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Subgenomic mRNA

Subgenomic mRNAs (sgmRNAs) are a class of positive-sense, single-stranded RNA molecules generated by certain positive-strand RNA viruses, which are shorter than the full-length viral genomic RNA and serve primarily as messenger RNAs for the translation of viral structural and accessory proteins essential for virion assembly and host interaction.^[1] These transcripts are a key feature of the viral replication strategy in families such as Coronaviridae and Togaviridae, enabling efficient expression of downstream genes without requiring the entire genome to be translated.^[2] Unlike the genomic RNA, which encodes non-structural replication proteins, sgmRNAs are produced in a nested, 3'-coterminal set, each initiating at specific internal sites to direct the synthesis of proteins like spike, envelope, membrane, and nucleocapsid in coronaviruses.^[1] In coronaviruses, the production of sgmRNAs occurs through a discontinuous transcription mechanism during the synthesis of negative-sense RNA intermediates by the viral RNA-dependent RNA polymerase complex.^[2] This process involves template-switching at conserved transcription-regulating sequences (TRSs), where the polymerase pauses at body TRSs in the genomic template and jumps to the 5'-leader TRS, fusing a short leader sequence (approximately 65-90 nucleotides) to the 3'-proximal portions of the genome, resulting in 5-8 distinct sgmRNAs ranging from about 0.8 to 27 kb in length.^[1] Recent studies have identified emerging novel sgmRNAs in SARS-CoV-2 that may enhance replication and influence viral evolution.^[3] The abundance of these sgmRNAs increases progressively toward the 3' end of the genome, with the most 3'-proximal transcript (often encoding the nucleocapsid protein) being the most plentiful, up to 5,000 molecules per infected cell at peak replication around 6-8 hours post-infection.^[1] This hierarchical expression supports coordinated viral protein production and has implications for pathogenesis, as accessory proteins translated from sgmRNAs can modulate host immune responses and act as virulence factors.^[2] Beyond coronaviruses, sgmRNAs are also produced by alphaviruses (family Togaviridae), where the mechanism differs and involves internal promoter-driven transcription from a negative-sense RNA intermediate to generate a single, abundant subgenomic RNA of approximately 4 kb that encodes all structural proteins, including capsid and envelope glycoproteins.^[4] In alphaviruses like Sindbis or Chikungunya virus, this subgenomic RNA is synthesized after the processing of non-structural polyproteins, which regulates the switch from genomic replication to subgenomic transcription, ensuring high-level expression of structural components for virion morphogenesis.^[4] This strategy highlights the diversity of sgmRNA production across RNA viruses, adapting to genome organization while optimizing protein synthesis in infected cells.^[4]

Overview

Definition

Subgenomic mRNAs (sgRNAs) are virus-specific messenger RNAs that are shorter than the full-length viral genomic RNA and are derived from specific subgenomic regions of the genome. They are primarily found in positive-sense single-stranded RNA (+ssRNA) viruses, where they serve as templates for the translation of individual viral proteins or subsets of proteins, particularly those located downstream in the polycistronic genome.^[5] Unlike the complete genomic RNA, which functions dually as both the viral genome and an mRNA for producing non-structural proteins such as the RNA-dependent RNA polymerase, sgRNAs are dedicated to expressing structural proteins (e.g., capsid and envelope components) and accessory proteins essential for viral assembly and host interaction.^[6] This specialization allows efficient protein production without the need to translate the entire lengthy genome, optimizing resource use during infection.^[5] The production of sgRNAs occurs as part of the viral transcription process, where the viral polymerase generates these transcripts from internal promoter sites on the negative-sense RNA intermediate, resulting in mRNAs that share the 3' end with the genomic RNA but have truncated 5' ends aligned to specific open reading frames. Mechanisms vary by virus family, such as discontinuous transcription in coronaviruses versus internal initiation in alphaviruses.^[7] This mechanism ensures that sgRNAs possess the necessary 5' cap and 3' poly(A) tail for efficient translation by host ribosomes, while lacking the full genomic sequences required for packaging into new virions.^[5] By focusing translation on late-expressed viral components, sgRNAs play a critical role in temporal regulation of the viral lifecycle, distinguishing them from the genomic mRNA's primary role in early replication and non-structural protein synthesis.^[6] Subgenomic mRNAs were first described in the late 1970s through studies on coronaviruses, such as mouse hepatitis virus (MHV), where multiple nested subgenomic transcripts were identified using RNA fingerprinting techniques, revealing their leader-body fusion structure.^[8] Concurrently, research on togaviruses, including alphaviruses like Sindbis virus, documented a single major subgenomic mRNA responsible for structural protein expression, marking an early recognition of this strategy across +ssRNA virus families.^[9]

Role in Viral Replication

Subgenomic mRNAs (sgRNAs) play a pivotal role in the viral replication cycle of positive-sense single-stranded RNA viruses, particularly those with large genomes like coronaviruses, by facilitating the temporal regulation of gene expression. In the early phase of infection, the incoming genomic RNA serves as an mRNA template for translating non-structural replicase proteins, which form the replication-transcription complexes essential for subsequent RNA synthesis. As infection progresses to the late phase, sgRNAs are transcribed from negative-strand intermediates, enabling the production of structural proteins required for virion assembly and release. This temporal separation ensures efficient progression through the replication cycle, with sgRNA synthesis peaking around 6-8 hours post-infection in coronaviruses.^[10]^[2]^[1] For viruses with expansive genomes, such as coronaviruses spanning 27-32 kb, sgRNAs provide a critical mechanism to circumvent the inefficiencies associated with translating long polycistronic RNAs. The genomic RNA, while capable of encoding multiple proteins, faces challenges in ribosomal scanning and initiation for downstream open reading frames (ORFs), leading to suboptimal expression of 3'-proximal genes. In contrast, sgRNAs are typically monocistronic—translating primarily the 5'-most ORF—or occasionally dicistronic, allowing dedicated and efficient translation of individual structural or accessory genes without interference from upstream sequences. This strategy supports the expression of diverse proteins from a single genome template, optimizing resource allocation during replication.^[1]^[2]^[11] Following transcription, sgRNAs are translated in the host cell cytoplasm by cellular ribosomes, yielding key viral components such as the nucleocapsid (N) protein for genome packaging, envelope proteins (S, E, M) for virion morphogenesis and host cell entry, and accessory proteins that modulate host interactions and immune responses. These proteins accumulate in the endoplasmic reticulum and other cytoplasmic compartments, where they assemble with replicated genomic RNA to form infectious virions. The cytoplasmic localization of sgRNA translation integrates seamlessly with the host's protein synthesis machinery, hijacking it to prioritize viral needs while supporting the final stages of the replication cycle.^[10]^[2] From an evolutionary perspective, sgRNAs confer advantages by enabling subgenomic amplification, which generates higher copy numbers of transcripts for essential structural and accessory proteins without proportionally increasing full-genome replication. This amplification, driven by internal template-switching during negative-strand synthesis, enhances virion production efficiency and supports the maintenance of large genomes under replication constraints. Additionally, by limiting the expression of full-length genomic RNA in the cytoplasm, sgRNAs may reduce exposure to host immune sensors that detect extensive double-stranded RNA intermediates, thereby aiding viral persistence.^[1]^[12]

Synthesis Mechanisms

Discontinuous Transcription

Discontinuous transcription represents the primary mechanism for subgenomic mRNA (sgRNA) synthesis in many positive-sense single-stranded RNA viruses, particularly within the Nidovirales order, including the families Coronaviridae and Arteriviridae.^[13]^[14] In this process, the viral RNA-dependent RNA polymerase (RdRp, often nsp12 in coronaviruses, along with cofactors nsp7 and nsp8) initiates negative-strand RNA synthesis on the positive-sense genomic RNA (gRNA) template, starting from the 3' poly(A) tail and proceeding toward the 5' end.^[10] The polymerase pauses upon reaching a body transcription-regulating sequence (TRS-B) located immediately upstream of the target open reading frame (ORF). At this point, the 3' end of the nascent negative strand, which contains the complement of the TRS-B (anti-TRS-B), base-pairs with the leader TRS (TRS-L) at the 5' end of the gRNA template, facilitating a template switch.^[14]^[13] This base-pairing interaction, driven by sequence complementarity in the conserved core motif (typically 5'-CUAAAC-3' in coronaviruses), allows the polymerase to relocate to the 5' end, resume synthesis by copying the leader sequence (approximately 70-100 nucleotides long), and complete the negative sgRNA strand, which is chimeric with an anti-leader at the 5' end fused to the anti-body sequence.^[14]^[10] The resulting negative sgRNA then serves as a template for positive-strand synthesis, yielding the mature sgRNA with a common 5' leader sequence fused to the gene-specific body and a 3' poly(A) tail.^[10] The efficiency of this template-switching mechanism relies on the sequence similarity and flanking regions of TRS-L and TRS-B, which enhance base-pairing stability (often quantified by free energy changes, ΔG, with favorable interactions exceeding -35 kcal/mol).^[14] Mutations disrupting this complementarity, as demonstrated in arteriviruses like equine arteritis virus, abolish or severely reduce sgRNA production for specific genes, while compensatory mutations restore it, confirming the guiding role of base pairing.^[13] In coronaviruses, the core sequence is nonessential but amplifies transcription efficiency by up to 1,000-fold when present.^[14] Polymerase fidelity during switching may involve viral cofactors for processivity and host factors, such as the RNA helicase DDX1 interacting with nucleocapsid protein, to stabilize replication-transcription complexes within double-membrane vesicles.^[10] This mechanism produces a nested set of sgRNAs, with those from 3'-proximal ORFs being most abundant due to proximity to the initiation site.^[1] Studies on bovine coronavirus show sgRNA accumulation rates 10- to 100-fold higher than full-length genomic RNA during the amplification phase, reaching up to 5,000 molecules per cell for certain sgRNAs compared to approximately 20 for the genome at peak infection.^[1] This disparity underscores the selective advantage of discontinuous transcription for efficient expression of downstream genes without replicating the entire genome repeatedly.^[1]

Alternative Pathways

In alphaviruses, which belong to the Togaviridae family, subgenomic mRNA (sgRNA) synthesis proceeds via continuous transcription initiated at an internal promoter on the negative-strand RNA template, distinct from the template-switching required in discontinuous mechanisms. This subgenomic promoter, located in the junction region between the non-structural and structural gene regions, spans roughly -98 to +14 nucleotides relative to the transcription start site and is recognized by the viral RNA-dependent RNA polymerase complex. The resulting 26S sgRNA is 3'-coterminal with the genomic RNA but lacks a 5' leader sequence, directly encoding the viral capsid and envelope proteins through ribosomal scanning from its capped 5' end. The non-structural protein nsP2 functions as a key regulator, binding the promoter to enhance replicase recruitment and modulate synthesis efficiency, ensuring temporal control during infection.^[15]^[16] Certain plant-infecting positive-strand RNA viruses employ structural rearrangements in the genomic RNA to activate sgRNA promoters without polymerase jumping. In umbraviruses, such as those in the Umbravirus genus, dimerization of the plus-strand genomic RNA via a kissing-loop interaction between complementary stem-loop structures positions distant regulatory elements to stimulate transcription of the sgRNA. This base-pairing-mediated process, detailed in a 2023 study, facilitates expression of the ORF3 movement protein essential for viral spread in plants, operating independently of host factors and highlighting RNA folding as a regulatory switch. The mechanism ensures sgRNA production only upon genome dimerization, which occurs during replication, thereby linking RNA packaging to gene expression.^[17] Premature termination of transcription represents another alternative route in some positive-strand RNA viruses, generating truncated templates for sgRNA synthesis. For example, in tombusviruses like tomato bushy stunt virus, the RNA-dependent RNA polymerase halts synthesis at promoter-proximal sites during negative-strand production, yielding shorter antigenomic templates that direct sgRNA transcription for downstream genes. This process is governed by cis-acting RNA elements and long-distance interactions that stabilize termination signals, allowing regulated expression without full-length genomic traversal. In togaviruses, while primary sgRNA synthesis relies on internal initiation, polyprotein processing by viral proteases indirectly influences rates by cleaving non-structural precursors, thereby activating replicase components needed for promoter-driven transcription.^[11]^[18] Although subgenomic mRNAs in the classical sense are uncommon in negative-sense RNA viruses, paramyxoviruses achieve analogous functional diversity through overlapping genes and co-transcriptional mRNA editing. In viruses like respiratory syncytial virus, the phosphoprotein (P) gene features overlapping reading frames, enabling multiple protein isoforms from a single transcript via alternative start sites. Additionally, P mRNA editing involves polymerase stuttering at a template G-run, inserting non-templated G residues to shift the reading frame and produce the essential P protein, effectively generating sgRNA-like variants that expand coding potential from compact genomes. These strategies prioritize precise control over gene expression in the context of sequential transcription from the 3' end.^[19] In select positive-strand RNA viruses lacking conventional leader-body fusion, sgRNAs support cap-independent translation via internal ribosome entry sites (IRES), as observed in some picornaviruses and flaviviruses where genomic RNAs harbor IRES elements for internal ORF access, mimicking subgenomic output without separate RNA species. However, true sgRNA generation in these families remains limited, with expression relying on polyprotein cleavage rather than distinct transcripts.^[11]

Structural Features

Leader Sequence

In viruses that employ discontinuous transcription, such as coronaviruses and related nidoviruses, the leader sequence of subgenomic mRNAs (sgRNAs) is a short, conserved segment, typically 50–220 nucleotides in length, located at the 5′ end of all sgRNAs within a given virus and identical to the 5′ terminus of the viral genomic RNA.^[13] This sequence includes a 5′ cap structure acquired during synthesis, which mimics eukaryotic mRNA features, and incorporates promoter elements such as the leader transcription regulatory sequence (TRS-L) that guide the viral RNA-dependent RNA polymerase (RdRp) for discontinuous transcription initiation.^[10] In coronaviruses, the leader is approximately 65–98 nucleotides long, while in related nidoviruses like arteriviruses, it extends to 156–221 nucleotides, reflecting family-specific adaptations in sgRNA production.^[13] In contrast, alphaviruses (family Togaviridae) produce a single sgRNA via internal promoter-driven transcription, featuring a distinct short 5′ untranslated region (UTR) of about 40–60 nucleotides that is not identical to the genomic RNA's longer 5′ UTR (~250 nucleotides in Sindbis virus).^[20] Functionally, in nidoviruses, the leader sequence serves multiple critical roles in sgRNA stability and utilization. The 5′ cap protects the mRNA from 5′ exonucleolytic degradation by host cellular enzymes, enhancing its longevity within infected cells.^[10] It also facilitates efficient binding of host ribosomes for translation initiation, as the unstructured or structured elements in the leader promote scanning or direct recruitment, bypassing some host antiviral translation shutoff mechanisms like those mediated by SARS-CoV-2 nsp1.^[10] Additionally, the embedded TRS-L motif enables polymerase recognition and template switching during discontinuous synthesis, ensuring the leader is fused to diverse body sequences downstream of body TRS (TRS-B) sites.^[10] The leader sequence exhibits high conservation across sgRNAs and viral strains, underscoring its essentiality; in coronaviruses, it often features elevated GC content, particularly in the 5′ untranslated region, which supports stable RNA secondary structures like stem-loops for regulatory functions.^[21] Mutations within the leader or TRS-L, such as alterations disrupting base-pairing with TRS-B, significantly impair sgRNA production and viral replication, as demonstrated in mutagenesis studies on SARS-CoV-2 and related coronaviruses.^[10] For instance, variants with changes in these motifs show reduced abundance of specific sgRNAs, highlighting the sequence's vulnerability and role in viral fitness.^[10]

Body and Poly(A) Tail

The body of a subgenomic mRNA (sgRNA) constitutes the variable central region, initiating immediately downstream of the body transcription regulatory sequence (TRS), and extends to the 3' end of the RNA molecule. This region encodes one or more open reading frames (ORFs) specific to viral structural or accessory proteins, such as the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins in coronaviruses. Unlike the full genomic RNA, which is polycistronic and primarily serves replication functions, the sgRNA body is structured to prioritize translation of its 5'-most ORF, with downstream ORFs often accessed via alternative mechanisms like ribosomal frameshifting or internal ribosome entry.^[22] The poly(A) tail is a hallmark 3' modification of sgRNAs, added post-transcriptionally and identical in sequence and function to that of the genomic RNA. Typically ranging from 40 to 100 nucleotides in length—though varying dynamically during infection, as observed in mouse hepatitis virus where tails shorten from ~65 nt early to ~30 nt late—this homopolymeric adenosine stretch is generated through slippage of the viral RNA-dependent RNA polymerase on U-rich sequences in the negative-strand template. This process, akin to stuttering during synthesis, ensures the tail's addition without requiring host poly(A) polymerase in most cases. The poly(A) tail is essential for mRNA stability by protecting against exonucleolytic degradation, facilitating nuclear export (though coronaviral replication occurs in the cytoplasm), and promoting longevity within host cells.^[23]^[24]^[22] Furthermore, the poly(A) tail interacts with the 5' cap structure to enable mRNA circularization, enhancing translation efficiency by recruiting ribosomes and eukaryotic initiation factors. In coronaviruses, this stabilization is critical for efficient protein production from sgRNAs. Compared to the genomic RNA, which spans 26-32 kb and encodes non-structural proteins across its length, sgRNA bodies are markedly shorter, typically 1-8 kb depending on the targeted ORF, thereby reducing the translational burden on host machinery by limiting the polycistronic complexity and focusing on discrete viral gene expression.^[24]^[22]

Examples in Viruses

Coronaviridae Family

In the Coronaviridae family, subgenomic mRNAs (sgRNAs) are produced as a nested set of 6-10 transcripts during viral replication, enabling the expression of structural and accessory proteins downstream of the genomic RNA. Each sgRNA shares a common 5' leader sequence but possesses a unique body transcription-regulating sequence (TRS) that directs discontinuous transcription for specific genes, such as the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. This nested structure ensures efficient translation primarily from the 5'-proximal open reading frame of each sgRNA, with examples like SARS-CoV-2 generating up to 10 canonical sgRNAs alongside noncanonical variants.^[25] In SARS-CoV-2, a prominent member of the family, nine canonical sgRNAs have been consistently detected in infected individuals, persisting in clinical samples up to 17 days after symptom onset. These sgRNAs correspond to key genes including S, E, M, and N, with varying abundances reflecting active viral gene expression. Variants such as Alpha (B.1.1.7) and Delta exhibit altered sgRNA profiles; for instance, Alpha shows elevated levels of S, M, E, N, and ORF6 sgRNAs compared to Delta, which displays intermediate abundances, potentially contributing to differences in disease severity observed with these lineages.^[26]^[25]^[27]^[28] The production of these sgRNAs relies on the high-fidelity RNA-dependent RNA polymerase (RdRp), nsp12, which forms a holoenzyme complex with cofactors nsp7 and nsp8 to facilitate precise recognition of TRS elements during template switching. This complex enhances processivity and accuracy in discontinuous minus-strand synthesis, incorporating the leader TRS to generate the nested sgRNA set while minimizing errors through proofreading mechanisms.^[10] SgRNAs in coronaviruses like SARS-CoV-2 serve as potential markers of active viral replication in diagnostics, as their detection often correlates more closely with viable, replication-competent virus than persistent genomic RNA, which can linger in samples without ongoing infection.^[29]^[30]

Other RNA Virus Families

Members of the Togaviridae family, such as Sindbis virus, generate a single subgenomic RNA (sgRNA) that encodes the viral structural proteins, synthesized via internal initiation at a subgenomic promoter located within the junction between nonstructural and structural genes on the negative-strand RNA template.^[31] This 26S sgRNA, approximately 4 kb in length, is produced by the viral RNA-dependent RNA polymerase (RdRp) through continuous transcription starting at an internal site, effectively acting as a premature termination of full-length genomic synthesis to yield a shorter mRNA.^[32] The promoter region, spanning about 19–68 nucleotides upstream of the start site, includes conserved stem-loop structures that direct RdRp binding and initiation, ensuring efficient expression of capsid, envelope, and glycoprotein genes during late infection stages.^[33] This mechanism contrasts with discontinuous strategies in other families, relying instead on promoter-driven internal entry for sgRNA production.^[34] In the Umbraviridae family of plant viruses, such as Pea enation mosaic virus 2 (PEMV2), a single RdRp-mediated sgRNA encodes the movement protein essential for cell-to-cell spread, with transcription activated by dimerization of the plus-strand genomic RNA via a kissing-loop interaction in the 5' region.^[35] This 2023 study revealed that genome dimerization exposes or stabilizes an internal promoter, allowing the RdRp to initiate sgRNA synthesis downstream of the replicase gene, thereby regulating the temporal switch from replication to movement protein expression. The process involves base-pairing between two RNA stem-loops, one near the 5' end and another in the replicase coding region, which is critical for efficient sg mRNA production in infected plant cells.^[36] Umbraviruses lack a capsid and rely on helper viruses for transmission, making this dimerization-dependent mechanism a unique adaptation for sgRNA control in their lifecycle.^[37] Arteriviridae viruses, including porcine reproductive and respiratory syndrome virus (PRRSV), produce 3–4 major sgRNAs through a discontinuous synthesis mechanism analogous to that in coronaviruses, involving fusion of a common 5' leader sequence with body sequences at transcription-regulatory sequences (TRSs) to form junction sites.^[13] These sgRNAs encode accessory and structural proteins, with synthesis guided by base-pairing between the genomic 5' end and TRS elements during minus-strand RNA production, leading to template switching by the RdRp.^[38] A conserved RNA hairpin in the leader region further regulates the discontinuous step, ensuring precise junction formation and varying sgRNA abundances based on TRS strength and spacing.^[39] This results in fewer sgRNAs compared to coronaviruses, reflecting the more compact arteriviral genome of about 15 kb.^[40]

Biological and Diagnostic Importance

Regulation of Gene Expression

Subgenomic mRNAs (sgRNAs) in positive-sense RNA viruses facilitate temporal regulation of gene expression by enabling a phased approach to viral protein synthesis. Transcription of sgRNAs typically ramps up after the initial establishment and translation of the replicase complex from the genomic RNA, allowing the virus to first prioritize non-structural proteins essential for replication machinery before shifting to structural and accessory proteins. This temporal shift is evident in SARS-CoV-2 infections, where sgRNA production becomes prominent around 4 hours post-infection, peaking at later stages as replication organelles mature and support exponential RNA synthesis.^[41] The molecular basis involves replication-transcription complexes that favor discontinuous synthesis at body transcription regulatory sequences (TRS-B) only after replicase polyproteins are processed, ensuring coordinated progression of the viral lifecycle.^[10] Gene prioritization is achieved through a hierarchy of TRS strengths, where variations in TRS sequence, length, and flanking elements dictate sgRNA abundance, with stronger TRS promoting higher transcription rates for critical genes. In coronaviruses like transmissible gastroenteritis virus, the nucleocapsid (N) gene TRS, spanning 88 nucleotides, generates 2-4 times more sgRNA than those for membrane (M) or spike (S) genes due to optimal core sequences and stability. Similarly, in SARS-CoV-2, the 3'-proximal N TRS results in the highest sgRNA levels among the nine canonical species, reflecting positional and sequence-based efficiency that biases toward structural proteins needed for virion assembly. This hierarchy maintains consistent sgRNA-to-genomic RNA ratios across infection stages, fine-tuning protein stoichiometry without requiring post-transcriptional adjustments.^[42]^[10] Translational efficiency of sgRNAs is enhanced by shared structural features that mimic host mRNAs, promoting selective viral protein synthesis in a competitive cellular environment. The conserved 5' leader sequence (~70-75 nucleotides), identical across sgRNAs, facilitates cap-dependent ribosome scanning from the 5' cap added during synthesis, with the leader's stem-loop structures boosting initiation at upstream open reading frames (ORFs). For polycistronic sgRNAs encoding multiple proteins, downstream ORFs employ leaky scanning—where ribosomes bypass suboptimal upstream start codons—or internal ribosome entry sites (IRES) embedded in RNA elements to enable cap-independent initiation, as observed in infectious bronchitis virus mRNA 3 and mouse hepatitis virus mRNA 5.^[24] This dual mechanism allows efficient expression of accessory proteins without compromising the primary ORF translation.^[24] Quantitative control of sgRNA levels directly influences protein output, with abundance correlating to functional demands such as virion packaging. In SARS-CoV-2, the N gene sgRNA is the most abundant, often comprising up to 40% of total viral transcripts in infected cells, underscoring its prioritization for encapsidating genomic RNA during late infection stages. This disparity in sgRNA quantities—N exceeding others like S or E by several fold—ensures stoichiometric balance for assembly while minimizing resource waste on less essential genes.^[43] SgRNAs interact with host defenses by structurally resembling cellular mRNAs, thereby evading innate immune detection, but dysregulation can provoke antiviral responses. Coronaviruses employ non-structural proteins like nsp16 to add 2'-O-methylation to the 5' cap of sgRNAs, mimicking the "self" signature of host transcripts and reducing recognition by sensors such as RIG-I and MDA5, which suppresses type I interferon (IFN) production. However, if this capping or methylation is impaired—such as through nsp16 mutations—sgRNAs become more immunogenic, triggering robust IFN responses and limiting viral replication. This evasion strategy highlights the delicate balance viruses maintain to exploit host translation machinery without alerting immunity.^[44]^[45]

Applications in Virology and Diagnostics

Subgenomic mRNAs (sgRNAs) serve as valuable markers in virology research for monitoring viral replication dynamics. Profiling of sgRNAs using reverse transcription quantitative PCR (RT-qPCR) enables precise tracking of replication kinetics in infected cells, as sgRNA abundance correlates directly with active transcription and viral productivity.^[25] For instance, time-course RT-qPCR assays have quantified sgRNA levels during SARS-CoV-2 infection, revealing that subgenomic transcripts for structural genes like N and E peak around 24-48 hours post-infection, providing insights into the temporal progression of discontinuous transcription.^[46] Additionally, CRISPR-based approaches targeting transcription-regulatory sequence (TRS) junctions have demonstrated potent inhibition of sgRNA production; post-2020 studies using CRISPR-Cas13d to cleave TRS-adjacent regions reduced sgRNA yields by over 90% in cell models of SARS-CoV-2 and other coronaviruses, highlighting their utility in antiviral screening.^[47] In diagnostics, sgRNA detection offers a specific indicator of ongoing viral replication, distinguishing active infection from residual genomic RNA remnants. Assays targeting SARS-CoV-2 sgRNAs for the E or N genes via RT-qPCR show higher sensitivity for viable virus, as these transcripts are rapidly degraded and thus absent in non-replicating samples.^[48] For example, sgN RNA detection in nasopharyngeal swabs correlates with culturable virus isolation, with cycle threshold values below 25 indicating high replication competence, unlike genomic RNA which persists longer post-recovery.^[49] A 2023 study in eBioMedicine analyzed sgRNA profiles across SARS-CoV-2 variants (Alpha, Delta, Omicron sublineages), revealing variant-specific imbalances—such as higher levels of S, M, and Orf6 sgRNAs in Omicron BA.5—that aid in subvariant identification and infectivity assessment during surveillance.^[50] Therapeutically, sgRNA-inspired platforms have advanced vaccine development, particularly self-amplifying mRNAs (saRNAs) that mimic sgRNA structures for enhanced antigen expression. saRNA vaccines, derived from alphavirus replicons, incorporate subgenomic promoters to drive high-level, transient production of SARS-CoV-2 spike protein, achieving protective immunity in nonhuman primates with doses as low as 2 μg.^[51] These constructs amplify intracellularly, yielding sgRNA-like transcripts that boost humoral responses 10-fold over conventional mRNAs.^[52] Furthermore, inhibitors targeting discontinuous synthesis show promise as broad-spectrum antivirals; remdesivir (GS-5734) disrupts TRS-mediated template switching, significantly reducing sgRNA output across betacoronaviruses in vitro and in vivo models.^[53] Despite these applications, sgRNAs necessitate highly sensitive assays like digital droplet PCR for reliable detection in low-abundance samples.^[54] Emerging research as of 2025 is exploring sgRNA monitoring for long COVID, where persistent viral RNA may signal ongoing reservoirs in some symptomatic cases, informing targeted interventions.^[55]

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Feb 1, 2025 · Current data indicate that sgRNA detection is more sensitive and specific for viable viruses than genomic RNA analysis [8]. Despite some ...
[28]
Profiling of SARS-CoV-2 Subgenomic RNAs in Clinical Specimens
Mar 21, 2022 · The sgRNAs contain a common 5′ leader sequence of approximately 70 nucleotides fused to different segments from the 3′ end of the viral genome ...
[29]
Mechanism and structural diversity of exoribonuclease-resistant ...
Jan 9, 2018 · Subgenomic flavivirus RNAs result when the 5′–3′ progression of cellular exoribonuclease Xrn1 is blocked by RNA elements called Xrn1-resistant ...
[30]
The subgenomic flaviviral RNA suppresses RNA interference ...
Jan 30, 2024 · Importantly, ZIKV sfRNA acts as a potent viral suppressor of RNAi (VSR) by competing with siRNAs for binding RISC components, RHA and PACT. The ...
[31]
Subgenomic flavivirus RNA binds the mosquito DEAD/H-box ... - PNAS
Sep 5, 2019 · All flaviviruses, including those that exclusively replicate in mosquitoes, produce a highly abundant, noncoding subgenomic flavivirus RNA ( ...
[32]
Subgenomic Flaviviral RNAs of Dengue Viruses - PMC
Nov 24, 2023 · The most important role of DENV sfRNAs is to inhibit host antiviral responses by interacting with viral and host proteins, thereby influencing ...
[33]
Zika Virus Subgenomic Flavivirus RNA Generation Requires ...
A common feature of flavivirus-infected cells is the accumulation of viral noncoding subgenomic RNAs by partial degradation of the viral genome, known as sfRNAs ...
[34]
Promoter for Sindbis virus RNA-dependent subgenomic ... - PMC - NIH
Two species of mRNA are synthesized in cells infected with Sindbis virus; one, the 49S RNA, is the genomic RNA; the other, the 26S RNA, is a subgenomic RNA ...
[35]
Distinct Sites on the Sindbis Virus RNA-Dependent ... - ASM Journals
Sindbis virus-infected cells make two positive-strand RNAs, a genomic (G) RNA and a subgenomic (SG) RNA. Here we report the amino acid sequence in ...
[36]
Specific Nucleotide Changes in the Subgenomic Promoter Region ...
This subgenomic mRNA is identical to the 3′ third of the genomic RNA that encodes the virus' structural proteins [3], which are required for progeny virion ...
[37]
Cis-acting RNA elements at the 59 end of Sindbis virus genome ...
The 59 end of Sindbis virus RNA contains core promoter elements for both minus- and plus-strand synthesis, regulating RNA synthesis.
[38]
Dimerization of an umbravirus RNA genome activates subgenomic ...
Jul 3, 2023 · Here we report that an umbravirus activates sg mRNA transcription via base pair-mediated dimerization of its plus-strand RNA genome.
[39]
Dimerization of an umbravirus RNA genome activates subgenomic ...
Here we report that an umbravirus activates sg mRNA transcription via base pair-mediated dimerization of its plus-strand RNA genome.
[40]
Umbravirus-like RNA viruses are capable of independent systemic ...
Apr 25, 2024 · Dimerization of an umbravirus RNA genome activates subgenomic mRNA transcription. Nucleic Acids Res. 2023;51:8787–8804. doi: 10.1093/nar ...
[41]
Discontinuous Subgenomic RNA Synthesis in Arteriviruses Is ...
We hypothesize that a conformational switch in the LTH region regulates the role of the 5′-proximal region of the arterivirus genome in subgenomic RNA synthesis ...
[42]
New insights about the regulation of Nidovirus subgenomic mRNA ...
The initial model, a leader-primed transcription model (Lai, 1986) suggested that discontinuous transcription occurred during the synthesis of plus strand RNA ...<|control11|><|separator|>
[43]
Regulation of Relative Abundance of Arterivirus Subgenomic mRNAs
Their 5′ common leader sequence is derived from the genomic 5′-proximal region. Fusion of sg RNA leader and “body” segments involves a discontinuous ...
[44]
A high-resolution temporal atlas of the SARS-CoV-2 translatome ...
Aug 25, 2021 · SARS-CoV-2 has a ~30 kb single-stranded positive-sense RNA genome that is used as a template for subgenomic RNA (sgRNA) transcription. Two ...
[45]
Transcription Regulatory Sequences and mRNA Expression Levels ...
The coronavirus RNA genome has a length ranging from 27.6 to 31.5 kb. About two-thirds of the entire RNA comprises open reading frames (ORFs) 1a and 1ab, ...
[46]
The Architecture of SARS-CoV-2 Transcriptome - ScienceDirect.com
May 14, 2020 · In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or ...Missing: seminal | Show results with:seminal
[47]
The Interplay Between Coronavirus and Type I IFN Response
Coronaviruses have evolved nsp16 with 2′-O-methyltransferase activity, which autonomously modifies viral mRNAs with a 5′ cap structure, mimicking host mRNA.
[48]
Coronavirus takeover of host cell translation and intracellular ...
Jan 10, 2024 · This review provides an overview of how coronaviruses control viral and host translation during different stages of infection<|separator|>
[49]
Tracking the Transcription Kinetic of SARS-CoV-2 in Human Cells ...
We found that SARS-CoV-2 takes around 6 h to hijack the cells before the initiation of viral transcription process in human cells.
[50]
https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00234-7/fulltext
[51]
https://www.nature.com/articles/s41467-022-31005-z/
[52]
Correlation of SARS-CoV-2 Subgenomic RNA with Antigen ... - CDC
Aug 23, 2021 · sgRNA was detectable in 13 (81.2%) of 16 nasopharyngeal swab specimens from antigen-negative persons. Days after symptom onset (when the sample ...Missing: post- | Show results with:post-
[53]
https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1520811/full
[54]
Self-Amplifying RNA: A Second Revolution of mRNA Vaccines ...
Mar 17, 2024 · A special type of mRNA vaccine is based on self-amplifying RNA (saRNA) derived from the genome of RNA viruses, mainly alphaviruses.
[55]
Advancements in the development of antivirals against SARS ...
Jan 22, 2025 · Both viruses utilise a discontinuous transcription ... Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses.
[56]
SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical ...
Jul 20, 2021 · SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication . Nat Commun. 2020. ;. 11. : 6059.