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RNA-dependent RNA polymerase (RdRp)

An enzyme that uses an RNA template to make new RNA.

Positive-sense RNA (+RNA)

RNA that can generally function directly as mRNA for translation.

Negative-sense RNA (−RNA)

RNA complementary to mRNA; it must be copied into positive-sense RNA before translation.

Double-stranded RNA (dsRNA)

A genome made of two complementary RNA strands that cannot be directly translated.

Segmented RNA genome

A viral genome divided into separate RNA segments, each carrying part of the genetic information

Viral transcription

The process of making mRNA from a viral genome so host ribosomes can produce viral proteins

Viral genome replication

The process of copying the viral genome to produce new genomes for future virus particles.

RNA intermediate

A temporary RNA copy used as a template to produce new viral RNA genomes

RNA amplification

The production of many RNA copies from viral RNA templates, increasing the amount of viral genetic material

Intergenic region (ig)

A region between viral genes that can signal RdRp to stop transcription and begin another mRNA

Vesicular stomatitis virus (VSV)

A non-segmented negative-sense RNA virus that makes separate mRNAs through sequential transcription

VSV transcription termination

RdRp stops at intergenic signals to produce separate mRNAs for individual viral proteins

VSV genome replication

RdRp produces a full-length RNA copy instead of stopping at each intergenic region

Nucleocapsid (N) protein

A viral protein that binds and coats RNA, helping protect it and support genome replication

Influenza genome organization

Has eight negative-sense RNA genome segments

Influenza mRNA production

RdRp makes positive-sense mRNAs from negative-sense genome segments for viral protein production

Influenza genome replication

A positive-sense RNA intermediate is copied to produce new negative-sense genome segments

Rotavirus genome

A double-stranded RNA genome kept protected inside the viral core

Rotavirus core

RdRp-containing viral structure where RNA transcription occurs while the dsRNA genome remains protected

Rotavirus transcription

RdRp makes mRNAs inside the core; the mRNAs exit and are translated by host ribosomes

Rotavirus genome replication

New viral cores replicate RNA to produce double-stranded RNA genomes

Poliovirus genome

A positive-sense RNA genome that can be translated directly into one long polyprotein

Polyprotein

A long protein precursor that is cleaved into multiple functional viral proteins

Viral protease

An enzyme that cuts a polyprotein into separate functional proteins

Poliovirus RNA replication proteins

RNA replication proteins Proteolytic processing produces proteins needed for replication, including VPg and RdRp (3D polymerase)

Rubella structural protein production

RdRp makes a smaller subgenomic mRNA that is translated into structural proteins, including capsid

Subgenomic mRNA

A shorter RNA transcript used to produce specific viral proteins, such as structural proteins

VPg

A poliovirus protein linked to the viral RNA replication process that can serve as an RNA synthesis primer

VPg uridylylation

The addition of two uridine groups to VPg, producing VPg-pUpU for RNA synthesis

VPg-pUpU

A primer that allows poliovirus RdRp to begin extending a new RNA strand

RNA cloverleaf

A structured region of poliovirus RNA involved in recognition and regulation of RNA replication

CRE (cis-acting replication element)

A specific RNA structure that helps support poliovirus RNA replication

Pseudoknot

An RNA structure formed by interactions between different parts of an RNA strand that can contribute to replication signals

De novo RNA synthesis

RNA synthesis that begins without a separate primer

Primer-dependent RNA synthesis

RNA synthesis that begins using a primer, such as poliovirus VPg-pUpU

Polymerase domain conservation

Similarities in polymerase protein regions that reflect shared features of nucleic acid synthesis

DNA polymerase

An enzyme that uses DNA as a template to synthesize DNA

Reverse transcriptase

An enzyme that uses an RNA template to synthesize DNA

SARS-CoV-2 spike protein

The viral protein that binds host receptors and mediates membrane fusion after activation

TMPRSS2

A host cell-surface protease that activates SARS-CoV-2 spike for cell-surface entry

Cathepsins

Host proteases that can activate SARS-CoV-2 spike during entry through acidified endosomes

Cell-surface viral entry

A route where viral fusion machinery is activated at the plasma membrane, allowing entry into the cell

Endosomal viral entry

A route where viruses enter through endocytosis and use endosomal conditions to activate entry or fusion

Endosomal acidification

A decrease in endosomal pH that can activate viral proteins or promote capsid changes needed for entry

Adenovirus

A non-enveloped virus that enters cells through receptor-mediated uptake and delivers its DNA to the nucleus

Adenovirus fiber proteins

Viral surface proteins that help bind host cell receptors during attachment

Integrins

Host cell proteins that can help adenovirus internalization after attachment

Adenovirus capsid destabilization

Changes in the capsid, promoted by endosomal conditions, that help the virus escape the endosome

Adenovirus protein VI

A viral protein that disrupts the endosomal membrane, allowing the virus to escape into the cytoplasm

Adenovirus genome release

The viral capsid reaches the nuclear pore, where viral DNA is delivered into the nucleus

Poliovirus versus rubella

Translates one polyprotein that is cleaved; rubella uses subgenomic mRNA to produce structural proteins

Why rotavirus protects its dsRNA

Keeping dsRNA inside the core protects the genome while allowing mRNAs to be produced and exported for translation

Why negative-sense RNA needs RdRp

Host ribosomes cannot translate negative-sense RNA directly, so viral RdRp must first make positive-sense mRNA

replication

makes new copies of the viral genome

Transcription

makes mRNAs for protein production