Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein

Rao, R. Shyama Prasad; Ahsan, Nagib; Xu, Chunhui; Su, Lingtao; Verburgt, Jacob; Fornelli, Luca; Xu, Dong

doi:10.1177/11769343211064616

Cited by 11 publications

(8 citation statements)

References 77 publications

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“…Sequence, structural property, and phylogenetic tree analyses of Mibgl3. (a) Alignment of amino acid sequences of Mibgl3, HvExo, BoGH3, AoGH, and EmGH performed using Clustal Omega () and ENDscript server (). , The accession numbers were WP_067196459 for Mibgl3, 1EX1 for HvExoI, 5JP0 for BoGH3, 5YOT for AoGH, and 5Z87 for EmGH1. The amino acid residues that are conserved in all four proteins, are denoted with white letters and highlighted in red.…”

Section: Resultsmentioning

confidence: 99%

“…Enzyme annotation was performed by the Carbohydrate Active Enzyme Annotation web server (dbCAN, ) . Alignment of amino acid sequences of different β-glucosidases was performed using Clustal Omega () and the ENDscript server (). , The amino acid sequence of Mibgl3 was submitted to the National Center for Biotechnology Information database, and the BLASTp tool was used for sequence alignment to download amino acid sequences of related GH3 proteins with high homology. Developmental tree mapping and analysis were performed using MEGA 7.0 …”

Section: Methodsmentioning

confidence: 99%

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Novel β-Glucosidase Mibgl3 fromMicrobacteriumsp. XT11 with Oligoxanthan-Hydrolyzing Activity

Wang

et al. 2022

J. Agric. Food Chem.

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The enzymatic pathway of xanthan depolymerization has been predicted previously; however, the β-glucosidase and unsaturated glucuronyl hydrolase in this system have not been cloned and characterized. This lack of knowledge hinders rational modification of xanthan and exploration of new applications. In this work, we report on the properties of Mibgl3, a xanthandegrading enzyme isolated from Microbacterium sp. XT11. Mibgl3 exhibits typical structural features of the GH3 family but shares low sequence identity with reported GH3 enzymes. The activity of Mibgl3 can be inhibited by Cu 2+ , Fe 2+ , Zn 2+ , and glucose. Unlike most β-glucosidases, Mibgl3 can tolerate a wide pH range and is activated by high concentrations of NaCl. This improves the commercial value of Mibgl3. In particular, Mibgl3 exhibits higher substrate specificity toward oligoxanthan than other β-glucosidases. Ion chromatography, ultrahigh-performance liquid chromatography−mass spectrometry (UPLC−MS), and GC−MS results showed that Mibgl3 could effectively hydrolyze oligoxanthan to release glucose and glucuronate. Therefore, Mibgl3 might play an important role in xanthan depolymerization by functioning as hydrolase of both the xanthan backbone and sidechains. This knowledge of the enzymatic properties and hydrolysis mechanism of a β-glucosidase will be beneficial for future applications.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Novel β-Glucosidase Mibgl3 fromMicrobacteriumsp. XT11 with Oligoxanthan-Hydrolyzing Activity

Wang

et al. 2022

J. Agric. Food Chem.

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“…Others have called variants with other tools such as DeepSNV (20) and VarScan (21). DeepSNV was not used as it only investigates SNVs (22), when indels have been found to confer selective advantages (23). Freebayes has been observed to perform slightly superiorly than VarScan when calling variants in wastewater samples (24) and in internal benchmarking (data not shown).…”

Section: Methodsmentioning

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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“…While highly similar sequences lead to nonspecific primer/probe binding and lead to ambiguous detection of OPVs, highly divergent or variable sequence regions pose considerable challenge to detection. As in other viruses (Rao et al, 2021), comparison among OPVs such as VACV and VARV revealed that indels of 3-25 bp are common events in poxviruses (Coulson and Upton, 2011). The A27L (ATI) gene is one such hypervariable target containing variations including truncations, deletions, insertions, and base changes in the two clades of MPXV (Meyer et al, 1997).…”

Section: Detection Of Mpxv -Challenges and Opportunitiesmentioning

confidence: 99%

Molecular detection of monkeypox and related viruses – Challenges and opportunities

Ghate¹,

Suravajhala²,

Patil³

et al. 2022

Preprint

Self Cite

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The recent widespread emergence of monkeypox, a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R0 ≈ 0.58) and fatality rate (0-3%) are low, as it causes prolonged morbidity, monkeypox is leading to considerable public health anxiety. Thus, effective containment and disease management require quick and efficient detection of MPXV. In this bioinformatic overview, we summarize the numerous molecular tests available for MPXV, and discuss the diversity of genes and primers used in the PCR-based detection. Over 90 primer/probe sets are used for the detection of poxviruses. While hemagglutinin and A-type inclusion protein are the most common target genes, TNF receptor and complement binding protein genes are frequently used for distinguishing Congo and west-African clades of MPXV. Problems and possibilities in the detection of MPXV have been discussed.

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Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein

Cited by 11 publications

References 77 publications

Novel β-Glucosidase Mibgl3 fromMicrobacteriumsp. XT11 with Oligoxanthan-Hydrolyzing Activity

Novel β-Glucosidase Mibgl3 fromMicrobacteriumsp. XT11 with Oligoxanthan-Hydrolyzing Activity

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

Molecular detection of monkeypox and related viruses – Challenges and opportunities

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