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1. Ecological and Evolutionary Insights About Emerging Infectious Diseases from the COVID-19 Pandemic

   https://doi.org/10.1146/annurev-ecolsys-102320-101234  

   Kilpatrick, A Marm (November 2023, Annual Review of Ecology, Evolution, and Systematics)

   The coronavirus disease 2019 (COVID-19) pandemic challenged the workings of human society, but in doing so, it advanced our understanding of the ecology and evolution of infectious diseases. Fluctuating transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demonstrated the highly dynamic nature of human social behavior, often without government intervention. Evolution of SARS-CoV-2 in the first two years following spillover resulted primarily in increased transmissibility, while in the third year, the globally dominant virus variants had all evolved substantial immune evasion. The combination of viral evolution and the buildup of host immunity through vaccination and infection greatly decreased the realized virulence of SARS-CoV-2 due to the age dependence of disease severity. The COVID-19 pandemic was exacerbated by presymptomatic, asymptomatic, and highly heterogeneous transmission, as well as highly variable disease severity and the broad host range of SARS-CoV-2. Insights and tools developed during the COVID-19 pandemic could provide a stronger scientific basis for preventing, mitigating, and controlling future pandemics. 

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2. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

   https://doi.org/10.1038/s41467-021-24467-0  

   Bui, Linh T.; Winters, Nichelle I.; Chung, Mei-I; Joseph, Chitra; Gutierrez, Austin J.; Habermann, Arun C.; Adams, Taylor S.; Schupp, Jonas C.; Poli, Sergio; Peter, Lance M.; et al (December 2021, Nature Communications)

   null (Ed.)

   Abstract Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyze the transcriptomes of 611,398 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observe a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD AT2 cells express higher levels of genes linked directly to the efficiency of viral replication and the innate immune response. Additionally, we identify basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection. 

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3. An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

   https://doi.org/10.1093/molbev/msab118  

   Kumar, Sudhir; Tao, Qiqing; Weaver, Steven; Sanderford, Maxwell; Caraballo-Ortiz, Marcos A; Sharma, Sudip; Pond, Sergei L; Miura, Sayaka (May 2021, Molecular Biology and Evolution)

   Yeager, Meredith (Ed.)

   Abstract Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the United States harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains that have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia as well as continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/). 

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4. Host Immune Response Driving SARS-CoV-2 Evolution

   https://doi.org/10.3390/v12101095  

   Wang, Rui; Hozumi, Yuta; Zheng, Yong-Hui; Yin, Changchuan; Wei, Guo-Wei (October 2020, Viruses)

   null (Ed.)

   The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance in controlling and combating the coronavirus disease 2019 (COVID-19) pandemic. Currently, over 15,000 SARS-CoV-2 single mutations have been recorded, which have a great impact on the development of diagnostics, vaccines, antibody therapies, and drugs. However, little is known about SARS-CoV-2’s evolutionary characteristics and general trend. In this work, we present a comprehensive genotyping analysis of existing SARS-CoV-2 mutations. We reveal that host immune response via APOBEC and ADAR gene editing gives rise to near 65% of recorded mutations. Additionally, we show that children under age five and the elderly may be at high risk from COVID-19 because of their overreaction to the viral infection. Moreover, we uncover that populations of Oceania and Africa react significantly more intensively to SARS-CoV-2 infection than those of Europe and Asia, which may explain why African Americans were shown to be at increased risk of dying from COVID-19, in addition to their high risk of COVID-19 infection caused by systemic health and social inequities. Finally, our study indicates that for two viral genome sequences of the same origin, their evolution order may be determined from the ratio of mutation type, C > T over T > C. 

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5. Understanding Neutrophil Dynamics during COVID-19 Infection

   https://doi.org/10.3390/app13042409  

   Murphy, Quiyana M.; Ciupe, Stanca M. (February 2023, Applied Sciences)

   Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in varied clinical outcomes, with virus-induced chronic inflammation and tissue injury being associated with enhanced disease pathogenesis. To determine the role of tissue damage on immune populations recruitment and function, a mathematical model of innate immunity following SARS-CoV-2 infection has been proposed. The model was fitted to published longitudinal immune marker data from patients with mild and severe COVID-19 disease and key parameters were estimated for each clinical outcome. Analytical, bifurcation, and numerical investigations were conducted to determine the effect of parameters and initial conditions on long-term dynamics. The results were used to suggest changes needed to achieve immune resolution. 

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