 and microbiome approaches, respectively. Secondly, we illustrated current strategies of microbiome methods to assist three aspects of SARS-CoV-2, namely source tracking, treatment and prevention, respectively. We summarized the promise of microbiome approaches on SARS-CoV-2, and provided perspectives for future studies on faster and more effective SARS-CoV-2 epidemiology and pathogenetics based on microbiome approaches. We also tested several machine learning source-tracking methods for deducting possible sources of samples containing SARS-CoV-2. Both tests were based on microbiome data from different cohorts. Results have shown that the source-tracking of samples containing SARS-CoV-2 could reach accuracies higher than 96% based on microbiome data. Together, we summarized that microbiome approaches could assist in SARS-CoV-2 source tracking, treatment and prevention of COVID-19.

• Tipo de recurso: Article of investigation
• Fecha de publicación: 2020
• Institución: Universidad de Bogotá Jorge Tadeo Lozano
• Repositorio: Expeditio: repositorio UTadeo
• Idioma: eng
• OAI Identifier: oai:expeditiorepositorio.utadeo.edu.co:20.500.12010/16002
• Acceso en línea: https://doi.org/10.1016/j.csbj.2020.11.027; http://hdl.handle.net/20.500.12010/16002
• Palabra clave: Utilizing microbiome; Treatment and prevention; COVID-19; Síndrome respiratorio agudo grave; COVID-19; SARS-CoV-2; Coronavirus
• License: Abierto (Texto Completo)