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Article ; Online: Shell disorder and the HIV vaccine mystery: lessons from the legendary Oswald Avery.

Goh, Gerard Kian-Meng / Uversky, Vladimir N

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 12, Page(s) 5702–5711

Abstract: The search for a human immunodeficiency virus (HIV) vaccine has spanned nearly four decades without much success. A much needed paradigm shift can be found in the abnormally high levels of intrinsic disorder in the outer shells of HIVs, the hepatitis C ... ...

Abstract	The search for a human immunodeficiency virus (HIV) vaccine has spanned nearly four decades without much success. A much needed paradigm shift can be found in the abnormally high levels of intrinsic disorder in the outer shells of HIVs, the hepatitis C virus (HCV), and herpes simplex viruses (HSVs), for which successful vaccines have not been established. On the other hand, this feature (high levels of intrinsic disorder in the outer shells) is completely absent in classic viruses for which effective vaccines are found, such as the rabies virus. The motions arising from the disordered outer shell result in the inability of antibodies to bind tightly to the polysaccharides on the viral surface proteins, and, therefore, induce inadequate immune response. Experiments conducted by the legendary Avery Oswald in the 1920s form the theoretical underpinning of this new model. Failures of the vaccines based on the HIV glycoprotein Gp120 and other vaccines can be traced back to the lack of understanding of the important roles of shell disorder in a "Trojan-horse" immune evasion mechanism utilized by the virus.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	AIDS Vaccines ; Humans ; Immune Evasion
Chemical Substances	AIDS Vaccines
Language	English
Publishing date	2021-01-07
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1870562
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Article: Computational, Experimental, and Clinical Evidence of a Specific but Peculiar Evolutionary Nature of (COVID-19) SARS-CoV-2

Goh, Gerard Kian-Meng / Dunker, A. Keith / Foster, James A. / Uversky, Vladimir N.

Journal of proteome research. 2022 Feb. 10, v. 21, no. 4

2022

Abstract: The shell disorder models have predicted that SARS-CoV-2 is of a specific but peculiar evolutionary nature. All coronaviruses (CoVs) closely related to SARS-CoV-2 have been found to have the hardest outer shells (M protein) among CoVs. This hard shell ( ... ...

Abstract	The shell disorder models have predicted that SARS-CoV-2 is of a specific but peculiar evolutionary nature. All coronaviruses (CoVs) closely related to SARS-CoV-2 have been found to have the hardest outer shells (M protein) among CoVs. This hard shell (low M percentage of intrinsic disorder (PID)) is associated with burrowing animals, for example, pangolins, and is believed to be responsible for the high contagiousness of SARS-CoV-2 because it will be more resistant to antimicrobial enzymes found in saliva/mucus. Incoming clinical and experimental data do support this along with a prediction based on another aspect of the shell (N, inner shell) disorder models that SARS-CoV-1 is more virulent than SARS-CoV-2 because SARS-CoV-2 produces fewer virus copies in vital organs even if large amounts of infections particles are shed orally and nasally. A phylogenetic study using M reveals a closer relationship of SARS-CoV to pangolin-CoVs than the bat-RaTG13 found in Yunnan, China. Previous studies may have been confused by recombinations that were poorly handled. The shell disorder models suggest that a pangolin-CoV strain may have entered the human population in 2017 or before as an attenuated virus, which could explain why SARS-CoV is found to be highly adapted to humans.
Keywords	COVID-19 infection ; Pholidota (mammals) ; Severe acute respiratory syndrome coronavirus ; Severe acute respiratory syndrome coronavirus 2 ; human population ; mucus ; phylogeny ; prediction ; proteome ; research ; saliva ; virulence ; viruses ; China
Language	English
Dates of publication	2022-0210
Size	p. 874-890.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2.

Goh, Gerard Kian-Meng / Dunker, A Keith / Foster, James A / Uversky, Vladimir N

Biomolecules

2022 Volume 12, Issue 5

Abstract: Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov- ... ...

Abstract	Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. The SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9%-lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants and pangolin-CoV-2017 (5.4% vs. 5.9%). COVID-19-related CoVs have the lowest M-PIDs (hardest outer shell) among all CoVs. This is likely to be responsible for the higher contagiousness of SARS-CoV-2 and Omicron, since hard outer shell protects the virion from salivary/mucosal antimicrobial enzymes. Phylogenetic study using M reveals that Omicron branched off from an ancestor of the Wuhan-Hu-1 strain closely related to pangolin-CoVs. M, being evolutionarily conserved in COVID-19, is most ideal for COVID-19 phylogenetic study. Omicron may have been hiding among burrowing animals (e.g., pangolins) that provide optimal evolutionary environments for attenuation and increase shell hardness, which is essential for fecal-oral-respiratory transmission via buried feces. Incoming data support SDM e.g., the presence of fewer infectious particles in the lungs than in the bronchi upon infection.
MeSH term(s)	Animals ; COVID-19 ; Chiroptera ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2022-04-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12050631
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Article ; Online: A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation.

Goh, Gerard Kian-Meng / Dunker, A Keith / Foster, James A / Uversky, Vladimir N

Biomolecules

2022 Volume 12, Issue 10

Abstract: The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID-percentage of intrinsic disorder-of the membrane protein M, PID ... M ... ) and higher flexibility of the inner shell ...

Abstract	The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID-percentage of intrinsic disorder-of the membrane protein M, PID<sub>M</sub>) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PID<sub>N</sub>) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations. The first observation demonstrated lesser and greater presence of the Omicron particles in the lungs and bronchial tissues, respectively, as there is a greater level of mucus in the bronchi. The other observation revealed that there are lower viral loads in 2017-pangolin-CoV, which is predicted to have similarly low PID<sub>N</sub> as Omicron. The abnormally hard M, which is very rarely seen in coronaviruses, arose from the fecal-oral behaviors of pangolins via exposure to buried feces. Pangolins provide an environment for coronavirus (CoV) attenuation, which is seen in Omicron. Phylogenetic study using M shows that COVID-19-related bat-CoVs from Laos and Omicron are clustered in close proximity to pangolin-CoVs, which suggests the recurrence of interspecies transmissions. Hard M may have implications for long COVID-19, with immune systems having difficulty degrading viral proteins/particles.
MeSH term(s)	Humans ; Animals ; SARS-CoV-2 ; COVID-19 ; Pangolins ; Phylogeny ; Reproducibility of Results ; Viral Proteins ; Nucleocapsid Proteins/genetics ; Membrane Proteins
Chemical Substances	Viral Proteins ; Nucleocapsid Proteins ; Membrane Proteins
Language	English
Publishing date	2022-09-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12101353
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Article ; Online: Computational, Experimental, and Clinical Evidence of a Specific but Peculiar Evolutionary Nature of (COVID-19) SARS-CoV-2.

Goh, Gerard Kian-Meng / Dunker, A Keith / Foster, James A / Uversky, Vladimir N

Journal of proteome research

2022 Volume 21, Issue 4, Page(s) 874–890

Abstract	The shell disorder models have predicted that SARS-CoV-2 is of a specific but peculiar evolutionary nature. All coronaviruses (CoVs) closely related to SARS-CoV-2 have been found to have the hardest outer shells (M protein) among CoVs. This hard shell (low M percentage of intrinsic disorder (PID)) is associated with burrowing animals, for example, pangolins, and is believed to be responsible for the high contagiousness of SARS-CoV-2 because it will be more resistant to antimicrobial enzymes found in saliva/mucus. Incoming clinical and experimental data do support this along with a prediction based on another aspect of the shell (N, inner shell) disorder models that SARS-CoV-1 is more virulent than SARS-CoV-2 because SARS-CoV-2 produces fewer virus copies in vital organs even if large amounts of infections particles are shed orally and nasally. A phylogenetic study using M reveals a closer relationship of SARS-CoV to pangolin-CoVs than the bat-RaTG13 found in Yunnan, China. Previous studies may have been confused by recombinations that were poorly handled. The shell disorder models suggest that a pangolin-CoV strain may have entered the human population in 2017 or before as an attenuated virus, which could explain why SARS-CoV is found to be highly adapted to humans.
MeSH term(s)	Animals ; COVID-19 ; China ; Phylogeny ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-02-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00001
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Article ; Online: Feasibility of the vaccine development for SARS-CoV-2 and other viruses using the shell disorder analysis.

Goh, Gerard Kian-Meng / Dunker, A Keith / Foster, James A / Uversky, Vladimir N

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

2021 Volume 26, Page(s) 143–153

Abstract: Several related viral shell disorder (disorder of shell proteins of viruses) models were built using a disorder predictor via AI. The parent model detected the presence of high levels of disorder at the outer shell in viruses, for which vaccines are not ... ...

Abstract	Several related viral shell disorder (disorder of shell proteins of viruses) models were built using a disorder predictor via AI. The parent model detected the presence of high levels of disorder at the outer shell in viruses, for which vaccines are not available. Another model found correlations between inner shell disorder and viral virulence. A third model was able to positively correlate the levels of respiratory transmission of coronaviruses (CoVs). These models are linked together by the fact that they have uncovered two novel immune evading strategies employed by the various viruses. The first involve the use of highly disordered "shape-shifting" outer shell to prevent antibodies from binding tightly to the virus thus leading to vaccine failure. The second usually involves a more disordered inner shell that provides for more efficient binding in the rapid replication of viral particles before any host immune response. This "Trojan horse" immune evasion often backfires on the virus, when the viral load becomes too great at a vital organ, which leads to death of the host. Just as such virulence entails the viral load to exceed at a vital organ, a minimal viral load in the saliva/mucus is necessary for respiratory transmission to be feasible. As for the SARS-CoV-2, no high levels of disorder can be detected at the outer shell membrane (M) protein, but some evidence of correlation between virulence and inner shell (nucleocapsid, N) disorder has been observed. This suggests that not only the development of vaccine for SARS-CoV-2, unlike HIV, HSV and HCV, is feasible but its attenuated vaccine strain can either be found in nature or generated by genetically modifying N.
MeSH term(s)	Animals ; COVID-19 ; COVID-19 Vaccines ; Computational Biology ; Feasibility Studies ; Horses ; Humans ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2021-03-09
Publishing country	United States
Document type	Journal Article
ISSN	2335-6936
ISSN (online)	2335-6936
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity

Gerard Kian-Meng Goh / A. Keith Dunker / James A. Foster / Vladimir N. Uversky

Biomolecules, Vol 10, Iss 2, p

2020 Volume 331

Abstract: The world is currently witnessing an outbreak of a new coronavirus spreading quickly across China and affecting at least 24 other countries. With almost 65,000 infected, a worldwide death toll of at least 1370 (as of 14 February 2020), and with the ... ...

Abstract	The world is currently witnessing an outbreak of a new coronavirus spreading quickly across China and affecting at least 24 other countries. With almost 65,000 infected, a worldwide death toll of at least 1370 (as of 14 February 2020), and with the potential to affect up to two-thirds of the world population, COVID-19 is considered by the World Health Organization (WHO) to be a global health emergency. The speed of spread and infectivity of COVID-19 (also known as Wuhan-2019-nCoV) are dramatically exceeding those of the Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV). In fact, since September 2012, the WHO has been notified of 2494 laboratory-confirmed cases of infection with MERS-CoV, whereas the 2002−2003 epidemic of SARS affected 26 countries and resulted in more than 8000 cases. Therefore, although SARS, MERS, and COVID-19 are all the result of coronaviral infections, the causes of the coronaviruses differ dramatically in their transmissibility. It is likely that these differences in infectivity of coronaviruses can be attributed to the differences in the rigidity of their shells which can be evaluated using computational tools for predicting intrinsic disorder predisposition of the corresponding viral proteins.
Keywords	covid-19 ; wuhan-2019-ncov ; protein intrinsic disorder ; shell disorder ; virulence ; transmission ; nucleocapsid protein ; membrane protein ; Microbiology ; QR1-502 ; covid19
Subject code	612
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity

Gerard Kian-Meng Goh / A. Keith Dunker / James A. Foster / Vladimir N. Uversky

Biomolecules ; Volume 10 ; Issue 2

2020

Abstract	The world is currently witnessing an outbreak of a new coronavirus spreading quickly across China and affecting at least 24 other countries. With almost 65,000 infected, a worldwide death toll of at least 1370 (as of 14 February 2020), and with the potential to affect up to two-thirds of the world population, COVID-19 is considered by the World Health Organization (WHO) to be a global health emergency. The speed of spread and infectivity of COVID-19 (also known as Wuhan-2019-nCoV) are dramatically exceeding those of the Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV). In fact, since September 2012, the WHO has been notified of 2494 laboratory-confirmed cases of infection with MERS-CoV, whereas the 2002– 2003 epidemic of SARS affected 26 countries and resulted in more than 8000 cases. Therefore, although SARS, MERS, and COVID-19 are all the result of coronaviral infections, the causes of the coronaviruses differ dramatically in their transmissibility. It is likely that these differences in infectivity of coronaviruses can be attributed to the differences in the rigidity of their shells which can be evaluated using computational tools for predicting intrinsic disorder predisposition of the corresponding viral proteins.
Keywords	COVID-19 ; Wuhan-2019-nCoV ; protein intrinsic disorder ; shell disorder ; virulence ; transmission ; nucleocapsid protein ; membrane protein ; covid19
Subject code	612
Language	English
Publishing date	2020-02-19
Publisher	Multidisciplinary Digital Publishing Institute
Publishing country	ch
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Shell Disorder Analysis Suggests That Pangolins Offered a Window for a Silent Spread of an Attenuated SARS-CoV-2 Precursor among Humans.

Goh, Gerard Kian-Meng / Dunker, A Keith / Foster, James A / Uversky, Vladimir N

Journal of proteome research

2020 Volume 19, Issue 11, Page(s) 4543–4552

Abstract: A model to predict the relative levels of respiratory and fecal-oral transmission potentials of coronaviruses (CoVs) by measuring the percentage of protein intrinsic disorder (PID) of the M (Membrane) and N (Nucleoprotein) proteins in their outer and ... ...

Abstract	A model to predict the relative levels of respiratory and fecal-oral transmission potentials of coronaviruses (CoVs) by measuring the percentage of protein intrinsic disorder (PID) of the M (Membrane) and N (Nucleoprotein) proteins in their outer and inner shells, respectively, was built before the MERS-CoV outbreak. With M
MeSH term(s)	Animals ; Betacoronavirus/chemistry ; COVID-19 ; Coronavirus Infections/transmission ; Coronavirus Infections/veterinary ; Coronavirus Infections/virology ; Coronavirus Nucleocapsid Proteins ; Eutheria/virology ; Humans ; Intrinsically Disordered Proteins ; Nucleocapsid Proteins ; Pandemics/veterinary ; Phosphoproteins ; Pneumonia, Viral/transmission ; Pneumonia, Viral/veterinary ; Pneumonia, Viral/virology ; Rabbits/virology ; SARS-CoV-2 ; Viral Proteins
Chemical Substances	Coronavirus Nucleocapsid Proteins ; Intrinsically Disordered Proteins ; Nucleocapsid Proteins ; Phosphoproteins ; Viral Proteins ; nucleocapsid phosphoprotein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-08-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00460
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Article ; Online: Nipah shell disorder, modes of infection, and virulence.

Goh, Gerard Kian-Meng / Dunker, A Keith / Foster, James A / Uversky, Vladimir N

Microbial pathogenesis

2020 Volume 141, Page(s) 103976

Abstract: The Nipah Virus (NiV) was first isolated during a 1998-9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher ... ...

Abstract	The Nipah Virus (NiV) was first isolated during a 1998-9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (~71%, 2001-5, ~93%, 2008-12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r
MeSH term(s)	Amino Acid Sequence ; Animals ; Disease Outbreaks ; Disease Susceptibility ; Evolution, Molecular ; Genome, Viral ; Henipavirus Infections/epidemiology ; Henipavirus Infections/virology ; Humans ; Models, Biological ; Mortality ; Nipah Virus/classification ; Nipah Virus/genetics ; Nipah Virus/pathogenicity ; Phylogeny ; Protein Conformation ; Sequence Analysis, DNA ; Swine ; Swine Diseases/epidemiology ; Swine Diseases/virology ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Virulence
Chemical Substances	Viral Proteins
Keywords	covid19
Language	English
Publishing date	2020-01-12
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2020.103976
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