Identification and molecular docking of novel chikungunya virus NSP4 inhibitory peptides from camel milk proteins.

The chikungunya (CHIK) virus is an arbovirus belonging to the alphavirus (Togaviridae family). Around 85% of infected individuals suffer from symptoms such as high fever and severe joint pain; about 30 to 40% will develop a chronic joint illness. The Nsp4 protease is the most conserved protein in the alphavirus family and serves as an RNA-dependent RNA polymerase (RdRp). Targeting this enzyme might inhibit the CHIKV replication cycle. This work aims to in silico study the CHIKV RdRp inhibitory effect of peptides derived from camel milk protein as antiviral peptides. Various bioinformatics tools were recruited to identify, screen, predict and assess peptides obtained from camel milk as antiviral peptides (AVPs). During this study, CHIKV Nsp4 (polymerase) was used as a target to be inhibited by interaction with peptides derived from camel milk protein. Among 91 putative bioactive peptides, the best predicted 5 were further evaluated. Molecular docking showed that the top 5 AVPs generated better docking scores and interacted well with active sites of Nsp4 by the formation of different hydrogen bonds as well as other bonds. AVP63 and AVP20 showed the best Molecular docking and MD simulation results. The residue 315ASP of the GDD motif (catalytic core) exhibited a favorable interaction with the AVPs. The findings of this study suggest that the AVP20 derived from camel milk protein can be a potential novel CHIKV polymerase inhibitor.Communicated by Ramaswamy H. Sarma.

The First Genomic Characterization of the Chikungunya Virus in Saudi Arabia.

BACKGROUND: Chikungunya is an arboviral infection caused by the Chikungunya virus (CHIKV) transmitted to humans by mosquitoes of Aedes spp. CHIKV has been confined to African countries and South-East Asia up to 2004, but since then, the pathogen has become more global, and its high morbidity rate has become more visible. Saudi Arabia is not an endemic region of CHIKV, and the virus's origin is not yet fully understood. This study aimed to characterize the genome of CHIKV from samples detected in Jeddah in 2018. METHOD: Twenty-two sets of primers were designed to amplify near-full length genome of CHIKV. RT-PCR was conducted from clinical samples. Two samples were used for studying near complete genome sequence while the remaining samples were used to study the E1 gene. Different bioinformatics tools were utilized. RESULTS: Phylogenetic analysis showed that the CHIKV strains clustered with strains isolated from Kenya during 2017-2018 and belonged to ECSA genotype. E1: L136F, K211E and I317V mutations were identified in our strains. Also, E2: M74I, A76T, and V264A mutations were documented. Additionally, the capsid N79S substitution was also detected. CONCLUSION: The genome of CHIKV was analyzed for the first time in Saudi Arabia to better understand the origin of the CHIKV and its genetic diversity, which showed high similarity with IE-a subclade of CHIKV strains detected in Mombasa (Kenya) indicating its possible origin.

Evaluation of CD4+:CD8+ Ratio in Patients With Cervical Cancer and the Levels of Inflammatory Markers.

BACKGROUND/AIM: Cervical cancer remains a major public health concern. The ratio of CD4+:CD8+ T-cells is used to evaluate the immune system function. This study aimed to explore the CD4+:CD8+ T-cell ratio in relation to the glycemic status, inflammatory markers, vitamin D, and vitamin B12 in patients with early diagnosed cervical cancer. PATIENTS AND METHODS: This is a cross-sectional study. Blood samples were collected for flow cytometry analysis. Information regarding Papanicolaou (Pap) smears and colposcopy investigations were collected from 152 women with type 2 diabetes admitted to East Jeddah Hospital, Jeddah, Saudi Arabia, between January 2018 and January 2021. RESULTS: Patients with early cervical carcinoma and a higher CD4+:CD8+ ratio (>1.2) had a higher C-reactive protein (CRP) level than those with a lower CD4+:CD8+ ratio (Mean±SD=13.75±13.3 vs. 10.85±8.1; p-value=0.034). Patients with early cervical carcinoma, diabetes, and higher CD4+:CD8+ ratio (>1.2) had a higher blood HbA1c percent than those with a lower CD4+:CD8+ ratio. CONCLUSION: A high CD4+:CD8+ T-cells ratio was associated with an increased HbA1c% and CRP levels in women with diabetes diagnosed with early cervical carcinoma, which can induce inflammation in early diagnosed patients with cervical cancer.

High seroprevalence of SARS-CoV-2 among high-density communities in Saudi Arabia.

BACKGROUND: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection had been investigated utilizing serology. MATERIALS AND METHODS: This community-based sero-survey was carried out in the neighborhoods of three cities in Saudi Arabia. RESULTS: Of 5629 participants, 2766 (49.1%) were women; and 2148 (38.1%) were 18-34 years of age, and 3645 (64.7%) were from South East Asia. Positive serology was seen in 2825 (50.2% (95% CI: 48.8-51.5%) for SARS-CoV-2 anti-S1 IgG antibodies by ECLIA. Being in the age category of 18-34 years and being from Eastern Mediterranean Region (country A) were associated with higher COVID-19 seropositivity with estimated odds ratio of 1.3 [95% CI 1.1-1.8] and 2.5 [95% CI 1.1.5-4.2] respectively. Gender, social status, education, nationality, symptoms, presence of comorbidities and activity style were positively associated with increased seropositivity. Factors associated negatively with the rate of seropositivity were higher education and having outdoor activity with estimated OR of 0.92 [95% CI 0.46-0.95] and 0.59 [95% CI 0.47-0.74], respectively. CONCLUSION: The study showed high seroprevalence of SARS-CoV-2 among high density population. Health education campaigns should target middle-aged, those with low education, those living in lower standards and indoor workers.

Seroprevalence of antibodies to SARS-CoV-2 among blood donors in the early months of the pandemic in Saudi Arabia.

BACKGROUND: Serologic testing provides better understanding of SARS-CoV-2 prevalence and its transmission. This study was an investigation of the prevalence of antibodies to SARS-CoV-2 among blood donors in Saudi Arabia. OBJECTIVE: To estimate the seroprevalence of anti-SARS-CoV-2 antibodies among blood donors in Saudi Arabia during the early phase of the COVID-19 pandemic. METHODS: Serology results and epidemiological data were analyzed for 837 adult blood donors, with no confirmed SARS-CoV-2 infection, in Saudi Arabia from 20th to 25th May 2020. Seroprevalence was determined using electrochemical immunoassay to detect anti-SARS-CoV-2 antibodies. RESULTS: The overall seroprevalence of anti-SARS-CoV-2 antibodies was 1.4% (12/837). Non-citizens had higher seroprevalence compared with citizens (OR 13.6, p = 0.001). Secondary education was significantly associated with higher seroprevalence compared with higher education (OR 6.8, p = 0.005). The data showed that the highest seroprevalence was in Makkah (8.1%). Uisng Makkah seroprevalence as the reference, the seroprevalence in other areas was: Madinah 4.1% (OR 0.48, 95% CI 0.12-1.94), Jeddah 2.3% (OR 0.27, 95% CI 0.31-2.25), and Qassim 2.9 % (OR 0.34, 95% CI 0.04-2.89) and these were not statistically different from seroprevalence in the Makkah region. CONCLUSIONS: At the early months of the COVID-19 pandemic in Saudi Arabia, the seroprevalence of antibodies to SARS-CoV-2 among blood donors was low, but was higher among non-citizens. These findings may indicate that non-citizens and less educated individuals may be less attentive to preventive measures. Monitoring seroprevalence trends over time require repeated sampling.