SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants

Chung, Hoyin; Noh, Ji Yeong; Koo, Bon‐Sang; Hong, Jung Joo; Kim, Hye Kwon

doi:10.1016/j.csbj.2022.04.022

Cited by 17 publications

(16 citation statements)

References 27 publications

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“…The K417N, N440K, 30 S477N, 31 T478K, E484A, 32 and N501Y 33 , 34 mutations were shown to evade neutralization by convalescent sera, some monoclonal antibodies (mAbs), and postvaccine serum. 35 , 36 , 37 …”

Section: Introductionmentioning

confidence: 99%

“…Molecular evidence pointed out that mutations (such as K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, and N501Y) could cause a reduction in neutralizing activity of mAbs, convalescent plasma, and serum‐induced by vaccines. 35 , 36 , 37 , 66 BA.2 has an additional three deletions and seven substitutions compared to BA.1, three of which lie in the RBD. 14 Structure and molecular analysis demonstrated that mutations in BA.1 (S371L, G446S, and G496S) and BA.2 (S371F, T376A, D405N, and R408S) have the potential to affect antibody binding.…”

Section: Introductionmentioning

confidence: 99%

“…However, some in silico analyses 28,29 predict that the Omicron spike has a higher binding affinity to ACE2 than Delta (Delta is 60% more transmissible than the highly infectious Alpha variant). The K417N, N440K, 30 S477N, 31 T478K, E484A, 32 and N501Y 33,34 mutations were shown to evade neutralization by convalescent sera, some monoclonal antibodies (mAbs), and postvaccine serum 35–37 …”

Section: Introductionmentioning

confidence: 99%

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The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Zhou

Zhi

Teng

2022

Journal of Medical Virology

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As of November 2021, several SARS‐CoV‐2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID‐19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) ( https://www.gisaid.org/ ). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild‐type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Zhou

Zhi

Teng

2022

Journal of Medical Virology

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“…Both pseudovirus experiments and structural modeling indicate that mutations (K417N, N440K [ 19 ], G446S, S477N [ 20 ], T478K [ 21 ], E484A [ 22 ], G496S, N501Y [ 23 ], Q498R [ 24 ], and Y505H, all of which were located in the BA.5 spike) increased the transmissibility of the SARS-CoV-2 variants by increasing the binding affinity and the tightness of RBD to human angiotensin-converting enzyme 2 (hACE2) [ 25 , 26 ] or generated the immune escape of the SARS-CoV-2 variants [ 27 , 28 , 29 ], as shown in Figure 3 . Additionally, BA.5 has also “H655Y + N679K + P681H” mutations located at the S1/S2 border, which could significantly promote the S1/S2 cleavage and activation of the S protein, thus enhancing viral fusogenicity [ 30 , 31 , 32 ].…”

Section: The Characteristics Of Sars-cov-2 Omicron Ba5 Spike Mutationsmentioning

confidence: 99%

The Epidemiological Features of the SARS-CoV-2 Omicron Subvariant BA.5 and Its Evasion of the Neutralizing Activity of Vaccination and Prior Infection

et al. 2022

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From December 2021 to May 2022, the Omicron BA.1 and BA.2 subvariants successively became the most dominant strains in many countries around the world. Subsequently, Omicron subvariants have emerged, and Omicron has been classified into five main lineages, including BA.1, BA.2, BA.3, BA.4, BA.5, and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6, BA.5.1, and BA.5.2) . The recent emergence of several Omicron subvariants has generated new concerns about further escape from immunity induced by prior infection and vaccination and the creation of new COVID-19 waves globally. In particular, BA.5 (first found in southern Africa, February 2022) displays a higher transmissibility than other Omicron subvariants and is replacing the previously circulating BA.1 and BA.2 in several countries.

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“…Since these studies, new lineages arisen, with the present being Omicron, negatively impacting treatment efficacy (1). Others have studied viral dynamics using recent lineages in serial passages in cells, observing similar development of directional selection and clinically concerning mutations (16, 17). Given the pandemic’s prolonged nature, understanding longitudinal viral changes in a mammalian host is pressing.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 evolution in the absence of selective immune pressures, results in antibody resistance, interferon suppression and phenotypic differences by lineage

Willett

Gravel

Dubuc

et al. 2023

Preprint

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Background: The continuing COVID-19 pandemic is partially due to viral evolution decreasing vaccine and treatment efficacies. Predicting viral evolution is difficult. Others have found that serial infections of the original SARS-CoV-2 isolate in non transgenic mice is accompanied with selection of alleles (such as Spike 417N, 493H and 501Y) conferring adaptation and greater binding affinity for the murine ACE2 receptor, enhanced infectivity, and lethal phenotype in mice. We designed a study to investigate long-term viral evolution's impact in K18-ACE2 mice with virus closer related to the Omicron sub-lineage. Methods: We serially infected SARS-CoV-2-naive mice with either the B.1.351 (Beta) or the B.1.617.2 (Delta) variant across twenty passages without selective pressures. We sequenced virus across passages, annotating variant alleles changing in frequency using published tools, tracking alleles suspected of decreasing vaccine/treatment efficacy. We evaluated virulence in animals infected with virus isolated at study completion and determined antibody neutralization sensitivity using sera from vaccinated individuals. Results and Conclusions: We observed variant alleles with documented roles in vaccine-elicited immunity evasion. This included the Omicron-associated mutation spike S371F that arose de-novo during our study. Passage 20 (P20) viruses were more virulent that their P0 counterpart with P20 Delta lineage being significantly more resistant to antibody neutralization. These developments occurred within two months of the study starting, suggesting that our model can rapidly emulate pandemic progression in mammals. While our model lacked selective pressures, such as pre-existing SARS-CoV-2 immunity, these conditions could readily be adapted. Such modeling could enable development of more evolution-resistant treatments.

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SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants

Cited by 17 publications

References 27 publications

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

The Epidemiological Features of the SARS-CoV-2 Omicron Subvariant BA.5 and Its Evasion of the Neutralizing Activity of Vaccination and Prior Infection

SARS-CoV-2 evolution in the absence of selective immune pressures, results in antibody resistance, interferon suppression and phenotypic differences by lineage

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