scholarly journals A Routine Sanger Sequencing Target Specific Mutation Assay for SARS-CoV-2 Variants of Concern and Interest

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2386
Author(s):  
Sin Hang Lee
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Sanger Sequencing ◽  
Biological Behavior ◽  
Human Populations ◽  
Rt Pcr ◽  
Genetic Changes ◽  
S Protein ◽  
Amino Acid Mutations

As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have a potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein, along with certain mutations in other regions within the S protein as specific variants, in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.

scholarly journals A Routine Sanger Sequencing Target Specific Mutation Assay For SARS-CoV-2 Variants Of Concern And Interest

2021 ◽  
Author(s):  
Sin Hang Lee
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Sanger Sequencing ◽  
Biological Behavior ◽  
Human Populations ◽  
Rt Pcr ◽  
Genetic Changes ◽  
S Protein ◽  
Amino Acid Mutations

As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein along with certain mutations in other regions within the S protein as specific variants in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.

scholarly journals A Routine Sanger Sequencing Target Specific Mutation Assay For SARS-CoV-2 Variants Of Concern And Interest

2021 ◽  
Author(s):  
Sin Hang Lee
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Sanger Sequencing ◽  
Biological Behavior ◽  
Human Populations ◽  
Rt Pcr ◽  
Genetic Changes ◽  
S Protein ◽  
Amino Acid Mutations

As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein along with certain mutations in other regions within the S protein as specific variants in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.

scholarly journals The amino acid sequence of the B-protein of bacteriophage ZJ-2

1972 ◽  
Vol 127 (1) ◽  
pp. 167-178 ◽  
Author(s):  
D. T. Snell ◽  
R. E. Offord
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Protein Component ◽  
Major Coat Protein ◽  
Male Specific

1. Bacteriophage ZJ-2 is a filamentous male-specific coliphage. Methods are given for its preparation and separation into nucleic acid and the major coat-protein component (B-protein). 2. The determination of the amino acid sequence of the B-protein of bacteriophage ZJ-2 is described. The principal features of this aspect of the work were the special procedures dictated by the insolubility of the protein and the extreme insolubility of its fragments. The sequence is compared with that obtained by other workers for the coat protein of the related bacteriophage fd.

scholarly journals The N-terminal domain of Spike protein contributes to antigenicity difference between porcine epidemic diarrhea virus genotypes G1 and G2

2021 ◽  
Author(s):  
Qi-long Qiao ◽  
Ning Li ◽  
Ming-zhen Song ◽  
Jing Chen ◽  
Pan pan Yang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Porcine Epidemic Diarrhea Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
S Protein ◽  
Diarrhea Virus ◽  
Terminal Domain ◽  
Porcine Epidemic Diarrhea ◽  
Amino Acid Mutations ◽  
Multiple Amino Acid ◽  
S Proteins

Porcine epidemic diarrhea virus (PEDV) strains have been clarified into two genotypes, G1 and G2, based on the sequence of the spike (S) gene. Amino acid mutations that distinguish the two PEDV genotypes were mostly located in the N-terminal domain (NTD) (aa 1-380) of S protein. The fact of increased outbreaks of G2 subtype PEDV and the failure of G1 subtype PEDV strain (CV777)-based vaccine in China since 2010 suggested that multiple amino acid mutations located in the NTD altered the antigenicity of S protein. To determine the role of the NTD of S protein in the antigenicity difference, the NTD of the CV777 vaccine strain (G1) and CH/ZMDZY/11 strain (G2) was expressed in E. coli, respectively. polyclonal antibodies (PAbs) against genotype-specific S proteins were prepared by immunizing BALB/c mice using purified S proteins. Antigenicity was systematically compared by detection of PAbs against two genotype PEDV strains and purified S proteins using Western blot, indirect enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence assay (IFA), and serum cross-neutralization assay (SN). Consistent with the multiple amino acid mutations in the NTD of S protein, different antigenic cross-reactivity between the two genotypes was demonstrated. There was six-fold and more than twenty-fold difference in ELISA and SN titer between anti-CV777 S protein antibodies against G1 and G2 subtype strains, respectively. There was twofold and eight-fold difference in ELISA and SN titer between anti-ZMDZY S protein antibodies against G1 and G2 genotype strains, respectively. The results proved that the NTD of S protein contributes to the antigenicity difference between PEDV genotypes G1 and G2, and highlighted a G2 strain should be used to develop a vaccine for providing better protection against prevalent genotype of PEDV.

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