SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia.

INTRODUCTION: In December 2019, a new severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China, causing coronavirus disease 2019. The present study investigated genetic profiles and variations of SARS-CoV-2 distributed in different regions of Saudi Arabia to begin to understand the pathogenesis and transmission of SARS-CoV-2 in this country and analyzed associations of these variations with host factors. METHODOLOGY: In total, 774 SARS-CoV-2 genomic sequences obtained and annotated by the Global Initiative on Sharing All Influenza Data (GISAID) were captured and analyzed. RESULTS: The most common SARS-CoV-2 clades in Saudi Arabia were GH followed by O, GR, G, and S. Statistically significant associations were detected between clades and patient outcome. Age, as a host factor, was significantly associated with many variables, including virus geographical location, clade, and patient outcome. The most common variants detected were the NSP12_P323L mutation 94.9%, followed by the D614G mutation (76%) and the NS3_Q57H mutation (71.4%). The concerned variants B.1.1.7, B.1.351, and P.1 were not detected in our population. D614G was associated with higher morbidities than the wild-type virus, including higher rates of death and hospitalization. The NS3_Q57H mutation was the only variant associated with better patient outcome than the wild type. Risk of death was highest with the NSP12_P323L mutation (OR = 1.84; 95% CI = 0.37-9.30) and lowest with the NS3_Q57H mutation (OR = 0.43; 95% CI = 0.25-0.727). CONCLUSIONS: SARS-CoV-2 has evolved uniquely and independently in Saudi Arabia. Our findings provide evidence to begin linking the evolutionary implications to host factors and their effects on the virus severity and transmission.

Demand management and optimization of clinical laboratory services in a tertiary referral center in Saudi Arabia.

BACKGROUND: Demand for clinical laboratory services in our insti.tution has increased by 7% each year in the past 5 years, while the amount budgeted for services has remained fixed. To address the issue, we conducted a pilot study to curb inappropriate demand by implementing a minimum retest interval (time-based restrictions on the ordering certain tests) and thus reduce costs. OBJECTIVE: Explore the impact (financial and work volume) of restricting overuse of laboratory tests that add to costs but provide no additional clinical value. DESIGN: Pilot study of means to reduce costs and workload. SETTING: Clinical laboratory that provides diagnostic support to a tertiary care center specializing in transplantation and oncology. METHODS: With the engagement of clinical colleagues, we selected 13 tests characterized by high volume, high cost, or a perception of overuse that adds no clinical value. The selection was also based on established lock-out frequencies identified in a literature review. Data was captured on test numbers before and after initiating computer-based lock-outs along with the reference laboratory cost of these tests for the first 6 months of 2016 and 2017. MAIN OUTCOME MEASURES: Alterations in testing patterns (mimimum retest intervals) and frequencies for tests. RESULTS: The number of tests ordered during the 6-month period in 2017 were reduced by an average of 6.6% versus the same period for 2016, saving 2.03 million Saudi Arabian Riyals (SAR). Given a 7% annual growth in the preceding 5 years, the volume was reduced by 13% in real terms. The percentage reduction in number of tests ranged from as little as 0.2% for PT to 70.3% for an enzyme immunoassay. Savings were 1.4 million SAR in hematology and 0.36 million SAR in microbiology over the 6-month period. CONCLUSION: Minimum retest intervals using computer-based rules are effective in supporting strategies to manage demand. LIMITATIONS: This approach may not be applicable to all laboratory tests; however, the success of this pilot study would encourage more widespread use of this approach. CONFLICT OF INTEREST: None.

Phylogenetic and nucleotide sequence analysis of influenza A (H1N1) HA and NA genes of strains isolated from Saudi Arabia.

INTRODUCTION: In early 2009, a novel influenza A (H1N1) virus appeared in Mexico and rapidly disseminated worldwide. Little is known about the phylogeny and evolutionary dynamics of the H1N1 strain found in Saudi Arabia. METHODOLOGY: Nucleotide sequencing and bioinformatics analyses were used to study molecular variation between the virus isolates. RESULTS: In this report, 72 hemagglutinin (HA) and 45 neuraminidase (NA) H1N1 virus gene sequences, isolated in 2009 from various regions of Saudi Arabia, were analyzed. Genetic characterization indicated that viruses from two different clades, 6 and 7, were circulating in the region, with clade 7, the most widely circulating H1N1 clade globally in 2009, being predominant. Sequence analysis of the HA and NA genes revealed a high degree of sequence identity with the corresponding genes from viruses circulating in the South East Asia region and with the A/California/7/2009 strain. New mutations in the HA gene of pandemic H1N1 (pH1N1) viruses, that could alter viral fitness, were identified. Relaxed-clock and Bayesian Skyline Plot analyses, based on the isolates used in this study and closely related globally representative strains, indicated marginally higher substitution rates than the type strain (5.14×10-3 and 4.18×10-3 substitutions/nucleotide/year in the HA and NA genes, respectively). CONCLUSIONS: The Saudi isolates were antigenically homogeneous and closely related to the prototype vaccine strain A/California/7/2009. The antigenic site of the HA gene had acquired novel mutations in some isolates, making continued monitoring of these viruses vital for the identification of potentially highly virulent and drug resistant variants.

Mycobacterium chelonae complex bacteremia from a post-renal transplant patient: case report and literature review.

In this report we present a case of a young lady with abdominal abscesses and septicemia caused by Mycobacterium chelonae complex. Identification of the organism and initiation of the appropriate antimicrobial therapy was delayed, resulting in significant morbidity and multiple hospital admissions. Gram staining of these organisms from blood culture can be easily overlooked or confused with either debris or diptheroids. We concluded that detection of Gram-positive rod colonies should prompt an acid-fast stain to distinguish diphtheroids from rapidly growing mycobacteria in immunosuppressed patients.