COVID-19: Establishing, implementing and assessment safety strategy, descriptive interventional study.

The increase in severe acute respiratory syndrome SARS-CoV-2 has invariably affected medical professionals in their training, academic and professional development. The present study was an interventional descriptive study aimed at reducing the risk of exposure to COVID-19 and enabling physical attendance to the practical session for applied medical students by establishing and implementing a safety strategy. The adopted safety strategy has eight conditions and 50 requirements. Compliance with the safety strategy along with the serological diagnosis of COVID-19 was used as a key performance indicator for assessing the efficiency of the safety strategy. A total of 197 students were enrolled at the beginning of the study. The overall results showed that 78.1% of the respondents strictly followed the protocol, 14.5% of the individuals partially responded to the protocol and 7.4% of the individuals did not respond to the protocol. Twenty-two (12.6%) out of the 175 participants who completed the study had positive COVID-19 during the study period, whereas the remaining 153 participants (87.4%) appeared to be healthy. The serological results showed that 68 (38.9%) and 66 (37.7%) individuals of the study population had positive IgM+IgA and IgG of COVID-19, respectively; the majority of the participants who developed antibodies did not show symptoms and appeared to be healthy during the study. The physical distancing condition was the only condition that displayed a significant relationship with seropositive IgM+IgA. The compiling of standardized protocols along with serological diagnoses can be an effective tool in measuring the effectiveness of safety protocol and reducing the risk of exposure to COVID-19.

West Nile virus IgG antibodies among blood donors in Sudan: a cross-sectional study.

while the world is concentrated on fighting SARS-CoV-2, other viruses such as West Nile virus (WNV) attack the communities silently. West Nile Virus (WNV) is established as one of the infectious agents that transmissible blood transfusion. The present study is cross-sectional, conducted in the central blood bank, Khartoum state, Sudan, and aimed to determine WNV IgG antibodies among blood donors. METHODS: the antibodies of the IgG class against West Nile virus in the serum were determined using the ELISA technique. Ninety blood donors participated in this study. RESULTS: the results showed that 67(74.4%) of participants had positive IgG for WNV. The majority of positive participants 28/67(41.8%) had an age between 28-37 years followed by an age group 18-27 years 24/67(35.8), the dominant blood group of the positive WNV IgG participants was A+ 26/67 (38.8%) followed by O+ 19/67(28.4%). The result displayed that 40(59.7%) of the positive IgG had donated blood several times and 58 (86.6%) had a blood transfusion. Statistical analysis showed an insignificant association between age group, blood group, blood donation, blood transfusion, and West Nile Virus. CONCLUSIONS: the high IgG seroprevalence (which indicated previous infection) in the present study suggests high virus circulation in Sudan. This situation proposed that WNF screening test should be part of blood transfusion screening tests in Sudan.

Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern.

This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).

In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations.

In-silico studies on SARS-CoV-2 genome are considered important to identify the significant pattern of variations and its possible effects on the structural and functional characteristics of the virus. The current study determined such genetic variations and their possible impact among SARS-CoV-2 variants isolated in India. A total of 546 SARS-CoV-2 genomic sequences (India) were retrieved from the gene bank (NCBI) and subjected to alignment against the Wuhan variant (NC_045512.2), the corresponding amino acid changes were analyzed using NCBI Protein-BLAST. These 546 variants revealed 841 mutations; most of these were non-synonymous 464/841 (55.1%), there was no identical variant compared to the original strain. All genes; coding and non-coding showed nucleotide changes, most of the structural genes showed frequent nonsynonymous mutations. The most affected genes were ORF1a/b followed by the S gene which showed 515/841 (61.2%) and 120/841 (14.3%) mutations, respectively. The most frequent non-synonymous mutation 486/546 (89.01%) occurred in the S gene (structural gene) at position 23,403 where A changed to G leading to the replacement of aspartic acid by glycine in position (D614G). Interestingly, four variants also showed deletion. The variants MT800923 and MT800925 showed 12 consecutive nucleotide deletion in position 21982-21993 resulting in 4 consecutive amino acid deletions that were leucine, glycine, valine, and tyrosine in positions 141, 142, 143, and 144 respectively. The present study exhibited a higher mutations rate per variant compared to other studies carried out in India.

Unique SARS-CoV-2 Variant Exhibiting Plenteous Missense Mutations in Structural and Nonstructural Genes.

Determining the variations in SARS-CoV-2 variant is considered main factor for understanding the pathogenic mechanisms, aid in diagnosis, prevention and treatment. The present study aimed to determine the genetic variations of SARS-CoV-2. The sequences of SARS-CoV-2 were obtained from National Center for Biotechnology Information (NCBI) and studied according to the time of isolation and their origin. The genome sequence of SARS-CoV-2 accession number NC_045512 which represented the first isolated sequence of SARS-CoV-2 (Wuhan strain) was used as the reference sequence. The obtained genome sequences of SARS-CoV-2 were aligned against this Wuhan strain and variations among nucleotides and proteins were examined. The sequence of SARS-CoV-2 accession number MT577016 showed very low homology 98.75% compared to Wuhan strain NC_045512. The analysis identified 301 nucleotide changes, which correspond to 258 different mutations; most of them 80% (207/258) were missense point mutations followed by 17.1% (44/258) silent point mutations. The critical mutations occurred in viral structural genes; 16.7% (43/258) mutations reported in S gene and 1 missense mutation was observed in E gene. Our finding showed the lowest homology and relatively distant phylogenetic relation of this SARS-CoV-2 variant with Wuhan strain along with high frequency of mutations including those in spike S and envelope E genes.

Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study.

SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico, cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.

Genetic variations among SARS-CoV-2 strains isolated in China.

The rapid spread of COVID-19, which has led to a global pandemic, has placed public health systems under severe pressure. Identifying variations in SARS-CoV-2 strains from different regions is a key factor for understanding the pathogenic mechanisms, aid in diagnosis, prevention and therapy of this disease. The present study is an analytical descriptive study aimed to determine genetic variations among SARS-CoV-2 strains isolated in China. Sixty six complete genome sequences of the virus were retrieved from NCBI, the sequence of original Wuhan strain accession number NC 045512 was used as the reference sequence. Each genome sequence was blasted against the original Wuhan strain; the analysis was done using NCBI Nucleo-blast. The collected sequences showed 10 different variants. One hundred and thirty four mutations were identified among the variants of SARS-CoV-2 in this study; most of them 52.2% (70/134) were missense point mutation, majority of the mutations 65.7% (88/134) occurred in the open reading frame a/b (ORFab), few mutations occurred in the structural viral genome, each of spike (S) gene and nucleocapsid (N) gene showed 4 mutations; 2 silent point mutations and 2 missense point mutations occurred in each gene whereas membrane (M) gene showed silent point mutation and no mutation observed in the envelope E gene. The remarkable observation in this study showed by Yunnan variant accession number MT226610 which exhibited high incidence of mutations, it displayed 28 different point mutations; only 3(10.7%) of them were silent mutations while the rest were missense mutations. Our analysis showed several mutations including spike S gene and membrane M gene which may be responsible for a change in the structures of target proteins.

Detection of multidrug resistant Mycobacterium tuberculosis in Tabuk, Saudi Arabia, using Genotype MTBDRplus.

BACKGROUND: The global increase in the rates of multidrug-resistant (MDR) tuberculosis (TB) has made the timely identification of resistant Mycobacterium tuberculosis complex strains an important emergence to achieve effective disease management and to prevent their spread in the community. The present study aimed to determine the MDR-TB in Tabuk province, north of the Kingdom of Saudi Arabia. METHODS: The GenoType MTBDRplus assay was used to determine the mutations associated with isoniazid (INH) and rifampicin (RIF) resistances. A total number of 61 confirmed M. tuberculosis positive-sputum samples were scanned for the mutation in the rpoB, inhA, and katG genes. RESULTS: The present study revealed that 67.2% of the samples were susceptible, 29.5% were monoresistant, and 3.3% were MDR. CONCLUSIONS: The monoresistant showed 26.2% for INH and 3.3% for RIF. The early detection of MDR could guide the starting of appropriate regimen of treatment.

Association between pulmonary tuberculosis and Type 2 diabetes in Sudanese patients.

INTRODUCTION: Tuberculosis (TB) and diabetes mellitus (DM) are both important health issues, and the association between DM and TB may be the next challenge for global TB control worldwide, type 2 DM (T2DM) responsible for 90% of DM cases. Persons with diabetes have a significantly increased risk of active TB, which is two to three times higher than in persons without diabetes. The aim of this study was to determine the association between pulmonary tuberculosis (PTB) and T2DM among Sudanese patients and also to determine the association between hemoglobin A1c (HbA1c) percentage in diabetic patients and development of PTB and effect of duration of T2DM in developing PTB. MATERIALS AND METHODS: A total of 120 sputum samples were collected from patients during 6 months in Ribat University Hospital, Khartoum, Sudan. Sixty of them were known type 2 diabetic patients categorized as study group and sixty were nondiabetic patients categorized as control group. Ziehl-Neelsen smear preparation and DNA were extracted from sputum for detection of Mycobacterium tuberculosis by polymerase chain reaction (PCR). RESULTS: Among the 120 sputum specimens, 72 (60%) were males and 48 (40%) were females. Fourteen (19.4%) males and 6 (12.5%) females had PTB, the difference was not statistically significant according to gender P = 0.229. According to treatment modalities, diabetic patients were treated with injectable insulin (36.7%), PCR positive was 4(33.3%) P value (0.853), oral hypoglycemic drugs (51.7%) PCR positive 7 (58.3%) P value (0.849) and dietary control (11.7%) PCR positive (1 (8.3%) P value (1.000) Were insignificant differences. The frequency of HbA1c of 58 patients with diabetes was 24 (41.4%) who had controlled DM (HbA1c level ≤ 6.5%) and 34 (58.6%) had uncontrolled DM. Of the 60 patients with diabetes, 12 had PTB with uncontrolled DM, with significant difference (P=0.000). The mean duration of diabetes mellitus was (6.92 years ± Std 6.801) and the frequency of diabetes mellitus in first 10 years was 47 (78.3%), in (11-20) years was 10 (16.7%) and in (21-30) years was 3 (5%), the PCR positive PTB showed 10(21.3%) for the first 10 years, (11-20) years was 2 (20%) and zero (0.0%) for (21-30) years, P-value (0.480) insignificant different. CONCLUSIONS: In summary, we found consistent evidence for an increased risk of TB among patients with uncontrolled DM (high-level HbA1c).

Cost effectiveness of adopted quality requirements in hospital laboratories.

BACKGROUND: The present study was designed in quasi-experiment to assess adoption of the essential clauses of particular clinical laboratory quality management requirements based on international organization for standardization (ISO 15189) in hospital laboratories and to evaluate the cost effectiveness of compliance to ISO 15189. METHODS: The quality management intervention based on ISO 15189 was conceded through three phases; pre - intervention phase, Intervention phase and Post-intervention phase. RESULTS: In pre-intervention phase the compliance to ISO 15189 was 49% for study group vs. 47% for control group with P value 0.48, while the post intervention results displayed 54% vs. 79% for study group and control group respectively in compliance to ISO 15189 and statistically significant difference (P value 0.00) with effect size (Cohen's d) of (0.00) in pre-intervention phase and (0.99) in post - intervention phase. The annual average cost per-test for the study group and control group was 1.80 ± 0.25 vs. 1.97 ± 0.39, respectively with P value 0.39 whereas the post-intervention results showed that the annual average total costs per-test for study group and control group was 1.57 ± 0.23 vs 2.08 ± 0.38, P value 0.019 respectively, with cost-effectiveness ratio of (0.88) in pre -intervention phase and (0.52) in post-intervention phase. CONCLUSION: The planned adoption of quality management requirements (QMS) in clinical laboratories had great effect to increase the compliance percent with quality management system requirement, raise the average total cost effectiveness, and improve the analytical process capability of the testing procedure.