A Systematic Review on Papers That Study on SNPs That Affect SARS-CoV-2 Infection & COVID-19 Severity

Background: COVID-19, caused by SARS-CoV-2 has become the most threatening issue to all populations around the world. It is directly and indirectly affecting all of us and thus, is a emergence topic dealt in global health. In order to avoid the infection, various studies have been done and still ongoing. Now having over 141 million cases of COVID19 and causing over 3 million deaths around the world, the tendency of infection and degree severity of the disease shown in different groups of people came up as an issue. Here, we reviewed 21 papers on SNPs related to SARS-CoV-2 infection severity and analyzed the results of them. Methods: The PubMed databases were searched for papers discussing SNPs associated with SARS-CoV-2 infection severity. Clinical studies with human patients and statistically showing relevance of the SNP with virus infection were included. Quality Assessment of all papers were done with Newcastle Ottawa Scale. Results: In the analysis, 21 full-text literatures out of 2956 screened titles and abstracts, including 63496 cases, were included. All were human based clinical studies, some based on certain regions gathered patient data and some based on big databases obtained online. ACE2, TMPRSS2, IFITM3 are the genes mentioned most frequently that are related with SARS-CoV-2 infection. 20 out of 21 studies mentioned one of more of those genes. The relevant genes according to SNPs were also analyzed. rs12252-C, rs143936283, rs2285666, rs41303171, and rs35803318 are the SNPs that were mentioned at least twice in two different studies. Conclusions: the data: type of trial, clinical and study outcomes, study population, statistically powerful results, and topic relevance. most of the papers that deal with genetic factors of SARS-CoV-2 infection severity, it clearly which factors should be focused and targeted. Also, by further studies of the genes and SNPs mentioned, which biological characteristics of people are comparably more vulnerable to the disease infection. Knowing which group are more vulnerable and what traits makes easier infection or disease development, prevention of epidemics may be improved.


Introduction & Background
In 2020, coronavirus disease 2019 (COVID-19) posed a serious global public health threat. According to JHU Coronavirus Resource Center live update, the total cases of COVID-19 has reached more than 144 million and caused over 3 million deaths over the globe. The COVID-19 pandemic has been studied from diverse perspectives, and health care professionals are trying their best to control the pandemic. As the consequences of COVID-19 are potentially severe, avoiding infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important. Ethnicity has been found to affect the severity of COVID-19. The virus rst emerged in East Asia, but relatively higher rates of morbidity and mortality have been identi ed in European populations. It is therefore important to determine the mechanism underlying the effect of ethnicity on the severity of COVID-19. With regard to the biochemistry of SARS-CoV-2, the binding of the viral spike (S) protein to cellular receptors and priming of the S protein by host cell proteases are signi cant factors affecting the entry of SARS-CoV-2 into the host cell. [1,2] Several studies have found that angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2) are involved in this step. ACE2 is the cellular receptor to which SARS-CoV-2 binds, thereby gaining entry into the host cell. ACE2 is involved in regulatory processes in our body. ACE2 is also the functional receptor for severe acute respiratory syndrome coronavirus (SARS-CoV). As the expression levels of ACE2 are high in the heart and lungs, COVID-19 patients can develop heart-and lung-related complications. TMPRSS2 cleaves the spike protein of SARS-CoV-2, leading to the activation of the virus and cellular membrane. [3] Given the involvement of these proteins in the entry of SARS-CoV-2 into host cells, it is possible that the relationship between ethnicity and disease severity is due to single-nucleotide polymorphisms (SNPs) in the corresponding genes. Therefore, in this systematic review, we aimed to discover the related SNPs of SARS-CoV-2 infection by going through all the SNPs mentioned in 21 papers of identical topic. We analyzed 21 papers on SNPs in the genes encoding mainly ACE2 and TMPRSS2 and their connections with

Paper selection
All the papers gained from searching using the Medline expression from above, were taken as initial 2956 papers. Then, the following exclusion criteria were used to exclude the papers inappropriate for inclusion in this systematic review.
The following exclusion criteria were applied: 1. Animal studies and studies with human subjects involving other coronaviruses, such as bovine coronavirus and deltacoronavirus.
3. Studies on irrelevant topics, such as porcine diarrhea.
4. Studies on COVID-19 that did not discuss genetics or the cellular infection mechanism.

Data extraction
Data extraction was performed by 2 of us independently. Any type of discord on the data selection or extraction were resolved through discussion. Following criteria were considered when extracting the data: type of trial, clinical and study outcomes, study population, statistically powerful results, and topic relevance.

Quality Assessment
The Newcastle Ottawa Scale (NOS) was used to assess the quality of the 21 included papers. This quality assessment tool was formed by a collaboration between two universities, the University of Newcastle, Australia, and the University of Ottawa, Canada. The NOS was created for the assessment of the quality of nonrandomized studies, such as case-control and cohort studies. There are 3 domains in the NOS: selection, comparability, and outcome. [4] Selection considers the representativeness of the exposed cohort, selection of the non-exposed cohort, ascertainment of exposure, and demonstration that the outcome of interest was not present at the start of the study. For questions 2 and 3 in the outcome section, which ask about follow-up, all papers had to be scored as "yes." COVID-19 is a recent issue; therefore, the follow-up duration could not be as long as in studies on other topics. The comparability of the duration of follow-up between the included studies and usual studies had to be deemed acceptable. There were 4 assessment questions under the selection section. For representativeness of the exposed cohort section, a) truly representative, and b)somewhat representative were both given one star. For selection of the non-exposed cohort, a) Drawn from the same community as the exposed cohort was given one star. For ascertainment of the exposure, both a)Secure record and b)Structured interview were given a star. Last question under the selection section, demonstrated that outcome of interest was not present at start of study, choice of a)Yes, is only given a star. The only criteria to assess the comparability, comparability of the cohorts on the basis of the design or analysis is controlled for cofounders, both choice a) The study controls for age, sex, and marital status and b) Study controls for other factors were given a star. Under the outcome section, there were three questions to follow in order to assess the corresponding criteria. For assessment of outcome, both choice a) Independent blind assessment and b) Record linkage were given a star. Second question under outcome section, was follow-up long enough for outcomes to occur, choice a)Yes is given a star. Last question for assessing outcome, adequacy of follow-up of cohorts, both answer of a) Complete follow-up all subject accounted for and b) Subjects lost to follow up unlikely to introduce bias-number lost less than or equal to 20% or description of those lost suggested no different from those followed are the choices given a star. [5] Results Out of 2956 papers searched initially, 21 academic papers were selected for the systematic review. equivalently. In total, the mean ± standard deviation number of patients per paper was 63496 ± 13889.90; the numbers of patients in the databases mentioned above were not taken into account. The average age of the subjects was 55 years old; however, this value is not accurate because multiple studies did not report age or only recorded the age range and not the average age. The genes investigated in these papers were mainly ACE2 and TMPRSS2. IFITM3, CD147, IFIH1, IL6, LZTFL1, and ACE1 were also mentioned in some papers. (Table 1)  All papers had equal quality assessment scores. (Table 2) The papers varied in terms of the representativeness of the cohort. Speci cally, the papers that used databases were categorized as "truly representative." The remaining papers, which were classi ed as "somewhat representative," collected genomic data from patients from a single hospital or region. Since the aim of this systematic review was to identify SNPs associated with infection with SARS-CoV-2 and the severity of COVID-19 regardless of other health factors, papers that were relevant to the purpose of the review were mostly assessed as being appropriate. In the 21 included papers, ACE2 was mentioned most frequently, and TMPRSS2 and IFITM3 were also mentioned in some papers. Overall, there were some SNPs reported in multiple studies as being related to infection with SARS-CoV-2 and the severity of COVID-19.
As the study was performed with limited data sources and the diversity of the study populations varied, it was di cult to identify common SNPs.

Discussion
This study is started from interest and curiosity on the studies that suggests a certain group of people has greater susceptibility to SARS-CoV-2. Therefore, aim of this study is to nd out genes and SNPs that are related to SARS-CoV-2 infection severity. 21 papers are in depth reviewed to analyze the highly associated or frequently mentioned genetic factors. We can conclude that genetic susceptibility to infection with SARS-CoV-2 mainly involves ACE2 and TMPRSS2. Second, the strength of the effects of these SNPs on susceptibility to infection with SARS-CoV-2 should be quanti ed in future studies. As progression disease is affected by the health status of the individual patient, the strength of the contribution of genetics could be challenging to quantify. However, the genes and SNPs could be ordered in terms of their relative contributions. Third, the SNPs that were mentioned to be related to certain gene's action, (Table 3 & Table 4) do not straight away affect the mechanism. Several SNPs affect the genes' action via indirect path; therefore, it may not always be applicable to all individuals. As they are from all different studies that had different approach, the SNPs collected may not necessarily affect COVID-19 infection. Lastly, as the COVID-19 pandemic developed recently and is ongoing, there were limitations with regard to performing a systematic review. The papers included in this review were mainly published in 2020, with a few published in 2021. As the pandemic started in late 2019, papers on the topic were limited to 2019-2021. This limited the duration of clinical follow-up. Therefore, in the outcome section of the quality assessment of the articles, the second criterion, which pertains to follow-up, had to be marked as "yes." Normally, clinical follow-up of less than one year would not be assessed as "yes." In this case, long-term follow-up was impossible due to the recent cause of the pandemic.

Conclusion
ACE2, TMPRSS2, IFITM3 were found to be the most frequently mentioned genes that are associated with SARS-CoV-2 infection. There were 5 SNPs that were found common in two or more studies (rs12252-C, rs143936283, rs2285666, rs41303171, rs35803318). These SNPs are all related to the genes mentioned above. Although there were some limitations due to lack of data range and follow up time, this study still suggests a general genetic characteristic of vulnerable SARS-CoV-2 infection. Future further research may be done to specify the exact impact of the SNP in terms of severity and degree of impact.

Declarations
Ethics approval, guidelines, and consent to participate: not needed as the research does not include a direct clinical testing Consent for publication: All the authors have approved Availability of data and materials: The studies included in the systematic review are all retrieved from PubMed.gov. All studies included can all be found at PubMed.gov.
Competing interests: Not applicable  Flow chart depicting literature search and selection process