Genetic analysis of human parainfluenza type 2 virus in Riyadh, Saudi Arabia.

The extensive mass gathering of pilgrims from all over the world, as well as the constant flow of foreign workers via country entry crossings, raises the likelihood of respiratory virus outbreaks spreading and evolving in Saudi Arabia. Here, we report the sequence and phylogenetic analysis of the human parainfluenza type-2 (HPIV-2) in nasopharyngeal aspirates (NPAs) collected from Riyadh, Saudi Arabia, from 2020/21 to 2021/22 seasons. RNA was extracted from the clinical samples and subjected to RT-PCR analysis for the detection of IAV and IBV. The full-length HN gene of HPIV-2 was amplified and sequenced. Multiple sequence alignments (both nucleotides and deduced amino acids) were aligned using Clustal W, MegAlign program of Lasergene software, and MEGA 7.0. HPIV-2 was found in (4; 2% of 200) NPAs. Sequence and phylogenetic analysis results showed that indicated a genotype shifting from G3 to G4a with 83% sequence homology 62-M786 from Japan, which was prominent throughout the winter seasons of 2008/09. Multiple amino acid sequence alignment revealed 25 sites of possible difference between G3 genotypes and G4a. A total of twenty- two of these locations were shared by the other G4a genotypes, whereas three positions, 67 V, 175 S, and 377Q, were exclusively shared by G3. Only eight conserved N-glycosylation sites were found at amino acids 6(NLS), 286(NTT), 335(NIT), 388(NNS), 498(NES), 504(NPT), 517(NTT), and 539(NGT) in four Riyadh isolates. Our findings also revealed that the G4a genotype of HPIV-2 predominated in our samples population during the winter seasons of 2020/21 and 2021/22. Further research with a larger sample size covering numerous regions of Saudi Arabia throughout different epidemic seasons is needed to achieve an improved knowledge of HPIV-2 circulation.

The emergence of subgenotype ON-1 of Human orthopneumovirus type A in Riyadh, Saudi Arabia: A new episode of the virus epidemiological dynamic.

Lower respiratory tract infections caused by Human orthopneumovirus are still a threat to the pediatric population worldwide. To date, the molecular epidemiology of the virus in Saudi Arabia has not been adequately charted. In this study, a total of 205 nasopharyngeal aspirate samples were collected from hospitalized children with lower respiratory tract symptoms during the winter seasons of 2014/15 and 2015/16. Human orthopneumovirus was detected in 89 (43.4%) samples, of which 56 (27.3%) were positive for type A and 33 (16.1%) were positive for type B viruses. The fragment that spans the two hypervariable regions (HVR1 and HVR2) of the G gene of Human orthopneumovirus A was amplified and sequenced. Sequence and phylogenetic analyses have revealed a genotype shift from NA1 to ON-1, which was prevalent during the winter seasons of 2007/08 and 2008/09. Based on the intergenotypic p-distance values, ON-1 was reclassified as a subgenotype of the most predominant genotype GA2. Three conserved N-glycosylation sites were observed in the HVR2 of Saudi ON-1 strains. The presence of a 23 amino acid duplicated region in ON-1 strains resulted in a higher number of O-glycosylation sites as compared to other genotypes. The data presented in this report outlined the replacement of NA1 and NA2 subgenotypes in Saudi Arabia with ON-1 within 7 to 8 years. The continuous evolution of Human orthopneumovirus through point mutations and nucleotide duplication may explain its ability to cause recurrent infections.

Viruses causing lower respiratory symptoms in young children: findings from the ORChID birth cohort.

INTRODUCTION: Viral acute respiratory infections (ARIs) cause substantial child morbidity. Sensitive molecular-based assays aid virus detection, but the clinical significance of positive tests remains uncertain as some viruses may be found in both acutely ill and healthy children. We describe disease-pathogen associations of respiratory viruses and quantify virus-specific attributable risk of ARIs in healthy children during the first 2 years of life. METHODS: One hundred fifty-eight term newborn babies in Brisbane, Australia, were recruited progressively into a longitudinal, community-based, birth cohort study conducted between September 2010 and October 2014. A daily tick-box diary captured predefined respiratory symptoms from birth until their second birthday. Weekly parent-collected nasal swabs were batch-tested for 17 respiratory viruses by PCR assays, allowing calculation of virus-specific attributable fractions in the exposed (AFE) to determine the proportion of virus-positive children whose ARI symptoms could be attributed to that particular virus. RESULTS: Of 8100 nasal swabs analysed, 2646 (32.7%) were virus-positive (275 virus codetections, 3.4%), with human rhinoviruses accounting for 2058/2646 (77.8%) positive swabs. Viruses were detected in 1154/1530 (75.4%) ARI episodes and in 984/4308 (22.8%) swabs from asymptomatic periods. Respiratory syncytial virus (AFE: 68% (95% CI 45% to 82%)) and human metapneumovirus (AFE: 69% (95% CI 43% to 83%)) were strongly associated with higher risk of lower respiratory symptoms. DISCUSSION: The strong association of respiratory syncytial virus and human metapneumovirus with ARIs and lower respiratory symptoms in young children managed within the community indicates successful development of vaccines against these two viruses should provide substantial health benefits.

A retrospective performance evaluation of an adenovirus real-time PCR assay.

Human adenoviruses (AdVs) cause a wide range of diseases. To date, there are at least 60 known human AdV types and, as these exhibit high levels of genetic variation this could impact potentially upon their detection by polymerase chain reaction (PCR)-based technology. Here, the sensitivity of a pan-AdV real-time PCR assay (AdV-PCR) used widely for testing clinical samples was determined retrospectively. An in silico analysis was performed initially using the 370 AdV sequences available on the Genbank database. To investigate for potential false-negative results, two additional AdV-PCR assays were used to re-evaluate 779 respiratory samples submitted for virus testing and 1,012 nasal swab samples collected as part of an ongoing community-based study. The results were then compared to those obtained by AdV-PCR. In silico analysis showed the presence of mismatches in the AdV-PCR primers and probe for most AdV sequences available on Genbank. Notably, 215 of the 370 (58%) sequences had at least three mismatches with the AdV-PCR forward primer. Of the 779 clinical samples, 88 were identified as AdV-positive, of which 84 were positive by the AdV-PCR. The four samples providing false-negative results in the AdV-PCR had high cycle threshold values in the other methods suggesting that sampling at low load, rather than sequence variation, was responsible for the negative results. No false-negative AdV-PCR results were observed for the community-based study samples. Reassuringly, the results show that despite the high level of sequence variation in the AdV-PCR assay oligonucleotide targets, the assay remains suitable for routine detection of human AdV strains.

Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control.

BACKGROUND: Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS: Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS: In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION: Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies.

Human bocavirus in Saudi Arabia: Molecular epidemiology and Co-infections among children with acute respiratory tract infections during 2014-2016.

Respiratory tract infections due to a variety of viruses continue to threaten the human population worldwide, particularly in developing countries. Among the responsible viruses, Human Bocavirus (HBoV), a novel discovered virus, causes respiratory tract and gastroenteritis disorders in young children. In Saudi Arabia, data regarding virus molecular epidemiology and evolution and its implication in respiratory tract infection are scarce. In the current study, genetic diversity and circulation pattern of HBoV-1 among hospitalized children due to acute respiratory tract infection (ARTI) during two consecutive years were charted. We found that 3.44% (2014/2015) and 11.25% (2015/2016) of children hospitalized due to ARTI were infected by HBoV-1. We have shown that HBoV was detected year-round without a marked seasonal peak. HBoV-1 also was co-detected with one or multiple other respiratory viruses. The multisequence analysis showed high sequence identity (∼99%) (few point mutation sites) between strains of each genotype and high sequence variation (∼79%) between HBoV-1 and the other 3 genotypes. Phylogenetic analysis showed the clustering of the study's isolates in the HBoV-1 subclade. Our data reveal that genetically conserved HBoV-1 was circulating among admitted children during the course of the study. Further epidemiological and molecular characterization of multiple HBoV-1 strains for different years and from all regions of Saudi Arabia are required to understand and monitor the virus evolution.

Distribution of Private Dental Healthcare Facilities in Riyadh City: A GIS-Based Approach.

BACKGROUND: The dental healthcare private sector in Riyadh city has been growing rapidly over the past few years; however, there is a lack of information on the accessibility and spatial distribution of private dental healthcare facilities (PDHFs) in the area. This study aimed to evaluate the spatial distribution of PDHFs in Riyadh city in relation to population density in each sub-municipality. METHODS: The current information regarding the number, location, and operability of PDHFs in Riyadh city was obtained from the Ministry of Health. A total of 632 operating PDHFs were included with the precise location plotted on Quantum Geographic Information System software (version 3.32.1, Essen, Germany) using Google Earth. Four levels of buffer zones-1 km, 3 km, 5 km, and >5 km-were determined. The population statistics and mean monthly individual income per district were gathered from Zadd.910ths. Microsoft Excel (version 16.0, Microsoft, Redmond, WA, USA) and RStudio software (version 4.1.3, Posit Software, PBC, Boston, MA, USA) were used for additional data analysis. RESULTS: There was an overall ratio of one PDHF per 9958 residents in Riyadh city. Olaya and Maather sub-municipalities had the largest PDHF-to-population ratios: (1:4566) and (1:4828), respectively. Only 36.3% of the city's total area was within a 1 km buffer zone from a PDHF. There was an overall weak positive correlation between the number of PDHFs and the total area in each sub-municipality (r = 0.29), and the distribution of PDHFs was uneven corresponding to the area (G* = 0.357). CONCLUSIONS: There was an uneven distribution of PDHFs in Riyadh city. Some areas were underserved while others were overserved in several sub-municipalities. Policy-makers and investors are encouraged to target underserved areas rather than areas with significant clustering to improve access to care.

Phytochemical analysis, antioxidant, anticancer, and antibacterial potential of Alpinia galanga (L.) rhizome.

Alpinia galanga (L.) Willd. (A. galanga) is extremely significant and is utilized extensively in traditional medicine throughout many nations. This study aimed to determine the chemical composition of A. galanga rhizome extract (AgRE) and to evaluate its antioxidant, anticancer, and antibacterial activities. The total phenolic content (TPC) and total flavonoid content (TFC) of AgRE were determined. The antioxidant activity, cytotoxic capability, and antibacterial of were assessed, as well as anti-apoptotic genes. Molecular docking (MD) was used to assess the binding affinity of the most enriched constituents in AgRE toward the active sites of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and p53 tumor suppressor protein (TP53). Gas chromatography-mass spectrometry (GC-MS) analysis demonstrated that AgRE is a rich source of turmerone. AgRE had moderate 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging properties, with the half-maximal inhibitory concentration (IC50) values of 79.34 ± 1.78 and 88.94 ± 2.28 µg/ml, respectively. AgRE preferentially reduced the viability of a subset of malignant MCF-7 and HepG2 cell lines, with IC50 of 125.35 ± 4.28 and 182.49 ± 3.19 µg/ml, respectively. AgRE exhibited considerable antimicrobial activity against all bacterial strains, with MIC values ranging from 7.81 ± 1.53 to 62.5 ± 3.28 µg/ml. The MD results revealed that ethyl-4-(2-methylpropyl)-benzene had the greatest binding energy with NADPH oxidase, with a Glide score of -6848 kcal/mol, followed by 2-methoxy-phenol (-5111 kcal/mol). Taken together, we report the interesting antioxidant, antibacterial, and anticancer properties of AgRE, which warrant further investigation. AgRE is a promising natural resource that could be used to combat complicated diseases such as cancer and bacterial infections.

Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia.

The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies.

Molecular Profiling of Inflammatory Mediators in Human Respiratory Syncytial Virus and Human Bocavirus Infection.

Infections due to human respiratory syncytial virus (HRSV) and human bocavirus (HBoV) can mediate the release of several pro-inflammatory cytokines such as IL-6, IL-8, and TNF-α, which are usually associated with disease severity in children. In this study, the change in the expression profile of cytokines and chemokines were determined during HRSV, HBoV, and HRSV coinfection with HBoV in 75 nasopharyngeal aspirates (NPAs) samples, positive real-time reverse transcriptase PCR Assay (rRT-PCR) for HRSV (n = 36), HBoV (n = 23) infection alone or HRSV coinfection with HBoV (n = 16). The samples were collected from hospitalized children. qPCR-based detection revealed that the levels of IL-6, IL-8, IL-10, IL-13, IL-33, and G-CSF were significantly (p < 0.05) greater in patients than in controls. IL-4, IL-17, GM-CSF, and CCL-5 were significantly elevated in children with HRSV coinfection with HBoV than in other groups (p < 0.05). TNF-α, IL-6, IL-8, IL-10, IL-13, and IL-33 in children with HRSV were significantly increased in severe infections compared to mild infections. Whereas, IL-10, IL-13, and IL-33 were significantly increased in severe infection in compared a mild infection in children with HBoV. Further large-scale investigations involving isolates are needed to enhance our knowledge of the association between viral infections and cytokine expression patterns during the different stages of HRSV and HBoV infection.