COVID‑19 is a devastating disease, and its control is difficult due to its high transmissibility rate and a long incubation average period (6.4 days). Additionally, more than half of the infected patients were asymptomatic young people or children. The asymptomatic virus transmission is the actual challenge to controlling the disease. Because of limited treatment options, diagnosis techniques have been the first focus all over the world, involving q-RT-PCR as a gold standard, serological tests, point of care studies, or RT-LAMP. Generally, nasopharyngeal, and oropharyngeal samples are preferred clinically as sources. However, alternative sources are being researched, particularly for healthcare professionals who have difficulty taking samples, patients who are afraid of giving samples, and pediatric patients. Herein, physiological saline has been utilized to offer an alternative source besides the swab samples for use in q-RT-PCR. In this study, 212 randomly chosen patients’ samples were studied, and we evaluated the concordance and accurate q-RT-PCR results in two different sources, obtained from swab and gargle samples of patients. Herein, physiological saline is utilized, which is widely used medically as a recommended irrigating and wound dressing solution. We obtained in our experiments with this method, the confidence interval determines 74.50% positivity when compared to the routine q-RT-PCR procedure as summarized. In addition, when only the gargle sampling method is studied in low-income countries, the cost of testing for COVID-19 will decrease significantly. Because this method does not require vNAT or VTM transport solution sterile swab sticks as shown. The plastic container with a lid in which the patient can gargle with SF and spit it out is an ideal method for this. Additionally, it provides a great cost-benefit in low-income countries.

ABSTRACT Patients immune phenotype/genotype data may be useful to understand the molecular mechanisms involved in SARS-CoV-2 infection and can contribute to the identify the different levels of disease severity. The roles of chemokines have been reported in the coronavirus-related diseases SARS and MERS and they may likewise play a critical role in the development of the symptoms of COVID-19 disease. We analyzed the association of the MCP-1-A2518 G, SDF-1-3’A, CCR5-delta32, CCR5-A55029 G, CXCR4-C138T and CCR2-V64I gene polymorphisms with COVID-19 severity to further unveil the immunological pathways leading to disease severity and death. Polymerase chain reaction(PCR)/Sanger sequencing analysis was performed for detection of the variations in 60 asymptomatic and 119 severe COVID-19 patients. In our study, we found that the frequencies of MCP-1 of GA genotype and G allele carriers were significantly higher in severe COVID-19 patients than the asymptomatic COVID-19 patients (p < .0001 and p: .005, respectively). However, no significant association was found for any of the other polymorphisms with the severity of COVID-19. Our findings suggest that there is a positive association between MCP-1-A2518 G gene variants with the severity of COVID-19. However, larger studies in different population which will focus on gene expression levels will help us to understand the capability of the mechanism role.

Bosnia and Herzegovina is located in the South-Eastern Europe, characterized by numerous historical influences, massive migration processes and complex population structure. For that reason, the aim of this study is to provide an accurate and precise update of the population genetics data of allele frequencies on 23 Y-STR loci in Bosnia and Herzegovina using larger sample size. For this purpose, 480 adult male individuals from the general population have been genotyped over 23 Y-STR loci contained in the PowerPlex Y23 system. Population genetics parameters have been calculated, namely allele and haplotype frequencies, gene and haplotype diversity, as well as Rst and P values for the assessment of interpopulation differences. The obtained results are in close agreement with previously published data for Bosnian-Herzegovinian population, as well as for local subpopulations. This study offers significantly increased resolution and information content, with 454 unique haplotypes. Population comparison reveals no statistically significant differences between the study population and 12 European populations used for comparison, as visualized through an MDS plot and neighbour-joining phylogenetic tree. This study offers representative data for local Y chromosomes that can be used for forensic applications, paternity and kinship testing, as well as for genealogical studies.

Human Y-chromosomal haplogroups are an important tool used in population genetics and forensic genetics. A conventional method used for Y haplogroup assignment is based on a set of Y-single nucleotide polymorphism (SNP) markers deployed, which exploits the low mutation rate nature of these markers. Y chromosome haplogroups can be successfully predicted from Y-short tandem repeat (STR) markers using different software packages, and this method gained much attention recently due to its labor-, time-, and cost-effectiveness. The present study was based on the analysis of a total of 480 adult male buccal swab samples collected from different regions of Bosnia and Herzegovina. Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. The results revealed the existence of 14 different haplogroups, with I2a, R1a, and E1b1b being the most prevalent with frequencies of 43.13, 14.79, and 14.58%, respectively. Compared to the previously published studies on Bosnian-Herzegovinian population based on Y-SNP and Y-STR data, this study represents an upgrade of molecular genetic data with a significantly larger number of samples, thus offering more accurate results and higher probability of detecting rare haplogroups.

We address the question of different representation of Bloch states for lattices with a basis, with a focus on topological systems. The representations differ in the relative phase of the Wannier functions corresponding to the diffferent basis members. We show that the phase can be chosen in such a way that the Wannier functions for the different sites in the basis both become eigenstates of the position operator in a particular band. A key step in showing this is the extension of the Brillouin zone. When the distance between sites within a unit cell is a rational number, $p/q$, the Brillouin extends by a factor of $q$. For irrational numbers, the Brillouin zone extends to infinity. In the case of rational distance, $p/q$, the Berry phase"lives"on a cyclic curve in the parameter space of the Hamiltonian, on the Brillouin zone extended by a factor of $q$. For irrational distances the most stable way to calculate the polarization is to approximate the distance as a rational sequence, and use the formulas derived here for rational numbers. The use of different bases are related to unitary transformations of the Hamiltonian, as such, the phase diagrams of topological systems are not altered, but each phase can acquire different topological characteristics when the basis is changed. In the example we use, an extended Su-Schrieffer-Heeger model, the use of the diagonal basis leads to toroidal knots in the Hamiltonian space, whose winding numbers give the polarization.

Background: The human angiotensin I converting enzyme 1 (ACE1) gene insertion/deletion (I/D) polymorphism is classified based on the presence or absence of a 287 bp Alu sequence. The ACE1 D allele is associated with higher ACE1 concentrations in tissues. Previous research has shown that susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is primarily determined by the affinity between the viral receptor-binding domain and the host human receptor angiotensin-converting enzyme 2 (hACE2) receptor. In the human genome, ACE2 is identified as a homolog to ACE1. Objective: The purpose of this study was to characterize the ACE1 D allele distribution in Bosnia and Herzegovina (B&H), so as to compare it to population data from other European countries and to investigate the potential correlation between D allele frequencies and coronavirus disease 2019 (COVID-19) epidemiological findings in selected European populations. Methods: The ACE1 D allele frequencies in 18 selected European populations were analyzed and compared with COVID-19 prevalence, mortality, and severity using multivariate linear regression analysis. Results and Discussion: The ACE1 D allele distribution within the B&H population was similar to its distribution in other European populations. Regression analysis showed no significant correlation between the D allele frequency and the incidence of infections between the examined populations, nor with the rates of fatality and severe cases. Conclusion: There is no clear statistical evidence that the ACE1 D allele is associated with increased or decreased COVID-19 incidence, mortality, and case severity within the investigated populations.

Abstract – Modern Bosnia and Herzegovina is a state consisting of multiple ethnicities and regions located in the Western Balkan, with a very complex history. The earliest historical findings show that its area was inhabited since the Paleolithic. From that time, this part of Europe, especially the region of the Modern Bosnia and Herzegovina, could be recognized as the crossroad for the different human migration and the meeting point for different cultures, religions and gene pools. Mitochondrial DNA is being used for maternal lineage testing, while the Y chromosome is being used for paternal lineage testing. Therefore, these markers are being referred to as lineage markers. Lineage markers are often used for parental lineage monitoring in population genetics, human genetics, as well as in forensic genetics. The main intention of this paper is to construct a short overview of the Y chromosome studies performed in Bosnia and Herzegovina within the last two decades.

This study was conducted to confirm preliminary anthropological research indicating the specificity of isolated Selška Valley populations and implement clear mapping of genetic distances between neighboring populations and similar "inland island" populations from the region. The sample consisted of 86 unrelated individuals born in the Selška Valley from the lowland villages (Bukovica, Ševlje, Dolenja Vas, Selca, Železniki and Zali Log) and the mountain villages (Podlonk, Prtovč, Spodnje Danje, Zgornja Sorica and Spodnja Sorica). The for mentioned 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA) were analyzed and statistical analysis was applied to determine population-genetics and forensic parameters. The frequencies of 15 STR loci from isolated populations of Slovenian villages, Slovenia, Bosnian mountain villages and Bosnia and Herzegovina were analyzed to calculate genetic distances between them. Our results confirmed a similar genetic pattern between the Selška Valley mountain villages and Slovenian general population as well as Bosnian mountain villages and general Bosnian population. Even if the sample size was relatively small and examined populations were geographically isolated, observed genetic variation within the whole population was relatively high and comparable with neighboring populations. Additional analysis proved that the Selška Valley population is genetically closest to the Slovenian and Austrian populations. On the other hand, comparison with similarly patterned populations confirmed that this population could be recognized as "inland island" population in genetic terms.

Aim To investigate the prevalence of common genetic variants that can serve as markers of thrombophilia and warfarin pharmacogenetics in Bosnia and Herzegovina. Methods The study was performed between August and October 2017 on 130 healthy unrelated adult volunteers from Bosnian-Herzegovinian population sample. The prevalence of the following genetic variants was determined: F5 c.1601G>A (factor V Leiden), F2 c.*97G>A (factor II or prothrombin mutation), F13A1 (factor XIII) c.103G>T, MTHFR (methylenetetrahydrofolate reductase) c.665C>T and c.1286A>C, as well as PAI-1 (plasminogen activator inhibitor 1) c.-816A>G and c.-844G>A as markers of thrombophilia risk, and *2 and *3 alleles of CYP2C9 (cytochrome P450 2C9) and five variants of VKORC1 (vitamin K epoxide reductase complex subunit 1) as markers of warfarin pharmacogenetics. DNA was isolated from buccal swabs using salting out method, while genotyping was performed using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Results Minor allele frequencies for two main thrombophilia risk factors, F5 c.1601G>A and F2 c.*97G>A were 0.023 and 0.008, respectively. Combined data for the markers of warfarin pharmacogenetics imply that 57.4% study participants can be expected to metabolize warfarin at an extensive, 40.3% at intermediate, and 2.3% at a poor rate. Conclusion This study reports the first extensive population genetic data for thrombophilia and warfarin pharmacogenetic markers in Bosnia and Herzegovina. Allele frequencies of genetic variants are within the general average for European populations, and their presence implies the necessity of introduction of personalized medicine in warfarin-mediated antithrombotic therapy.

Abstract The aim of this study is to provide an insight into Balkan populations’ genetic relations utilizing in silico analysis of Y-STR haplotypes and performing haplogroup predictions together with network analysis of the same haplotypes for visualization of the relations between chosen haplotypes and Balkan populations in general. The population dataset used in this study was obtained using 23, 17, 12, 9 and 7 Y-STR loci for 13 populations. The 13 populations include: Bosnia and Herzegovina (B&H), Croatia, Macedonia, Slovenia, Greece, Romany (Hungary), Hungary, Serbia, Montenegro, Albania, Kosovo, Romania and Bulgaria. The overall dataset contains a total of 2179 samples with 1878 different haplotypes. I2a was detected as the major haplogroup in four out of thirteen analysed Balkan populations. The four populations (B&H, Croatia, Montenegro and Serbia) which had I2a as the most prevalent haplogroup were all from the former Yugoslavian republic. The remaining two major populations from former Yugoslavia, Macedonia and Slovenia, had E1b1b and R1a haplogroups as the most prevalent, respectively. The populations with E1b1b haplogroup as the most prevalent one are Macedonian, Romanian, as well as Albanian populations from Kosovo and Albania. The I2a haplogroup cluster is more compact when compared to E1b1b and R1b haplogroup clusters, indicating a larger degree of homogeneity within the haplotypes that belong to the I2a haplogroup. Our study demonstrates that a combination of haplogroup prediction and network analysis represents an effective approach to utilize publicly available Y-STR datasets for population genetics.

The region of Western Balkans has been inhabited since the Paleolithic era and was the route of the spread of farming from the Middle East to Europe during the Neolithic era. In the present study, Y-STR data from European populations have been used to construct median-joining networks. The study was performed using Whit Athey’s Haplogroup Predictor, Y Utility and Network 4 software packages to predict Y haplogroups, construct networks, perform clustering of closely related Y chromosomes and calculate time estimates between individual nodes. The results of the study imply that geographically close populations cluster together at both Balkan and European levels. It was observed that an elevated number of study populations and individual haplogroups increases the possibility that individuals of different ethnic background cluster within the same or neighboring clades of network. Subsequent time estimates, performed based on the mutation frequency between the ancestral node and its descendant nodes, revealed that I2a haplogroup within the Western Balkan region has the most compact clustering (age, estimated at 3109 years), followed by Hg E1b1b which has the second most compact clustering (4896 years). The obtained results are nonetheless in accordance with previously published research investigating the frequency of Y haplogroups based on Y-SNP variant frequencies, indicating that Western Balkan countries are mainly represented by I2a subclade (average for six countries 32.3%), followed by E1b1b and R1a (average for six countries of 21.5% and 17%, respectively).

Since the introduction of the term low copy number DNA, also referred as low template DNA, touch DNA or trace DNA analysis, it has quickly become focal point of forensic DNA testing as well as other DNA based studies. Low template DNA (ltDNA) samples can be described as the samples which involve single source samples with template DNA in concentrations below 100 picograms (pg). Due to sensitivity of ltDNA samples to contamination, it is of great importance to optimize performance of the multiplex STR systems and existing protocols to increase chance of successful analysis. The main objective of this study was analysis of 20 challenging samples (skeletal remains, cigarette buts, chewing gum, poorly collected buccal swabs etc.) mostly low template DNA samples, preliminarily profiled by PowerPlex® 16 multiplex STR systems and additionally processed with new generation multiplex STR kit PowerPlex® Fusion. Sample isolation was done using a standard phenol-chloroform method for bone samples and DNeasy® Blood and Tissue Kit for other forensic samples. PowerPlex® 16 (PP16), multiplex STR system and PowerPlex® Fusion (PP Fusion) were used for co-amplification of 15 and 24 autosomal STR loci respectively. Results of this preliminary study suggest that PP Fusion primer set is better optimized for the analysis of ltDNA samples, and it is more robust regarding presence of the potential PCR inhibitors.