tetano
Editor, Senior Moderator
PeerJ
. 2022 Mar 21;10:e13136.
doi: 10.7717/peerj.13136. eCollection 2022.
An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
Sk Sarif Hassan[SUP] 1 [/SUP], Vaishnavi Kodakandla[SUP] 2 [/SUP], Elrashdy M Redwan[SUP] 3 [/SUP], Kenneth Lundstrom[SUP] 4 [/SUP], Pabitra Pal Choudhury[SUP] 5 [/SUP], Tarek Mohamed Abd El-Aziz[SUP] 6 [/SUP], Kazuo Takayama[SUP] 7 [/SUP], Ramesh Kandimalla[SUP] 8 [/SUP], Amos Lal[SUP] 9 [/SUP], Ángel Serrano-Aroca[SUP] 10 [/SUP], Gajendra Kumar Azad[SUP] 11 [/SUP], Alaa A A Aljabali[SUP] 12 [/SUP], Giorgio Palù[SUP] 13 [/SUP], Gaurav Chauhan[SUP] 14 [/SUP], Parise Adadi[SUP] 15 [/SUP], Murtaza Tambuwala[SUP] 16 [/SUP], Adam M Brufsky[SUP] 17 [/SUP], Wagner Baetas-da-Cruz[SUP] 18 [/SUP], Debmalya Barh[SUP] 19 [/SUP], Vasco Azevedo[SUP] 20 [/SUP], Nikolas G Bazan[SUP] 21 [/SUP], Bruno Silva Andrade[SUP] 22 [/SUP], Raner José Santana Silva[SUP] 23 [/SUP], Vladimir N Uversky[SUP] 24 [/SUP]
Affiliations
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
Keywords: COVID-19; Continent distribution; Intrinsically disordered region; ORF8; SARS-CoV-2; Truncated; Truncation mutation.
. 2022 Mar 21;10:e13136.
doi: 10.7717/peerj.13136. eCollection 2022.
An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
Sk Sarif Hassan[SUP] 1 [/SUP], Vaishnavi Kodakandla[SUP] 2 [/SUP], Elrashdy M Redwan[SUP] 3 [/SUP], Kenneth Lundstrom[SUP] 4 [/SUP], Pabitra Pal Choudhury[SUP] 5 [/SUP], Tarek Mohamed Abd El-Aziz[SUP] 6 [/SUP], Kazuo Takayama[SUP] 7 [/SUP], Ramesh Kandimalla[SUP] 8 [/SUP], Amos Lal[SUP] 9 [/SUP], Ángel Serrano-Aroca[SUP] 10 [/SUP], Gajendra Kumar Azad[SUP] 11 [/SUP], Alaa A A Aljabali[SUP] 12 [/SUP], Giorgio Palù[SUP] 13 [/SUP], Gaurav Chauhan[SUP] 14 [/SUP], Parise Adadi[SUP] 15 [/SUP], Murtaza Tambuwala[SUP] 16 [/SUP], Adam M Brufsky[SUP] 17 [/SUP], Wagner Baetas-da-Cruz[SUP] 18 [/SUP], Debmalya Barh[SUP] 19 [/SUP], Vasco Azevedo[SUP] 20 [/SUP], Nikolas G Bazan[SUP] 21 [/SUP], Bruno Silva Andrade[SUP] 22 [/SUP], Raner José Santana Silva[SUP] 23 [/SUP], Vladimir N Uversky[SUP] 24 [/SUP]
Affiliations
- PMID: 35341060
- PMCID: PMC8944340
- DOI: 10.7717/peerj.13136
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
Keywords: COVID-19; Continent distribution; Intrinsically disordered region; ORF8; SARS-CoV-2; Truncated; Truncation mutation.