Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2

Xi, Binbin; Meng, Yuhuan; Jiang, Dawei; Bai, Yunmeng; Chen, Zixi; Qu, Yimo; Li, Shuhua; Wei, Jinjia; Huang, Lizhen; Du, Hongli

doi:10.3390/v14030454

Cited by 4 publications

(1 citation statement)

References 39 publications

(61 reference statements)

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“…Based on our previous research on the evolution of SARS-CoV-2 consensus genomes ( 28 - 31 ), we investigated the characteristics of SARS-CoV-2 within-host diversity and the implications of iSNVs for viral immune evasion using almost 2,00,000 raw genome sequencing data of SARS-CoV-2. Our work provided insights into the possible mutation drivers or their mutational signatures for iSNVs and the evolutionary strategies of SARS-CoV-2 to escape human innate and adaptive immunity.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion

Zeng

Chen

et al. 2023

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving, bringing great challenges to the control of the virus. In the present study, we investigated the characteristics of SARS-CoV-2 within-host diversity of human hosts and its implications for immune evasion using about 2,00,000 high-depth next-generation genome sequencing data of SARS-CoV-2. A total of 44% of the samples showed within-host variations (iSNVs), and the average number of iSNVs in the samples with iSNV was 1.90. C-to-U is the dominant substitution pattern for iSNVs. C-to-U/G-to-A and A-to-G/U-to-C preferentially occur in 5′-CG-3′ and 5′-AU-3′ motifs, respectively. In addition, we found that SARS-CoV-2 within-host variations are under negative selection. About 15.6% iSNVs had an impact on the content of the CpG dinucleotide (CpG) in SARS-CoV-2 genomes. We detected signatures of faster loss of CpG-gaining iSNVs, possibly resulting from zinc-finger antiviral protein-mediated antiviral activities targeting CpG, which could be the major reason for CpG depletion in SARS-CoV-2 consensus genomes. The non-synonymous iSNVs in the S gene can largely alter the S protein’s antigenic features, and many of these iSNVs are distributed in the amino-terminal domain (NTD) and receptor-binding domain (RBD). These results suggest that SARS-CoV-2 interacts actively with human hosts and attempts to take different evolutionary strategies to escape human innate and adaptive immunity. These new findings further deepen and widen our understanding of the within-host evolutionary features of SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of the coronavirus disease 2019, has evolved rapidly since it was discovered. Recent studies have pointed out that some mutations in the SARS-CoV-2 S protein could confer SARS-CoV-2 the ability to evade the human adaptive immune system. In addition, it is observed that the content of the CpG dinucleotide in SARS-CoV-2 genome sequences has decreased over time, reflecting the adaptation to the human host. The significance of our research is revealing the characteristics of SARS-CoV-2 within-host diversity of human hosts, identifying the causes of CpG depletion in SARS-CoV-2 consensus genomes, and exploring the potential impacts of non-synonymous within-host variations in the S gene on immune escape, which could further deepen and widen our understanding of the evolutionary features of SARS-CoV-2.

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Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion

Zeng

Chen

et al. 2023

mBio

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Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2

Townsend,

Gaughran,

Hassler

et al. 2023

Preprint

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Over the past two decades the pace of spillovers from animal viruses to humans has accelerated, with COVID-19 becoming the most deadly zoonotic disease in living memory. Prior to zoonosis, it is conceivable that the virus might largely be subjected to purifying selection, requiring no additional selective changes for successful zoonotic transmission. Alternatively, selective changes occurring in the reservoir species may coincidentally preadapt the virus for human-to-human transmission, facilitating spread upon cross-species exposure. Here we quantify changes in the genomes of SARS-CoV-2 and SARS-CoV-1 proximate to zoonosis to evaluate the selection pressures acting on the viruses. Application of molecular-evolutionary and population-genetic approaches to quantify site-specific selection within both SARS-CoV genomes revealed strong purifying selection across many genes at the time of zoonosis. Even in the viral surface-protein Spike that has been fast-evolving in humans, there is little evidence of positive selection proximate to zoonosis. Nevertheless, in SARS-CoV-2, NSP12, a core protein for viral replication, exhibited a region under adaptive selection proximate to zoonosis. Furthermore, in both SARS-CoV-1 and SARS-CoV-2, regions of adaptive selection proximate to zoonosis were found in ORF7a, a putative Major Histocompatibility Complex modulatory gene. These findings suggest that these replication and immunomodulatory proteins have played a previously underappreciated role in the adaptation of SARS coronaviruses to human hosts.

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Positive Diagnosis of COVID-19 in an Integrated Teaching and Healthcare Service and Its Associated Factors

Delgado-Mendoza,

Gómez-Suyón,

Miranda-Cárdenas

et al. 2024

Healthcare

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Developing and implementing an epidemiological surveillance plan was necessary during the COVID-19 pandemic to ensure safe dental practice. This was due to the high risk faced by this occupational group during the COVID-19 pandemic. This study aimed to determine the factors associated with COVID-19 diagnosis in a Peruvian dental school’s integrated teaching and care service. A cross-sectional study was conducted with a population made up of the records of students, teachers, and administrative personnel in a COVID-19 epidemiological surveillance plan of a dental school during the years 2021 to 2022. The year 2022 was positively associated with a positive diagnosis of COVID-19 (aPR: 1.51; 95% CI: 1.10–2.07; p = 0.010) and not having had contact with a patient with COVID-19 was negatively associated with being diagnosed with that disease (aPR: 0.20; 95% CI: 0.14–0.27; p < 0.001). In conclusion, 2022 was positively associated with having a positive COVID-19 diagnosis. In addition, not having had contact with a COVID-19 patient was negatively associated with the disease diagnosis and with the development of moderate to severe COVID-19.

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Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2

Cited by 4 publications

References 39 publications

SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion

SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion

Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2

Positive Diagnosis of COVID-19 in an Integrated Teaching and Healthcare Service and Its Associated Factors

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