VIROLOGIC AND BIOINFORMATIC ANALYSIS OF SARS-COV-2 TO FACILITATE EVIDENCE-BASED PUBLIC-POLICY AND NEXT-GENERATION VACCINE DESIGN
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2023
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Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19), has been the scourge of the world for the past three years. Worldwide, over 619 million cases of COVID-19 have resulted in over 6.5 million deaths. Hawaiʻi has not been spared from this pandemic, with more than 349,000 cases of COVID-19 and 1,691 deaths, with considerable caseloads among ethnic populations. The work herein combines virology, bioinformatics, and algorithms to discover new mutations, evaluate COVID-19 public policy, and facilitate the standardization of next-generation vaccine design. A better understanding of the responses to the COVID-19 pandemic, SARS-CoV-2 evolution, and the future of SARS-CoV-2 in endemicity is needed.
First, we sequence the S gene of SARS-CoV-2 positive nasal and oropharyngeal swabs acquired from Hawaiʻi. These sequences were then phylogenetically evaluated against sequences from around the world to determine if multiple introductions of SARS-CoV-2 were evident in Hawaiʻi. After finding that multiple introductions were present, we evaluated the S gene of the sequences found in Hawaiʻi and discovered the P681H amino acid substitution. We then evaluated the P681H substitution against all worldwide sequences and demonstrated a worldwide emergence pattern.
Second, we furthered our studies on SARS-CoV-2 in Hawaiʻi by isolating the virus. Following isolation, we developed a whole genome sequencing workflow to identify the viral genome. Following whole genome sequencing, we evolved our statistical evaluation of emergence for the assigned lineages and individual amino acid substitutions. We compared this to in-silico predicted B and T cell epitopes to demonstrate the need for vaccine redesign. We then answer how to redesign vaccines by evolving the emergence statistical analysis into an algorithm to predict emergence according to vaccine manufacturing timelines.
Third, we used bioinformatic approaches to evaluate the effectiveness of quarantine early in the pandemic and to apply precision public-health genomics to Hawaiʻi. With the former, we developed a method demonstrating the quarantine delayed the spread of variants. With the latter, we identified the origin of all SARS-CoV-2 variants of concern found in Hawaiʻi. With this, we demonstrated that 76% of all sequences found in Hawaiʻi originate from California. Scientists and public-health officials can use the techniques we developed herein for use in future pandemic preparedness.
The studies herein provide a foundation for understanding the COVID-19 pandemic worldwide and in Hawaiʻi. Such an understanding will allow the world to respond more adequately to future pandemics and SARS-CoV-2 as it becomes endemic. This work provides sequencing data from Hawaiʻi and uses that, combined with the worldwide data, to show that quarantine was effective, to develop a rule-based algorithm to monitor and determine virus evolution and emergence worldwide for vaccine redesign, and to track viral entry into Hawaiʻi from around the world.
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Virology, Bioinformatics, Public health
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