Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia.

Purpose: Omicron (B.1.1.529) is one of the highly mutated variants of concern of SARS-CoV-2. Lineages of Omicron bear a remarkable degree of mutations leading to enhanced pathogenicity and upward transmission trajectory. Mutating Omicron lineages may trigger a fresh COVID-19 wave at any time in any region. We aimed at the whole-genome sequencing of SARS-CoV-2 to determine variants/subvariants and significant mutations which can foster virus evolution, monitoring of disease spread, and outbreak management. Methods: We used Illumina-NovaSeq 6000 for SARS-CoV-2 genome sequencing, MEGA 10.2 and nextstrain tools for phylogeny; CD-HIT program (version 4.8.1) and MUSCLE program for clustering and alignment. At the same time, UCSF Chimera was employed for protein visualization. Results: Predominant Omicron pango lineages in Al-Baha were BA.5.2/B22 (n=4, 57%), and other lineages were BA.2.12/21L (n=1, 14.28%), BV.1/22B (n=1, 14.28%) and BA.5.2.18/22B (n=1, 14.28%). 22B nextstrain clade was predominant, while only one lineage showed 21L. BA.5.2/22B, BA.5.2/22B harbored a maximum of n=24 mutations in the spike region. Twelve crucial RBD mutations: D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, and Y505H were identified except the lineage BA.5.2/22B in which F486V mutation was not observed. Critical deletions S106 in membrane protein NSP6, E31in nucleocapsid, and L24 in spike region were observed in all the lineages. Furthermore, we identified common mutations of Omicron variants of SARS-CoV-2 in therapeutic hot spot spike region: T19I, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, A653V, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, D1146D, L452R, F486V, N679K and D796Y. The effect of RBD-targeted mutations on neutralizing (NAbs) binding was considerable. Conclusion: The outcome of this first report on SARS-CoV-2 variants identification and mutation in the Al-Baha region could be used to lay down the policies to manage and impede the regional outbreak of COVID-19 effectively.

Study of Streptococcus mutans in Early Biofilms at the Surfaces of Various Dental Composite Resins.

BACKGROUND: Biofilm deposit on the composite restoration is a common phenomenon and bacterial growth follows the deposition. The study aims to evaluate Streptococcus mutans (S. mutans) early biofilm formation on the surfaces of various dental composite resins by using the real-time quantitative polymerase chain reaction (qPCR) technique. MATERIALS AND METHODS: Thirty-two discs, where eight discs were in each group of Filtek Supreme Ultra (FSU; 3M, St. Paul, MN), Clearfil AP-X (APX; Kuraray Noritake Dental Inc., Tokyo, Japan), Beautifil II (BE2; Shofu, Inc., Kyoto, Japan), and Estelite Sigma Quick (ESQ; Tokuyama Dental, Tokyo, Japan), were fabricated and subjected to S. mutans biofilm formation in an oral biofilm reactor for 12 hours. Contact angles (CA) were measured on the freshly fabricated specimen. The attached biofilms underwent fluorescent microscopy (FM). S. mutans from biofilms were analyzed using a qPCR technique. Surface roughness (Sa) measurements were taken before and after biofilm formation. Scanning electron microscopy (SEM), including energy dispersive X-ray spectrometer (EDS) analysis, was also performed for detecting relative elements on biofilms. RESULTS: The study showed that FSU demonstrated the lowest CA while APX presented the highest values. FM revealed that condensed biofilm clusters were most on FSU. The qPCR results indicated the highest S. mutans DNA copies in the biofilm were on FSU while BE2 was the lowest (p < 0.05). Sa test signified that APX was significantly the lowest among all materials while FSU was the highest (p < 0.05). SEM displayed areas with apparently glucan-free S. mutans more on BE2 compared to APX and ESQ, while FSU had the least. Small white particles detected predominantly on the biofilms of BE2 appeared to be Si, Al, and F extruded from the resin. CONCLUSION: Differences in early biofilm formation onto various composite resins are dependent on the differences in material compositions and their surface properties. BE2 showed the lowest quantity of biofilm accumulation compared to other resin composites (APX, ESQ, and FSU). This could be attributed to BE2 proprieties as a giomer and fluoride content.

Assessment of the Prevalence and Incidence of COVID-19 in Saudi Arabia.

The global pandemic of coronavirus disease 2019 (COVID 19) is reported to have started in Wuhan City, Hebei Province, China. It has spread rapidly all over the world, including Saudi Arabia, having a severe health emergency. This new virus was named as the 2019 novel coronavirus (2019-nCoV), and now severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on previous practice and phylogenetic and taxonomic investigations. SARS-CoV-2 belongs to the family of Coronaviridae, Betacoronavirus, Sarbecovirus subgenus, genome ß. Throughout the COVID 19 pandemic, several strains of SARS-CoV-2 have been recognized around the world. The SARS-CoV-2 variants have caused significant morbidity and mortality worldwide and in Saudi Arabia as well. The rate at which COVID-19 spread across borders and affected countries has highlighted the significance of health care systems to nations and global operations. This review focuses on the origin, epidemiology, pathophysiology, transmission, and the impact of this disease, while highlighting the knowledge about SARS-CoV-2 variants.

Uncomplicated falciparum malaria among schoolchildren in Bajil district of Hodeidah governorate, west of Yemen: association with anaemia and underweight.

BACKGROUND: Malaria, malnutrition and anaemia are major public health problems in Yemen, with Hodeidah being the most malaria-afflicted governorate. To address the lack of relevant studies, this study was conducted to determine the prevalence of Plasmodium falciparum and its relation to nutritional status and haematological indices among schoolchildren in Bajil district of Hodeidah governorate, west of Yemen. METHODS: A cross-sectional study was conducted among 400 schoolchildren selected randomly from four schools in Bajil district. Data about demographic characteristics, risk factors and anthropometric measurements of age, height and weight were collected. Duplicate thick and thin blood films were prepared, stained with Giemsa and examined microscopically for malaria parasites. The density of P. falciparum asexual stages was estimated on thick films. EDTA-blood samples were examined for the haematological indices of haemoglobin (Hb) and blood cell counts. RESULTS: Plasmodium falciparum was prevalent among 8.0% (32/400) of schoolchildren with a mean parasite density of 244.3 ± 299.3/µL of blood and most infections showing low-level parasitaemia, whereas Plasmodium vivax was detected in one child (0.25%). Residing near water collections was a significant independent predictor of falciparum malaria [adjusted odds ratio (AOR) = 2.6, 95.0% CI 1.20-5.72; p = 0.016] in schoolchildren. Mild anaemia was prevalent among more than half of P. falciparum-infected schoolchildren and significantly associated with falciparum malaria (AOR = 5.8, 95.0% CI 2.39-14.17; p < 0.001), with a mean Hb concentration of 10.7 ± 1.0 g/dL. Although the mean values of the total white blood cells, monocytes and platelets were significantly lower in infected than non-infected schoolchildren, they were within normal ranges. More than half of the children were malnourished, with stunting (39.3%) and underweight (36.0%) being the most prevalent forms of malnutrition; 6.3% of children were wasted. Underweight (AOR = 5.3, 95.0% CI 2.09-13.62; p < 0.001) but not stunting or wasting, was a significant predictor of falciparum malaria among schoolchildren. CONCLUSION: Asymptomatic falciparum malaria is prevalent among schoolchildren in Bajil district of Hodeidah Governorate, with predominance of low parasitaemic infections and significant association with mild anaemia and underweight. Residence near water collection is a significant predictor of infection with falciparum malaria among schoolchildren. Further studies among children with severe malaria and those with high parasite densities are recommended.

Circulating rotavirus G and P strains post rotavirus vaccination in Eastern Mediterranean Region.

OBJECTIVE: To detect changes in circulating strains of rotavirus in the Eastern Mediterranean Region post rotavirus immunization drive. METHODS: We searched MEDLINE, PubMed, ScienceDirect, and the Cochrane Library and specific database website (Nutrition and Food Sciences) for relevant articles. Our search included websites of a number of relevant organizations in addition to gray literature search. Of the 2198 articles found, we included only 35 studies after excluding irrelevant, ineligible, duplicated, and very low-quality papers. RESULTS: Thirty pre-vaccination studies reported frequent rotavirus strains among children below 5 years of age. G1P[8] has been identified as the most dominant type prior to vaccination in Eastern Mediterranean Region (EMR) countries. Five post-vaccination studies conducted in 3 countries (Saudi Arabia, Morocco, and Yemen) illustrated that G1P[8] is the most prevalent strain in Saudi Arabia, and the incidence of G2P[4] has increased from 21.6% to 33.3%. In Yemen, G1P[4] is the most prevalent strain (87.5%), followed by G9P[8] (57%) and G1P[8] (18.5%). Furthermore, in Yemen, G9P[8] were the most prevalent strains accounting to 57% and 14% in G9P[4], post vaccination. Finally, in Morocco, G1P[8] was not reported 3 years post vaccination; however, incidence of G9P[8] was reported at 67% and G2P[4] at 33%. CONCLUSIONS: Rotavirus circulating strain prevalence in EMR countries has changed post vaccination, and G9P[8], G2P[4], and G9P[4] have become more dominant. Proportion of rotavirus strains in these countries after vaccination has significantly reduced. There is an increase in circulating strain G2P[4] in the post-vaccination period, which needs further monitoring.

Evaluation of rapid PfHRP-2/pLDH-based tests in diagnosing microscopy-confirmed falciparum malaria in Hodeidah governorate, Yemen.

Along with the determination of malaria infection rate among suspected patients attending hospitals in Hodeidah governorate, the present study evaluated the accuracy of Plasmodium falciparum histidine-rich protein-2 (PfHRP-2)/parasite-specific lactate dehydrogenase (pLDH)-based rapid diagnostic test (RDT) for the diagnosis of microscopy-confirmed falciparum malaria. An overall malaria infection rate of 19.3% (57/295) among suspected patients attending hospitals was microscopically confirmed. The sensitivity of thin blood films for the detection of malaria parasites was 79.0% compared to thick films and was greatly affected by the parasite density, being 65.0% or less at parasite densities of ≤1000 parasites/µl of blood. Compared to light microscopy, the present study revealed sensitivity levels of 100.0% (95% CI: 92.0-100.0) vs. 94.7% (95% CI: 84.2-98.6), specificity levels of 97.3% (95% CI: 89.8-99.5) vs. 100.0% (95% CI: 93.9-100.0), positive predictive values of 89.9% (95% CI: 88.3-99.0) vs. 100.0 (95% CI: 91.6-100.0) and negative predictive values of 100.0% (95% CI: 93.9-100.0) vs. 98.7% (95% CI: 89.3-98.7) for the PfHRP-2 and pLDH components of SD BIOLINE® RDT, respectively, for falciparum malaria diagnosis. Therefore, the overall accuracy levels of the PfHRP-2 and pLDH components of the investigated RDT for the diagnosis of microscopy-confirmed falciparum malaria are 98.5% (95% CI: 94.6-99.6) and 97.7% (95% CI: 93.5-99.2), respectively.

The incidence rate of thyroid cancer among women in Saudi Arabia: an observational descriptive epidemiological analysis of data from Saudi Cancer Registry 2001-2008.

This study provides a descriptive epidemiological data of thyroid cancer cases diagnosed from 2001 to 2008 among Saudi women, including the frequency and percentage of cases, the crude incidence rate (CIR) and the age-standardised incidence rate (ASIR) stratified by the region and year of diagnosis. This is a retrospective descriptive epidemiological analysis of all Saudi thyroid cancer cases recorded in the Saudi Cancer Registry (SCR) between January 2001 and December 2008. The statistical analyses were applied using descriptive statistics with the Statistical Package for the Social Sciences version 20.0. A total of 2,930 cases were recorded in the SCR between January 2001 and December 2008. The region of Riyadh in Saudi Arabia had the highest overall ASIR at 9.43 per 100,000 women, followed by Tabuk at 7.11 and eastern region at 6.5, while Jazan and Jouf had the lowest average ASIRs at 1.97 and at 2.72, respectively. The region of Qassim recorded the greatest changes of ASIR at 5.5 per 100,000 women from 2001 to 2008. There was a slight increase in the CIRs and ASIRs for thyroid cancer in Saudi Arabia between 2001 and 2008. Riyadh, Tabuk and eastern region were the highest overall ASIR in Saudi Arabia. While, Jazan and Hail had the lowest rates. Finally, the region of Qassim had the highest changes in CIR and ASIR from 2001 to 2008. Further analytical studies are needed to determine the potential risk factors of thyroid cancer disease among Saudi women.

The pattern of Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive epidemiological analysis of data from the Saudi Ministry of Health.

PURPOSE: This study describes the epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia. PATIENTS AND METHODS: Epidemiological analysis was performed on data from all MERS-CoV cases recorded by the Saudi Ministry of Health between June 6, 2013 and May 14, 2014. The frequency of cases and deaths was calculated and adjusted by month, sex, age group, and region. The average monthly temperature and humidity of infected regions throughout the year was also calculated. RESULTS: A total of 425 cases were recorded over the study period. The highest number of cases and deaths occurred between April and May 2014. Disease occurrence among men (260 cases [62%]) was higher than in women (162 cases [38%]), and the case fatality rate was higher for men (52%) than for women (23%). In addition, those in the 45-59 years and ≥60 years age groups were most likely to be infected, and the case fatality rate for these people was higher than for other groups. The highest number of cases and deaths were reported in Riyadh (169 cases; 43 deaths), followed by Jeddah (156 cases; 36 deaths) and the Eastern Region (24 cases; 22 deaths). The highest case fatality rate was in the Eastern Region (92%), followed by Medinah (36%) and Najran (33%). MERS-CoV infection actively causes disease in environments with low relative humidity (<20%) and high temperature (15°C-35°C). CONCLUSION: MERS-CoV is considered an epidemic in Saudi Arabia. The frequency of cases and deaths is higher among men than women, and those above 45 years of age are most affected. Low relative humidity and high temperature can enhance the spread of this disease in the entire population. Further analytical studies are required to determine the source and mode of infection in Saudi Arabia.