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Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.

In poultry production, birds are raised under intensive conditions, which can enable rapid spread of infections, with Clostridium perfringens-caused necrotic enteritis (NE) being one of the most devastating for the industry. The current investigation was conducted to evaluate the effectiveness of Bacillus subtilis PB6 probiotic supplementation on bird's post NE recovery, based on chicken performance, cecal microbiota composition, ileum histomorphometric measurements, and short-chain fatty acid production in the cecum of the birds that were challenged with NE mid-production. Birds were split into four groups, including a negative control, positive control challenged with C. perfringens, group supplemented with B. subtilis probiotic, and NE challenged birds supplemented with B. subtilis probiotic. Following NE challenge birds were allowed to reach the end of production time at 40 days, and samples were collected to estimate if probiotic supplementation resulted in better post-NE recovery. Intestinal lesion score across the duodenum, jejunum, and ileum indicated that at the end of production timeline NE challenged birds supplemented with B. subtilis probiotic had lower intestinal lesion scores compared to NE challenged birds without probiotic supplementation implying improved recovery. Probiotic supplementation improved performance of NE challenged birds only in the post-NE recovery stage. NE challenged birds had a significant increase in cecal propionic acid, which was not observed in NE challenged birds supplemented with B.subtilus. Both B. subtilis supplemented groups (challenged and unchanged) were characterized by a significant rise in cecal acetic and butyric acid. Our results demonstrate that B. subtilis supplementation can assist the birds in dealing with NE outbreak and long term recovery.

Artemisia absinthium L., is a plant with established pharmacological properties, but the A. absinthium root extract (AARE) remains unexplored. The aim of this study was to examine the chemical composition of AARE and assess its biological activity, which included antidiabetic, antibacterial, anticancer, and antioxidant properties. GC-MS was used to analyze the chemical components. The antioxidant activity of the total phenolic and flavonoid content was evaluated. Antibacterial activity and cytotoxic effects were identified. Enzyme inhibition experiments were performed to determine its antidiabetic potential. Molecular docking was utilized to evaluate the potential antioxidant, antibacterial, and anticancer activities of the compounds from AARE using Maestro 11.5 from the Schrödinger suite. AARE exhibited moderate antioxidant activity in DPPH (IC50: 172.41 ± 3.15 μg/mL) and ABTS (IC50: 378.94 ± 2.18 μg/mL) assays. Cytotoxicity tests on MCF-7 and HepG2 cancer cells demonstrated significant anticancer effects, with IC50 values of 150.12 ± 0.74 μg/mL and 137.11 ± 1.33 μg/mL, respectively. Apoptotic studies indicated an upregulation of pro-apoptotic genes (caspase-3, 8, 9, Bax) and a downregulation of anti-apoptotic markers (Bcl-2 and Bcl-Xl). AARE also inhibited α-amylase and α-glucosidase, suggesting potential antidiabetic effects, with IC50 values of 224.12 ± 1.17 μg/mL and 243.35 ± 1.51 μg/mL. Antibacterial assays revealed strong activity against Gram-positive bacteria. Molecular docking and pharmacokinetic analysis identified promising inhibitory effects of key AARE compounds on NADPH oxidase, E. coli Gyrase B, and Topoisomerase IIα, with favorable drug-like properties. These findings suggest AARE’s potential in treating cancer, diabetes, and bacterial infections, warranting further in vivo and clinical studies.

MERS-CoV is a zoonotic virus that has emerged in humans in 2012 and caused severe respiratory illness with a mortality rate of 34.4%. Since its appearance, MERS-CoV has been reported in 27 countries and most of these cases were in Saudi Arabia. So far, dromedaries are considered to be the intermediate host and the only known source of human infection. This study was designed to determine the seroprevalence and the infection rate of MERS-CoV in slaughtered food-camels in Riyadh, Saudi Arabia. A total of 171 nasal swabs along with 161 serum samples were collected during the winter; from January to April 2019. Nasal swabs were examined by Rapid test and RT-PCR to detect MERS-CoV RNA, while serum samples were tested primarily using S1-based ELISA Kit to detect MERS-CoV (IgG) antibodies and subsequently by MERS pseudotyped viral particles (MERSpp) neutralization assay for confirmation. Genetic diversity of the positive isolates was determined based on the amplification and sequencing of the spike gene. Our results showed high prevalence (38.6%) of MERS-CoV infection in slaughtered camels and high seropositivity (70.8%) during the time of the study. These data indicate previous and ongoing MERS-CoV infection in camels. Phylogenic analysis revealed relatively low genetic variability among our isolated samples. When these isolates were aligned against published spike sequences of MERS-CoV, deposited in global databases, there was sequence similarity of 94%. High seroprevalence and high genetic stability of MERS-CoV in camels indicating that camels pose a public health threat. The widespread MERS-CoV infections in camels might lead to a risk of future zoonotic transmission into people with direct contact with these infected camels. This study confirms re-infections in camels, highlighting a challenge for vaccine development when it comes to protective immunity.

Background/Objectives: Although several studies have shed light on the epidemiology of the influenza A/H3N2 subtype in Saudi Arabia, the knowledge regarding the molecular epidemiology and genetic diversity of the A/H3N2 subtype in the Riyadh region is still significantly restricted. Thus, the current research intends to investigate the molecular epidemiology and circulation patterns of the influenza A/H3N2 subtype in Riyadh, Saudi Arabia, over the past 9 years. Methods: A total of 380 nasopharyngeal aspirate samples (NPAs) (winter seasons 2020–2023) were screened for the presence of A/H3N2 subtype. Results: Sixty-five samples (17.11%) were found to be positive for the influenza A virus (IAV). A/H3N2 subtype 35 (9.21%) slightly predominated over A/H1N1 pdm09 30 (7.89%), the incidence rate was high in males (16.47%), and the most affected group was the 0–4 age group (14, 14.75%). The phylogenetic analysis revealed that the majority of Riyadh A/H3N2 samples were categorized into the sub-clades 3c.2a1b.1a and 3c.2a1b.1b, which did not exhibit any exclusive clustering with the vaccine strains. Out of the 20 amino acid substitutions detected in the HA1 domain of A/H3N2 strains, 9 were not found in any of the vaccine strains. The HA protein from the Riyadh samples has 8–11 N-glycosylation sites, some of which have been recorded in vaccine strains, yet are lacking in all strains analyzed in this study. Conclusions: As a result, the flu vaccines administered in Saudi Arabia might need to be reevaluated to incorporate additional vaccine strains that are more pertinent to those currently circulating in the recent epidemic seasons in Saudi Arabia.

Background/Objectives: Human Respiratory Syncytial Virus (HRSV) is a major global cause of acute lower respiratory infections in children. With recent approval of pre-fusion F protein-based vaccines and monoclonal antibodies, ongoing molecular surveillance is critical. This study examined HRSV molecular epidemiology and evolution in Riyadh, focusing on mutations in the attachment (G) and fusion (F) glycoproteins and their potential impact on vaccine efficacy. Methods: Nasopharyngeal aspirates (NPAs) (200 samples) were collected from pediatric patients. HRSV-positive samples were typed, and the G gene hypervariable region and F gene were sequenced. Sequence and phylogenetic analyses were performed to identify circulating genotypes and amino acid substitutions. Results: HRSV was detected in 15% of samples, with HRSV-B slightly predominant over HRSV-A. Infants aged 2–5 months had the highest incidence rate of infection. The ON1 subgenotype remained dominant. The duplicated region of the G gene showed constrained evolution, with 18 variable and 6 conserved residues over 13 years. In the F protein, HRSV-A isolates exhibited high conservation, with only three amino acid substitutions in antigenic sites (Ø and II). Sites III, IV, and V remained fully conserved. In contrast, HRSV-B isolates displayed eight substitutions in antigenic sites, including six in site II (palivizumab-binding epitope). Conclusions: Given the highly effective HRSV prophylactics, including the approved vaccines and monoclonal antibodies, these mutations raise critical concerns regarding vaccine efficacy against HRSV-B. These findings underscore the necessity of sustained, seasonal molecular surveillance to monitor the emergence of variants and provide a molecular basis for further clinical studies.

Background/Objectives: Influenza A virus undergoes continuous antigenic drift, necessitating annual vaccine reformulation. Saudi Arabia faces unique epidemiological challenges owing to mass gatherings during religious pilgrimages and the dynamic movement of foreign workers. This study aimed to characterize the genetic diversity of hemagglutinin (HA) and neuraminidase (NA) genes of influenza A viruses circulating in Riyadh and to assess their match with vaccine strains during the 2024–2025 period. Methods: Nasopharyngeal samples (n = 363) were collected from patients presenting with influenza-like illness. RT-PCR was used for detection and subtyping. Sequence and phylogenetic analysis of the complete HA and NA gene sequences from A/H1N1pdm09 strains (n = 7) were then performed. Results: Of the 363 samples, 110 (30.3%) were positive for influenza A; among these, 68 (61.8%) were A/H1N1pdm09, and 42 (38.2%) were H3N2. Phylogenetic analysis revealed that all A/H1N1pdm09 strains belonged to clade 5a.1, distinct from vaccine strains. In comparison with the vaccine strain A/Wisconsin/67/2022, seven amino acid substitutions in the HA gene and eight in the NA gene were recorded in Saudi circulating strains. The significant genetic divergence between circulating A/H1N1pdm09 strains and current vaccine strains indicates potential vaccine mismatch. Conclusions: The significant genetic divergence between circulating A/H1N1pdm09 strains and current vaccine strains suggests potential vaccine mismatch. Continuous surveillance programs along with vaccination plans are necessary to tackle the changing influenza A virus strains in the special epidemiological context of Saudi Arabia.

SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations’ associations with clinical outcomes.

Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.

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.