SARS-CoV-2 variants show temperature-dependent enhanced polymerase activity in the upper respiratory tract and high transmissibility

Kim, Se‐Mi; Kim, Eunha; Casel, Mark Anthony B.; Kim, Young-il; Sun, Rong; Kwack, Mi-Jeong; Yoo, Ji‐Seung; Yoo, Min-Ah; Yoo, Kwang-Min; Jang, Seung-Gyu; Rollon, Rare; Choi, Jeong Ho; Gil, Juryeon; Eun, Kiyoung; Kim, Hyunggee; Ensser, Armin; Hwang, Jun Hyun; Song, Min‐Suk; Kim, Myung Hee; Jung, Jae U.; Choi, Young‐Ki

doi:10.1101/2022.09.27.509689

Cited by 6 publications

(3 citation statements)

References 33 publications

(35 reference statements)

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“…Although T4685A, N4992N, and G5063S in RdRp were associated with Delta mortality, no mutation in RdRp was found to be significantly associated with Omicron mortality (Saifi et al, 2022). SARS-CoV-2 variants containing the P323L or P323L/G671S mutation in RdRp exhibited enhanced replication at 33°C compared to 37°C and high transmissibility in ferrets (Kim et al, 2022). Detailed mechanisms for Omicron's adaptation to the low temperature require further studies.…”

Section: Omicron Is More Selectively Proliferated In the Upper Respir...mentioning

confidence: 96%

“…RNA-dependent RNA polymerase (RdRp) plays an essential role for the viral replication and some mutations may be associated with viral replication in a low temperature (Kim et al, 2022). Multiple intra-host single-nucleotide variations have been found in the RdRp coding region of the Omicron variant, such as A1892T, I189V, P314L, K38R, T492I and V57V (Bansal and Kumar, 2022).…”

Section: Omicron Is More Selectively Proliferated In the Upper Respir...mentioning

confidence: 99%

See 1 more Smart Citation

Whether SARS-CoV-2 May Become Lethal Again? By Reference to the 1918 Influenza Virus

Yuan,

Jiang,

Zhang

et al. 2023

Preprint

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Omicron variants have higher infectivity, more immune escape but lower risk of severe clinical outcomes than the ancestral variants. However, people are still wondering whether SARS-CoV-2 may become lethal again or whether some highly-pathogenic strain may emerge in the future. Omicron is more selective proliferation in the upper respiratory tract (URT). The temperature of human URT is 33–34°C, and the virus strains other than Omicron cannot replicate effectively at this temperature. While Omicron adapted to the low temperature environment, so its distribution mainly depends on the expression levels of ACE2 in cells. Similar distribution switch from lungs to URT has been observed for the 1918 H1N1 influenza virus, who vanished after 1921 and has been turned to be the seasonal human influenza A viruses. However, some relatively high-pathogenic SARS-CoV-2 strains and influenza-virus strains may still emerge in the future. Dynamic changes in the viral virulence should be monitored constantly.

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Section: Omicron Is More Selectively Proliferated In the Upper Respir...mentioning

confidence: 96%

Section: Omicron Is More Selectively Proliferated In the Upper Respir...mentioning

confidence: 99%

Whether SARS-CoV-2 May Become Lethal Again? By Reference to the 1918 Influenza Virus

Yuan,

Jiang,

Zhang

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Notably, the G671S mutation in the RNA-dependent RNA polymerase (RdRp; Nsp12) prevalent in delta is not observed in omicron. G671S mutation facilitates enhanced replication and increased transmission (20). Further, a three amino acid deletion (ΔSGF) mutation in Nsp6 (106-108) was observed in more than 80% of omicron variants.…”

Section: Non-structural Proteins (Nsp's)mentioning

confidence: 99%

Temporal Pattern of Mutation Accumulation in SARS-CoV-2 Proteins: Insights from Whole Genome Sequences Pan-India Using Data Mining Approach

Varun

2023

Preprint

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Mutation is a fundamental factor that affects host-pathogen biology and consequently viral survival and spread. Close monitoring and observation of such mutation help decipher essential changes in the SARS Cov2 genome. A plethora of mutations have been documented owing to increased whole genomic sequencing. Understanding how conserved the specific mutations are and the temporal pattern of mutation accumulation is of paramount interest. Using an in-house data mining approach, pan-India data was mined and analysed for 26 proteins expressed by SARS-CoV-2 to understand the spread of mutations over 28 months (January 2021- April 2023). It was observed that proteins such as Nsp3, Nsp4, ORF9b, among others, acquired mutations over the period. In contrast, proteins such as Nsp6-10 were highly stable, with no detectable conserved mutations. Further, it was observed that many of the mutations that were highly prevalent in the delta variants were not observed in the omicron variants, which probably influenced the host-pathogen relationship. The study attempts to catalogue and focus on well-conserved mutations across all the SARS-CoV-2 proteins, highlighting the importance of understanding non-spike mutations.

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Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation

Jeronimo,

Aksenen,

Duarte

et al. 2024

J Virol

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Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus’s adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.

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SARS-CoV-2 variants show temperature-dependent enhanced polymerase activity in the upper respiratory tract and high transmissibility

Cited by 6 publications

References 33 publications

Whether SARS-CoV-2 May Become Lethal Again? By Reference to the 1918 Influenza Virus

Whether SARS-CoV-2 May Become Lethal Again? By Reference to the 1918 Influenza Virus

Temporal Pattern of Mutation Accumulation in SARS-CoV-2 Proteins: Insights from Whole Genome Sequences Pan-India Using Data Mining Approach

Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation

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