ABSTRACT
This report describes SARS-CoV-2 genomic surveillance conducted by the Department of Defense (DoD) Global Emerging Infections Surveillance Branch and the Next-Generation Sequencing and Bioinformatics Consortium (NGSBC) in response to the COVID-19 pandemic. Samples and sequence data were from SARS-CoV-2 infections occurring among Military Health System (MHS) beneficiaries from 1 March to 31 December 2020. There were 1,366 MHS samples sequenced from 10 countries, 36 U.S states or territories, and 5 Geographic Combatant Commands, representing approxi-mately 2% of DoD cases in 2020. Genomes from these samples were compared with other public sequences;observed trends were similar to those of Centers for Disease Control and Prevention national surveillance in the U.S. with B.1, B.1.2, and other sub-lineages comprising the dominant variants of SARS-CoV-2. Sequence data were used to monitor transmission dynamics on U.S. Navy ships and at military training centers and installations. As new variants emerge, DoD medical and public health practitioners should maxi-mize the use of genomic surveillance resources within DoD to inform force health protection measures. © 2022, Armed Forces Health Surveillance Center. All rights reserved.
ABSTRACT
The first U.S. case of non-travel-related severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was detected in late February 2020 in California, but the prevailing delay in diagnostic testing and initial stringent testing criteria made it difficult to identify those who could have acquired the virus through community spread. The emergence of the virus in the western Pacific region in late 2019 and the global distribution of Department of Defense (DoD) personnel present the risk that DoD members may have been exposed and contracted the virus earlier then U.S. detections. Here, a retrospective study from residual samples collected from a global DoD Respiratory Surveillance Program was conducted to establish a tentative timeline of when this virus began circulating in the DoD population. Quantitative real-time reverse-transcription polymerase chain reaction testing for SARS-CoV-2 was performed and the specimen collection dates of positive results were compared to the dates of the first infections previously identified in respective states and counties. Twenty-four positive samples were identified out of approximately 7,000 tested. Although this retrospective testing found early cases in 8 locations, there were no results indicative of circulation before late February.
ABSTRACT
Introduction: As the world struggles to manage and move forward from the clinical effects of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the ability to test for viral genomic RNA in patient samples is critical. Currently, the development and performance of SARS-CoV-2 clinical tests is impaired by a diminished supply chain of reagents needed for the tests, compelling labs to seek alternative, readily-available reagents as substitutes. Aim: To evaluate the suitability of Phosphate-Buffered Saline (PBS) and RNAlater™ as substitutes for sample transport media, to preserve the fidelity of viral RNA for use in a SARSCoV-2 RT-PCR assay. Materials and Methods: This molecular study was conducted in Dayton, Ohio (USA) using synthetic materials and de-identified remnant patient specimens. Simulated standard clinical laboratory storage conditions were used, including prolonged storage up to 72 hours at 2-8°C and a freeze/thaw cycle. PCR amplification performance was measured for PBS and RNAlater™ against transport medium as a reference using purified viral RNA. Performance differences were determined using repeated-measures two-way ANOVA with a 5% false discovery rate. Results: Results indicate that both solutions were suitable for testing viral RNA in the short term, but the viral RNA stored in PBS began to degrade after just 24 hours at 2-8°C. In contrast, RNAlater™ preserved the viral RNA out to 72 hours when stored at 2-8°C, with no statistically significant decrease in the detection limits compared to freshly-prepared viral RNA dilutions. A single freeze/thaw cycle raised the lower limit of detection for RNAlater™-preserved viral RNA slightly. Conclusion: The current (as of April 2020) CDC sample guidelines permit the use of PBS, but have not published data to support this claim. These results offer an alternative to the transport options outlined in many Emergency Use Authorisations (EUA) currently authorised for use in diagnostic testing and may be used for possible long-term storage solutions for studies investigating SARS-CoV-2.