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Differential Gene Expression and Transcriptomics Reveal High M‐Gene Expression in JN.1 and KP.1/2 Omicron Sub‐Variants of SARS‐CoV‐2: Implications for Developing More Sensitive Diagnostic Tests
ABSTRACT SARS‐CoV‐2, a positive‐strand RNA virus, utilizes both genomic replication and subgenomic mRNA transcription. Whole genome sequencing (WGS) from clinical samples can estimate viral gene expression levels. WGS was conducted on 529 SARS‐CoV‐2 positive clinical samples from Assam and northeast...
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| Published in: | Journal of medical virology 2024-11, Vol.96 (11), p.e70074-n/a |
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| creator | Siddique, Aktarul Islam Sarmah, Neelanjana Bali, Nargis K. Nausch, Norman Borkakoty, Biswajyoti |
| description | ABSTRACT
SARS‐CoV‐2, a positive‐strand RNA virus, utilizes both genomic replication and subgenomic mRNA transcription. Whole genome sequencing (WGS) from clinical samples can estimate viral gene expression levels. WGS was conducted on 529 SARS‐CoV‐2 positive clinical samples from Assam and northeastern India to track viral emergence and assess gene expression patterns. The results reveal differential expression across structural, non‐structural, and accessory genes, with notable upregulation of the M gene, especially in the Omicron variant, followed by E and ORF6. The mean transcript per million (TPM) expression levels of the M gene were significantly higher in Omicron variants (175 611 ± 46 921), peaking in the KP.1/KP.2 sublineage (220 493 ± 34 917), compared to the Delta variant (129 717 ± 33 773). The relative fold change of M gene expression between Delta and Omicron 2024 subvariants showed a 1.6‐fold change. Variant‐wise gene expression analysis suggests a correlation between gene expression and viral mutation, impacting replication. As anticipated, the expression levels of genes surge with the increase in the virus mutation. The Chi‐square trend for average substitution count versus average TPM of the M gene was highly significant (72.78., p |
| doi_str_mv | 10.1002/jmv.70074 |
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SARS‐CoV‐2, a positive‐strand RNA virus, utilizes both genomic replication and subgenomic mRNA transcription. Whole genome sequencing (WGS) from clinical samples can estimate viral gene expression levels. WGS was conducted on 529 SARS‐CoV‐2 positive clinical samples from Assam and northeastern India to track viral emergence and assess gene expression patterns. The results reveal differential expression across structural, non‐structural, and accessory genes, with notable upregulation of the M gene, especially in the Omicron variant, followed by E and ORF6. The mean transcript per million (TPM) expression levels of the M gene were significantly higher in Omicron variants (175 611 ± 46 921), peaking in the KP.1/KP.2 sublineage (220 493 ± 34 917), compared to the Delta variant (129 717 ± 33 773). The relative fold change of M gene expression between Delta and Omicron 2024 subvariants showed a 1.6‐fold change. Variant‐wise gene expression analysis suggests a correlation between gene expression and viral mutation, impacting replication. As anticipated, the expression levels of genes surge with the increase in the virus mutation. The Chi‐square trend for average substitution count versus average TPM of the M gene was highly significant (72.78., p < 0.0001). The M gene's high expression and low mutation rate make it an ideal target for designing a real‐time RT‐PCR kit assay. These findings highlight the need for continuous surveillance and understanding of viral gene expression dynamics for effective COVID‐19 management. Further studies are necessary to elucidate the significance of these observations in viral pathogenesis and transmission dynamics.</description><identifier>ISSN: 0146-6615</identifier><identifier>ISSN: 1096-9071</identifier><identifier>EISSN: 1096-9071</identifier><identifier>DOI: 10.1002/jmv.70074</identifier><identifier>PMID: 39588700</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Adolescent ; Adult ; Aged ; Child ; COVID-19 ; COVID-19 - diagnosis ; COVID-19 - virology ; Female ; FPKM ; Gene expression ; Gene Expression Regulation, Viral ; Gene sequencing ; Genes ; Genome, Viral - genetics ; Humans ; India - epidemiology ; M gene ; Male ; Middle Aged ; Mutation ; Mutation rates ; Pathogenesis ; Replication ; RNA viruses ; SARS-CoV-2 - genetics ; SARS‐CoV‐2 ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; subgenomic discontinuous replication ; subgenomic mRNA ; TPM ; Transcriptome ; Transcriptomics ; Viral diseases ; Viruses ; Whole Genome Sequencing ; Young Adult</subject><ispartof>Journal of medical virology, 2024-11, Vol.96 (11), p.e70074-n/a</ispartof><rights>2024 Wiley Periodicals LLC.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2784-461ebedf8dc4dcbd3dd236aca93fe622613e56661349260009b652395613d90a3</cites><orcidid>0000-0002-6922-4198</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39588700$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Siddique, Aktarul Islam</creatorcontrib><creatorcontrib>Sarmah, Neelanjana</creatorcontrib><creatorcontrib>Bali, Nargis K.</creatorcontrib><creatorcontrib>Nausch, Norman</creatorcontrib><creatorcontrib>Borkakoty, Biswajyoti</creatorcontrib><title>Differential Gene Expression and Transcriptomics Reveal High M‐Gene Expression in JN.1 and KP.1/2 Omicron Sub‐Variants of SARS‐CoV‐2: Implications for Developing More Sensitive Diagnostic Tests</title><title>Journal of medical virology</title><addtitle>J Med Virol</addtitle><description>ABSTRACT
SARS‐CoV‐2, a positive‐strand RNA virus, utilizes both genomic replication and subgenomic mRNA transcription. Whole genome sequencing (WGS) from clinical samples can estimate viral gene expression levels. WGS was conducted on 529 SARS‐CoV‐2 positive clinical samples from Assam and northeastern India to track viral emergence and assess gene expression patterns. The results reveal differential expression across structural, non‐structural, and accessory genes, with notable upregulation of the M gene, especially in the Omicron variant, followed by E and ORF6. The mean transcript per million (TPM) expression levels of the M gene were significantly higher in Omicron variants (175 611 ± 46 921), peaking in the KP.1/KP.2 sublineage (220 493 ± 34 917), compared to the Delta variant (129 717 ± 33 773). The relative fold change of M gene expression between Delta and Omicron 2024 subvariants showed a 1.6‐fold change. Variant‐wise gene expression analysis suggests a correlation between gene expression and viral mutation, impacting replication. As anticipated, the expression levels of genes surge with the increase in the virus mutation. The Chi‐square trend for average substitution count versus average TPM of the M gene was highly significant (72.78., p < 0.0001). The M gene's high expression and low mutation rate make it an ideal target for designing a real‐time RT‐PCR kit assay. These findings highlight the need for continuous surveillance and understanding of viral gene expression dynamics for effective COVID‐19 management. Further studies are necessary to elucidate the significance of these observations in viral pathogenesis and transmission dynamics.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Child</subject><subject>COVID-19</subject><subject>COVID-19 - diagnosis</subject><subject>COVID-19 - virology</subject><subject>Female</subject><subject>FPKM</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Viral</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genome, Viral - genetics</subject><subject>Humans</subject><subject>India - epidemiology</subject><subject>M gene</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Mutation</subject><subject>Mutation rates</subject><subject>Pathogenesis</subject><subject>Replication</subject><subject>RNA viruses</subject><subject>SARS-CoV-2 - genetics</subject><subject>SARS‐CoV‐2</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>subgenomic discontinuous replication</subject><subject>subgenomic mRNA</subject><subject>TPM</subject><subject>Transcriptome</subject><subject>Transcriptomics</subject><subject>Viral diseases</subject><subject>Viruses</subject><subject>Whole Genome Sequencing</subject><subject>Young Adult</subject><issn>0146-6615</issn><issn>1096-9071</issn><issn>1096-9071</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNp1kc2O0zAUhS0EYsrAghdAltjAIq1_EjdhN2rnlymDpqXbyEluiqvEDnbSYXY8Aq_Fa_Ak3JkOLEZiY0vX3znXOoeQ15yNOWNism134ylj0_gJGXGWqShjU_6UjBiPVaQUTw7IixC2jLE0E-I5OZBZkqaoGJFfc1PX4MH2Rjf0FCzQ4--dhxCMs1Tbiq68tqH0putda8pAr2EHiJ6ZzVe6-P3j52ONsfTi05jfaz9-HvOJoFco9Pi0HAoUrLU32vaBupouj66XOJq5NZ7iAz1vu8aUukejQGvn6Ry3Na4zdkMXzgNdgg2mNzugc6M31oXelHQFoQ8vybNaNwFePdyH5MvJ8Wp2Fl1enZ7Pji6jUkzTOIoVhwKqOq3KuCqLSlaVkEqXOpM1KCEUl5AoDE3GmVAYWVaoRGBgOKkypuUhebf37bz7NuDmvDWhhKbRFtwQcsmlSONYJRzRt4_QrRu8xd_dUXIqOOcxUu_3FGYUgoc677xptb_NOcvv-s2x3_y-X2TfPDgORQvVP_JvoQhM9sCNaeD2_075xWK9t_wDTduzFw</recordid><startdate>202411</startdate><enddate>202411</enddate><creator>Siddique, Aktarul Islam</creator><creator>Sarmah, Neelanjana</creator><creator>Bali, Nargis K.</creator><creator>Nausch, Norman</creator><creator>Borkakoty, Biswajyoti</creator><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7TK</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-6922-4198</orcidid></search><sort><creationdate>202411</creationdate><title>Differential Gene Expression and Transcriptomics Reveal High M‐Gene Expression in JN.1 and KP.1/2 Omicron Sub‐Variants of SARS‐CoV‐2: Implications for Developing More Sensitive Diagnostic Tests</title><author>Siddique, Aktarul Islam ; 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SARS‐CoV‐2, a positive‐strand RNA virus, utilizes both genomic replication and subgenomic mRNA transcription. Whole genome sequencing (WGS) from clinical samples can estimate viral gene expression levels. WGS was conducted on 529 SARS‐CoV‐2 positive clinical samples from Assam and northeastern India to track viral emergence and assess gene expression patterns. The results reveal differential expression across structural, non‐structural, and accessory genes, with notable upregulation of the M gene, especially in the Omicron variant, followed by E and ORF6. The mean transcript per million (TPM) expression levels of the M gene were significantly higher in Omicron variants (175 611 ± 46 921), peaking in the KP.1/KP.2 sublineage (220 493 ± 34 917), compared to the Delta variant (129 717 ± 33 773). The relative fold change of M gene expression between Delta and Omicron 2024 subvariants showed a 1.6‐fold change. Variant‐wise gene expression analysis suggests a correlation between gene expression and viral mutation, impacting replication. As anticipated, the expression levels of genes surge with the increase in the virus mutation. The Chi‐square trend for average substitution count versus average TPM of the M gene was highly significant (72.78., p < 0.0001). The M gene's high expression and low mutation rate make it an ideal target for designing a real‐time RT‐PCR kit assay. These findings highlight the need for continuous surveillance and understanding of viral gene expression dynamics for effective COVID‐19 management. Further studies are necessary to elucidate the significance of these observations in viral pathogenesis and transmission dynamics.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>39588700</pmid><doi>10.1002/jmv.70074</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-6922-4198</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Adolescent Adult Aged Child COVID-19 COVID-19 - diagnosis COVID-19 - virology Female FPKM Gene expression Gene Expression Regulation, Viral Gene sequencing Genes Genome, Viral - genetics Humans India - epidemiology M gene Male Middle Aged Mutation Mutation rates Pathogenesis Replication RNA viruses SARS-CoV-2 - genetics SARS‐CoV‐2 Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 subgenomic discontinuous replication subgenomic mRNA TPM Transcriptome Transcriptomics Viral diseases Viruses Whole Genome Sequencing Young Adult |
| title | Differential Gene Expression and Transcriptomics Reveal High M‐Gene Expression in JN.1 and KP.1/2 Omicron Sub‐Variants of SARS‐CoV‐2: Implications for Developing More Sensitive Diagnostic Tests |
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