Methods in Microbiology最新文献

Since the SARS-CoV-2 virus triggered the beginning of the COVID-19 pandemic, scientists, government officials, and healthcare professionals around the world recognized the need for accessible, affordable, and accurate testing to predict and contain the spread of COVID-19. In the months that followed, research teams designed, tested, and rolled out hundreds of diagnostic assays, each with different sampling methods, diagnostic technologies, and sensitivity levels. However, the contagious virus continued to spread; SARS-CoV-2 travelled through airborne particles and spread rapidly, despite the widening use of diagnostic assays. As the pandemic continued, hundreds of millions of people contracted COVID-19 and millions died worldwide. With so many infections, SARS-CoV-2 received many opportunities to replicate and mutate, and from these mutations emerged more contagious, deadly, and difficult-to-diagnose viral mutants. Each change to the viral genome presented potential added challenges to containing the virus, and as such, researchers have continued developing and improving testing methods to keep up with COVID-19. In this chapter, we examine several SARS-CoV-2 variants that have emerged during the pandemic. Additionally, we discuss a few major COVID-19 diagnostic technique categories, including those involving real-time PCR, serology, CRISPR, and electronic biosensors. Finally, we address SARS-CoV-2 variants and diagnostic assays in the age of COVID-19 vaccines.

SARS-CoV-2 continues to evolve, even after implementation of public-wide vaccination, as can be observed by an increasing number of mutations over time. Compared to responses by the United States and European countries, the disease mitigation strategies employed by the Australian government have been swift and effective. This provides a unique opportunity to study the emergence of variants of concern (VOCs) at many latitude levels in a country that has been able to control infection for the majority of the pandemic. In the present study, we explored the occurrence and accumulation of major mutations typical of VOCs in different regions of Australia and the effects that latitude has on the establishment of VOC-induced disease. We also studied the constellation of mutations characteristic of VOCs to determine if the mutation sets acted as haplotypes. Our goal was to explore processes behind the emergence of VOCs as the viral disease progresses towards becoming endemic. Most reported COVID-19 cases were in largest cities located within a -30°S to - 50°S latitude corridor previously identified to be associated with seasonal behavior. Accumulation plots of individual amino acid variants of major VOCs showed that the first major haplotypes reported worldwide were also present in Australia. A classification of accumulation plots revealed the existence of 18 additional haplotypes associated with VOCs alpha, delta and omicron. Core mutant constellations for these VOCs and curve overlaps for variants in each set of haplotypes demonstrated significant decoupling patterns, suggesting processes of emergence. Finally, construction of a "haplotype network" that describes the viral population landscape of Australia throughout the COVID-19 pandemic revealed significant and unanticipated seasonal patterns of emergence and diversification. These results provide a unique window into our evolutionary understanding of a human pathogen of great significance. They may guide future research into mitigation and prediction strategies for future VOCs.