ABSTRACT
Introduction/Objective In both the past and for the foreseeable future, SARS-CoV-2 (the coronavirus that causes COVID-19 disease) will continue to evolve. This evolution has already and will lead to new variants that will then cause surges of infection. These outbreaks in the past with the variant responsible have previously been reported individually. However, a timeline perspective on the changing SARS-CoV-2 variant landscape is sparse in the literature, particularly for testing performed at a Veteran Affairs Medical Center (VAMC). The Veteran population has increased comorbidities compared to the general population leading to susceptibility to infection including SARS-CoV-2. Hence, it is of utmost importance to explore the trending variants of SARS-CoV-2 in the veteran population as this epidemiological information may help in preventing transmission, which remains key in the management of COVID-19. Methods/Case Report Samples from selected patients from March 2021 to June 2022 who tested positive for SARS- CoV-2 by reverse transcriptase polymerase chain reaction with a cycle threshold or number <30 (required for sequencing) were sent for SARS-CoV-2 sequencing analysis. Results (if a Case Study enter NA) There were a total of 19 VAMC patients who were sequenced during the entire study period (March 2021 to June 2022). From March to May 2021, there were 8 patients, from which 6 demonstrated Pango Lineage B.1.1.7, 1 demonstrated Pango Lineage B.1.526.1, and 1 demonstrated Pango Lineage B.1. Later in 2021 (August to October 2021), there were 4 patients all of which demonstrates the Delta variant;2 of these 4 demonstrated the Delta subvariant Pango Lineage AY.25 and the other 2 demonstrated Pango Lineage AY.44. By May to June 2022, there were 7 patients, all of whom demonstrated infection by the Omicron variant. Interestingly, 6 of these 7 patients demonstrated the newly emerging subvariant BA.2.12.1 and the remaining 1 demonstrated BA.2.9. Conclusion SARS-CoV-2 has continued to evolve throughout the course of the pandemic, which has led to variants and subvariants that have predominated for a time to cause an outbreak only to be replaced later by a different strain. This timeline epidemiological perspective demonstrates that the Veteran population has also been affected by the variants that have led to outbreaks in the past within the general population.
ABSTRACT
Introduction/Objective Much was unknown initially regarding the triaging of scarce resources to manage the COVID-19 disease, particularly for prognosticating hospital admission needs, which contributed to the healthcare resource supply crisis. Thus, the authors developed the simple Jhala Risk Scoring System (JRSS). There is no report in the English literature that has explored a risk scoring system in patients with a SARS-CoV-2 sequencing result demonstrating different SARS-CoV-2 strains;hence, presented here is a first report. Methods/Case Report The JRSS assesses risk factor points based on patient's age, ethnicity, pulmonary medical history, cardiovascular medical history, diabetes history, smoking history, and laboratory parameters. From the veteran patients who had been sequenced for COVID-19 from March 2021 to June 2022 with available clinical notes or follow-up, the JRSS was applied to obtain a JRSS score. This JRSS score was then compared with the patient's admission status, SARS-CoV-2 sequence result, and survival. A JRSS score of 7 or greater would designate higher risk. Results (if a Case Study enter NA) There were a total of 11 COVID-19 positive patients meeting the inclusion criteria during the study period. 4 of these 11 patients were from March to May 2021. The patient ages ranged from 55-80 years of age and consisted of 2 Caucasian Americans and 2 African Americans. Of these 4 patients, 1 was treated as an outpatient (JRSS score 2), 2 were treated in the intensive care unit within which 1 expired (both JRSS score 9), and 1 was treated on the medical floor (JRSS score 7). All 4 patients from March to May 2021 sequenced to have Pango Lineage B.1.1.7. 7 of the 11 patients were from May to June 2022. The patient ages ranged from 69-86 years of age and consisted of 4 Caucasian Americans, 2 African Americans, and 1 decline to state. Of these 7 patients, 1 patient expired in the CLC (JRSS score 10). 5 recovered within the CLC with JRSS scores of 5, 7, and 8 for 2, 1, and 2 patients respectively. One patient required hospitalization (JRSS of 6 based clinically only as lab parameters were not performed). All 7 patients except for 1 sequenced for BA.2.12.1, a subvariant of Omicron. The 1 patient who sequenced with a different Omicron subvariant (BA.2.9) was one of the 5 patients who recovered from infection within the CLC. Conclusion The JRSS, developed early in the pandemic, is a very simple and highly successful system that helps in prognostication even with the Omicron outbreak.
ABSTRACT
Introduction/Objective The extraordinary circumstances of the highly contagiousSARS-CoV-2 pandemic have led the FDA to approve diagnosticassays with emergency use authorizations (EUA). One of theseassays is the Abbott RealTime SARS-CoV-2 assay (Abbott Park, Ill.). However, the literature is sparse on the validation of EUAassays for SARS-CoV-2 assays for this crisis;therefore, wepresent the Veteran Affairs Medical Center (VAMC) experiencein validating/verifying this test for clinical use. Methods Validation/verification was performed in three parts as part of quality assurance/quality improvement;1) sample/patientcorrelation, 2) precision, and 3) validation/verification of accuracy at the lower limit of detection (LOD). The results from these studies was compiled, reviewed by the laboratory, and after performance was deemed satisfactory, the test would beput for clinical use. Results For the sample/patient correlation, a total of 68 known positive and 59 known negative samples were run;these included 56positive contrived samples or controls, 12 known positivepatient samples, 31 negative contrived or controls, and 28 known negative patient samples. All results from the assay were as expected with 100% positive and negative percent agreementexcept for one sample that was quantity not sufficient fortesting. The precision study with 4 known positive and 4 knownnegative samples run once per day for 5 days yielded perfect100% precision for both the positive and negative samples.Replicates to determine accuracy at the lower LOD (100 viruscopies/ml per instructions for use of the assay) demonstratedaccuracy even with dilutions down to 50 virus copies/ml. For this third step, 3 replicates each had been performed at 1000,500, 250, 70, 60 and 50 virus copies/ml. As 100 virus copies/ml was the provided manufacturer LOD, 7 replicates were performed at 100 virus copies/ml. Conclusion The validation/verification indicated that the Abbott RealTimeSARS-CoV-2 assay performed with expectations including with real patient samples and could be put into clinical use at theVAMC. After this validation/verification, the assay has been verysuccessfully used for in-house testing for SARS-CoV-2. In fact, the validation demonstrated an LOD as low as 50 viruscopies/ml, suggesting the assay may be even more sensitive tolow levels of viremia than is stated in the EUA.