Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion

Hossain, Anamica; Trishna, Shammi Akter; Rashid, Alfi Anjum; Khair, Sabik; Alam, A. S. M. Rubayet Ul

doi:10.1016/j.micpath.2022.105699

Cited by 52 publications

(61 citation statements)

References 103 publications

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“…4 ). For instance, we found that accumulated mutations in Omicron's N-proteins, which is critical for viral replication and features unique mutations that are absent in other VOCs [56] , results in the loss of binding sites of twelve miRNAs previously bound to Wuhan-Hu-1 ( Fig. 3 c and Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern

Capistrano

Richner

Schwartz

et al. 2023

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Diseas

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Section: Resultsmentioning

confidence: 99%

Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern

Capistrano

Richner

Schwartz

et al. 2023

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Diseas

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“…SARS-CoV-2 has frequently exhibited new mutations that have resulted in new variants, including Delta (B.1.617.2) and Omicron (B.1.1.529). Moreover, Omicron is evolving rapidly and its new subvariants are constantly emerging (e.g., BA.1, BA.2 and BA.5) [ 28 ]. The emergence of SARS-CoV-2 variants carrying mutations in the S gene raises concerns about the possibility of enhanced transmission during the ongoing COVID-19 pandemic [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Performance Analysis of Self-Collected Nasal and Oral Swabs for Detection of SARS-CoV-2

Lim

Baek²,

Park³

et al. 2022

Diagnostics

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third highly pathogenic human coronavirus and is rapidly transmitted by infected individuals regardless of their symptoms. During the COVID-19 pandemic, owing to the dearth of skilled healthcare workers (HCWs) to collect samples for early diagnosis, self-collection emerged as a viable alternative. To evaluate the reliability of self-collection, we compared the virus detection rate using 3990 self-collected swabs and HCW-collected swabs, procured from the same individuals and collected immediately after the self-collection. The results of multiplex reverse-transcription quantitative polymerase chain reaction revealed that the viral load in the HCW-collected swabs was marginally (18.4–28.8 times) higher than that in self-collected swabs. Self-collection showed no significant difference in sensitivity and specificity from HCW-collection (κ = 0.87, McNemar’s test; p = 0.19), indicating a comparable performance. These findings suggest that self-collected swabs are acceptable substitutes for HCW-collected swabs, and that their use improved the specimen screening efficiency and reduced the risk of SARS-CoV-2 infection among HCWs during and after the COVID-19 pandemic.

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“…Taken together, the results of our phylogeographic analysis permitted us to map the early dispersal patterns of the two recently emerged omicron subvariants both globally and within Europe. Omicron subvariants are genetically diverse, a feature that facilitates their evasion of antiviral immunity that was acquired through vaccination or natural infection with another variant [ 9 , 10 , 11 , 12 , 15 , 17 , 18 , 19 ]. By the time both BA.4 and BA.5 emerged, a large fraction of the population in Europe and other Western countries had been vaccinated or had recovered from an earlier SARS-CoV-2 infection.…”

Section: Discussionmentioning

confidence: 99%

“…Apart from the high genetic divergence of the omicron variants compared to all other previously circulating VOCs, the subvariants show extensive divergence within the omicron clade [ 11 , 12 ]. The initial virus dispersal featured subvariants BA.1 and BA.1.1; this was followed by several major subvariant families, including BA.2, BA.4, and BA.5 [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Mapping the Early Dispersal Patterns of SARS-CoV-2 Omicron BA.4 and BA.5 Subvariants in the Absence of Travel Restrictions and Testing at the Borders in Europe

Kostaki

Mossialos

Tseti

et al. 2022

Viruses

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The circulation of SARS-CoV-2 omicron BA.4 and BA.5 subvariants with enhanced transmissibility and capacity for immune evasion resulted in a recent pandemic wave that began in April–May of 2022. We performed a statistical phylogeographic study that aimed to define the cross-border transmission patterns of BA.4 and BA.5 at the earliest stages of virus dispersal. Our sample included all BA.4 and BA.5 sequences that were publicly available in the GISAID database through mid-May 2022. Viral dispersal patterns were inferred using maximum likelihood phylogenetic trees with bootstrap support. We identified South Africa as the major source of both BA.4 and BA.5 that migrated to other continents. By contrast, we detected no significant export of these subvariants from Europe. Belgium was identified as a major hub for BA.4 transmission within Europe, while Portugal and Israel were identified as major sources of BA.5. Western and Northern European countries exhibited the highest rates of cross-border transmission, as did several popular tourist destinations in Southern and Central/Western Europe. Our study provides a detailed map of the early dispersal patterns of two highly transmissible SARS-CoV-2 omicron subvariants at a time when there was an overall relaxation of public health measures in Europe.

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Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion

Cited by 52 publications

References 103 publications

Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern

Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern

Performance Analysis of Self-Collected Nasal and Oral Swabs for Detection of SARS-CoV-2

Mapping the Early Dispersal Patterns of SARS-CoV-2 Omicron BA.4 and BA.5 Subvariants in the Absence of Travel Restrictions and Testing at the Borders in Europe

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