Phylogenetic Changes in SARS-CoV-2 Virus in Bosnian-Herzegovinian Population Over the Period of Two Years.

Background: All viral genomes, including the SARS-CoV-2 virus, mutate over time, and some of these mutations can affect the characteristics of the virus, such as the ease of spread, the severity of the patient's clinical picture, or the effect of vaccines, therapeutic drugs, diagnostic tools or other measures of public health and social protection. Because of all the above, it is imperative to carry out continuous sequencing of this pathogen. Objective: The main goal of this research was to obtain the highest quality genomic sequences of the SARS-CoV-2 virus, to compare the obtained sequences with the reference Wuhan-Hu-1 sequence and to obtain a high-quality genomic alignment in order to reconstruct the appropriate phylogenetic tree. Methods: For the purposes of this research, a next-generation semiconductor sequencing method was chosen. In this research, a total of 47 samples of nasopharyngeal and oropharyngeal swabs from patients from the human population of Bosnia and Herzegovina with a clinical diagnosis of COVID-19 were collected. Results: In the processed 47 samples, there are several monophyletic groups on the constructed phylogenetic tree, of which one sample belongs to the same monophyletic group as the Wuhan-Hu-1 reference sequence. Conclusion: The greater number of samples is needed for a more comprehensive approach. Therefore, the results of this research can act as a guideline for the design of effective measures and strategies in order to solve problems regarding future pandemics as efficiently as possible.

Identification of human genetic variants modulating the course of COVID-19 infection with importance in other viral infections.

Introduction: COVID-19 has been a major focus of scientific research since early 2020. Due to its societal, economic, and clinical impact worldwide, research efforts aimed, among other questions, to address the effect of host genetics in susceptibility and severity of COVID-19. Methods: We, therefore, performed next-generation sequencing of coding and regulatory regions of 16 human genes, involved in maintenance of the immune system or encoding receptors for viral entry into the host cells, in a subset of 60 COVID-19 patients from the General Hospital Tesanj, Bosnia and Herzegovina, classified into three groups of clinical conditions of different severity ("mild," "moderate," and "severe"). Results: We confirmed that the male sex and older age are risk factors for severe clinical picture and identified 13 variants on seven genes (CD55, IL1B, IL4, IRF7, DDX58, TMPRSS2, and ACE2) with potential functional significance, either as genetic markers of modulated susceptibility to SARS-CoV-2 infection or modifiers of the infection severity. Our results include variants reported for the first time as potentially associated with COVID-19, but further research and larger patient cohorts are required to confirm their effect. Discussion: Such studies, focused on candidate genes and/or variants, have a potential to answer the questions regarding the effect of human genetic makeup on the expected infection outcome. In addition, loci we identified here were previously reported to have clinical significance in other diseases and viral infections, thus confirming a general, broader significance of COVID-19-related research results following the end of the pandemic period.

Comparative Analysis of SARS-CoV-2 Detection Kits.

Background: SARS-CoV-2 is a coronavirus that causes a respiratory disease, COVID-19. For COVID-19 testing, real-time PCR is considered gold standard and therefore many commercial SARS-Cov-2 detection kits are available. Objective: The aim of the study is to determine diagnostic values of 10 different commercially available SARS-CoV-2 detection kits, based on their Ct value. Methods: For this study thirty clinical nasopharyngeal samples were collected in ALEA Genetic Center. Twenty four of them were positive, while six were negative and used as a negative control. Positive samples were selected based on the day when first symptoms appeared. RNA was extracted using the same extraction method for all samples. For amplification and comparison of detection kits, the same RT- PCR instrument was used. Results: Accuracy, sensitivity, specificity and Cohen's kappa coefficient were estimated to evaluate diagnostic values of the tested kits. This study showed that all kits showed 100% specificity. Accuracy, sensitivity and kappa coefficient varied among examined assays. Based on clinical features, LabGunTM COVID-19 Assay by LabGenomics proved to be the most sensitive, the most accurate and most specific. Therefore this assay was used as a reference kit. Conclusion: If things from practice are taken into account, accuracy and reliability of the tested commercial kits can vary compared to those obtained in this study where results were based on ideal functioning of the kits. When choosing the convenient commercial SARS-CoV-2 detection kit using RT-PCR method, many parameters need to be considered.