SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.

A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient's samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.

Applicability and efficacy of a model for prevention of perinatal transmission of hepatitis B virus infection: single center study in Egypt.

AIM: To identify possible maternal risk factors for hepatitis B virus (HBV) acquisition and assess the efficacy of immunoprophylaxis given to infants born to hepatitis B virus surface antigen (HBsAg) positive mothers. METHODS: Screening of 2000 pregnant females was carried out using rapid test and confirmed by enzyme immunoassay. A questionnaire consisting of 20 questions about the possible risk factors for acquisition of HBV infection was filled for every pregnant HBsAg positive female in addition to at least 2 pregnant HBsAg negative females for each positive case. Infants of HBsAg positive women were offered passive and active immunoprophylaxis within the 1st 48 h after birth, in addition to 2nd and 3rd doses of HBV vaccine after 1 and 6 mo respectively. Infants were tested for HBsAg and hepatitis B surface antibodies (HBsAb) at six months of age. RESULTS: HBsAg was confirmed positive in 1.2% of tested pregnant women. Risk factors significantly associated with HBV positivity were; history of injections (OR = 5.65), history of seeking medical advice in a clinic (OR = 7.02), history of hospitalization (OR = 6.82), history of surgery (OR = 4) and family history of hepatitis (OR = 3.89) (P < 0.05). Dropout rate was 28% for HBsAg women whose rapid test was not confirmed and could not be reached to provide immunoprophylaxis for thier newborns. Immunoprophylaxis failure was detected in only one newborn (3.7%) who tested positive for HBsAg at 6 mo of age; and vaccine failure (seronegative to HBsAb after 4 doses of the vaccine) was detected in another one (3.7%). The success rate of the immunoprophylaxis regimen was 92.6%. CONCLUSION: This pilot study shows that a successful national program for prevention of perinatal transmission of HBV needs to be preceded by an awareness campaign to avoid a high dropout rate.

Morbidity and outcome of severe respiratory syncytial virus infection.

BACKGROUND: Respiratory syncytial virus (RSV) is the main cause of severe acute respiratory infection (SARI) in infants and young children. This study aimed to identify risk factors for intensive care unit (ICU) admission, prolonged length of stay (PLOS), and mortality in patients hospitalized with SARI caused by RSV. METHODS: This prospective cohort study included children hospitalized with SARI (according to the World Health Organization definition) and whose laboratory results proved RSV infection during the period from February 2010 to May 2011. RESULTS: Out of 240 enrolled patients, 24 patients (10%) were admitted to the ICU, 57 patients (24.3%) had a PLOS of >9 days and 12 patients (5%) died. The presence of cyanosis (P = 0.000; OR, 351.7) and lung consolidation (P = 0.006, OR, 9.3) were independent risk factors associated with ICU admission. The need for ICU admission (P = 0.000; OR, 6.1) and lung consolidation (P = 0.008, OR, 2.46) were independent risk factors associated with PLOS. The presence of an underlying congenital heart disease (P = 0.03, OR, 18.3), thrombocytopenia (P = 0.04, OR, 32.86) and mechanical ventilation (P = 0.000; OR, 449.4) were the only independent risk factors associated with mortality in our study. CONCLUSIONS: Early recognition of risk factors for complicated RSV disease on admission prompts early interventions and early ICU admissions for these children.

RAD51 and XRCC3 gene polymorphisms and the risk of developing acute myeloid leukemia.

RAD51 (Rec A homolog of E. coli) is a polymorphic gene and one of the central proteins in homologous recombination-DNA-double-stand breaks (HR-DNA-DSB) repair pathway, which is vital in maintaining genetic stability within a cell. The x-ray repair cross complementing (XRCC3) protein also functions in HR-DNA-DSB repair pathway and directly interacts with and stabilizes RAD51 and the closely related RAD51C. The aim of this study was to determine the prevalence of the RAD51 and XRCC3 repair gene polymorphisms among acute myeloid leukemia (AML) patients and to define their role in development of AML and its correlation with the clinical presentation, laboratory data as well as treatment outcome using polymerase chain reaction-restriction fragment length polymorphism assay in 50 de novo AML patients as well as 30 healthy subjects as a control group. Our study revealed that RAD51 G135C and XRCC3 Thr241Met alleles were associated with increased risk of AML with odds ratio (OR) of 2.833 and 2.909 and 95% confidence interval (CI) of 1.527 to 8.983 and 1.761 to 9.788, respectively. Moreover, when combining the 2 genes polymorphisms, a significant elevation of the risk of AML was found with OR of 3.124 and 95% CI of 1.872 to 11.243. As regards treatment outcome, a highly statistical significant difference was found between XRCC3 genotypes with P value of 0.001, whereas no significant difference was present between RAD51 genotypes with P value of 0.29. This clarifies that XRCC3 gene polymorphisms was found to have a significant impact on the risk of treatment failure with OR of 3.560 and 95% CI of 1.167 to 10.875; however, RAD51 gene polymorphism was not found to have an equivalent effect with OR of 2.813 and 95% CI of 0.933 to 10.828. So XRCC3 gene polymorphism might be considered as a prognostic marker in AML. In conclusion, RAD51 and XRCC3 genes polymorphisms may play an important role in the development of AML.