Virology(RNA virus)

# Virology(RNA virus) ###### tags: `共筆` <h2 id="Picorna">Picornavirus</h2> ### Picornaviridae family * <a href="#Enteroviruses">Enterovirus (腸病毒)</a> * <a href="#Poliovirus">Poliovirus (小兒麻痺病毒)</a> * Coxsackie A & B * Echovirus * Hepatovirus * Hepatitis A virus (A型肝炎病毒) * <a href="#Rhinovirus">Rhinovirus (鼻病毒)</a> ### Property * Naked, small, icosahedral capsid * **+ssRNA** * Resistant to pH~9, detergents, mild sewage treatment & heat > 可以經由**糞口傳染** > Except: Rhinovirus在酸中不穩定、最適生長溫度為33度 * Most viruses are cytolytic. * Viral RNA is translated into polyprotein. ### Life cycle #### Genome structure * 5' Noncoding Region * VPg * Covalently linked to the 5’ end of the genome * 留下的**primer** * IRES (internal ribosome entry site) * 促進mRNA轉錄(不需要CAP) * Capsid Proteins * Nonstructural Proteins * **Protein processing** (Cut **polyprotein**) * Host shutoff * Polio2A ^pro^ cleaves **eIF4G**, inactivating most cellular translation. > Polio mRNA用IRES而非5'-cap initiate translation > Causes **cell death** * RNA replication * 3' Noncoding Region (3'-poly(A) tail) #### RNA replication * Cell membrane-associated replication * Viral **RNA polymerase (RdRP)** * Host factors: accessory proteins ![](https://i.imgur.com/iQrmY50.png =600x) --- <h3 id="Enteroviruses">Enteroviruses</h3> * 腸病毒(Enteroviruses)++不常造成腸胃道疾病(Enteric disease)++ * **糞口傳染(fecal-oral route)**: 上呼吸道與口咽(Oropharynx)黏膜 -> Intestines 1. 於口咽部複製、亦會感染在小腸黏膜**培氏斑塊**(**Peyer’s patch**)的淋巴球 3. Primary viremia: blood stream 4. Target tissue (**tissue tropism** &cytolytic capacity ) * Skin: * Hand-foot-and-mouth disease(手口足症) * Rash, herpangina(疱疹性咽峽炎) * Muscle * Myocarditis(心肌炎) * Pericarditis(心包炎) * Brain * Encephalitis(腦炎) * Meninges * Meningitis(腦膜炎) * Liver * Hepatitis(肝炎) 5. Secondary viremia * Viral, rather than immune, **pathologic effects** are responsible for causing disease symptoms. <h3 id="Poliovirus"> Poliovirus</h3> * Asymptomatic illness (>90%) * Abortive poliomyelitis, the **minor illness** (5%): nonspecific febrile illness (高熱病) * Nonparalytic poliomyelitis or **aseptic meningitis**(無菌性腦膜炎) (1-2%): back pain(背痛) and muscle spasms(肌肉痙攣) * Paralytic polio, the **major illness** (0.1% to 2.0%) #### Vaccine * Sabin (沙賓) * **口服，活病毒** * **Life long immunity** * Risk of **vaccine-associated poliomyelitis** * Not safe for immunodeficient patients. * Salk (沙克) * 注射，死病毒 * Lack of induction of secretory Ab.(=>會被感染但不會有臨床症狀) * Need boost for life long immunity. <h3 id="Rhinovirus"> Rhinovirus</h3> * Most important cause of the **common cold** * Optimal replication temperature is 33°C or lower. --- <h2 id="Corona">Coronavirus</h2> ### Property * Enveloped, helical symmetry capsid * + ss RNA genome ~30 kb(gene很大的RNA病毒), **5’ capped** and **3’ polyadenylated** * **Glycoprotein**: **可以容忍腸胃道環境**，以**糞口傳遞** * Zoonotic (人畜共通) * Structure * N: Nucleocapsid * Binds to viral RNA * M (E1): Membrane * S (E2): Spike * **Receptor binding and fusion** * E: Small envelope * HE: Hemaglutinin esteras * Involved in **release of virus** from cell ### Life cycle #### Genome organization * 5’-Pol-S-E-M-N-3’ * Gene 1: ORF1a & ORF1b * Non-structural proteins * ORF1a: Viral proteases * ORF1b: Polymerase RNA helicase * Gens 2 to 7: subgenomic mRNAs * Structural proteins #### Transcription * **Ribosomal frameshift**: ORF1a & ORF1ab * Sub-genomic mRNAs share the same 5’ leader sequence and 3’ overlapping sequences > A nested set ![](https://i.imgur.com/6Rf6xUw.png =500x) #### Entry * Receptors for **spike proteins** of ++SARS-CoVand SARS-CoV2++ are **Angiotension-converting enzyme 2 (ACE2)**. (in **upper and lower respiratory tracts**) * Spike protein **needs to be processed** before fusion can occur. > by **Cellular proteases** ![](https://i.imgur.com/uQshERJ.png) ### Disease mechanisms * Human coronavirus infects and kills epithelial cells of the upper respiratory tract. (replicates best at 33~35°C) * SARS-CoV & MERS-CoV replicate at 37°C, kill cells and initiate inflammatory responses in the lung * The **glycoprotein** helps this enveloped virus **survive the gastrointestinal tract**. ### MERS-CoV * **Pneumonia & Renal failure** * Case–fatality rate: 34.4% * Majority of these cases were reported from **Saudi Arabia**. * Occur more readily in the **immunocompromised individuals** or those have another **comorbidity**(合併症). * Receptor: Dipeptyl peptidase 4 (DPP4) * Natural reservoir: dromedary camels ### SARS-CoV-2 (cause of Covid-19) * Beta-coronavirus * Cause ARDS (acute respiratory distress syndrome) #### Transmission for SARS-CoV2 * Respiratory droplets, contact * R~0~ (R naught, the basic reproduction number) * the average number of people who will catch a disease from **one contagious person** * Reduce R0 * (social) distancing * Isolating infected * Immunization, preventive antiviral treatment * Test, isolation, contact trancing #### Anti-viral drugs ![](https://i.imgur.com/iZo9FAB.png =500x) * Remdesivir (a nucleotide analogs) --- <h2 id="Calici">Calicivirus</h2> * Naked icosohedral capsid, +ssRNA, with a 5ʹ-terminal VPg and 3ʹ-terminal poly(A) * Causes acute gastroenteritis(急性腸胃炎) * 因為小腸上皮細胞被破壞 * Replication is similar to coronaviruses ### Norovirus (諾羅病毒) * **Norwalk virus (Norwalk agent)** * Resistant to environmental pressure, detergents, drying and acid > 要用漂白水消毒 * 由受汙染的水或食物**糞口傳染** * Cause outbreaks of **gastroenteritis**, **vomiting** * Disease ++resolves after 48 hours++, without serious consequences. --- <h2 id="Paramyxo">Paramyxovirus</h2> * -ssRNA, enveloped helical nucleocapsid * Infection induces **syncytia** (**cell-cell fusion**, ++multinucleated giant cell++) ### Structure * Surface glycoprotein * Larger glycoprotein (HN, H, G) (**viral attachment protein**) * H: Measles virus * HN: Parainfluenza virus 1~4 * G: Metapneumovirus * Smaller glycoprotein (F) (**fusion protien**) * Ribonucleoprotein (RNP) * Virion-associated polymerase * L (large-polymerase) * P (Phosphoprotein) * Helical nucleocapsid (**RNA plus NP protein**) * Neuraminidase can facilitate **release** (by removing **sialic acid**) * F protein needs to be ++cleaved into F1 and F2++ (Hydrophobic fusion peptide) by a **cellular protease** before it can function in membrane fusion. > Cause cell-cell fusion (**syncytia**) ### Life Cycle * Transcription begins at the exact **3’ end**. * RNA上每段基因間都有**intergenic gap**：有RNA二級結構，RdRP有兩成的機率無法解開而++掉下來++ * 當RNA被N protein bind住：不會產生Gap => RNA replication > High level of N leads encapsidation. ![](https://i.imgur.com/neDz30g.png =500x) * F protein facilitates fusion between membranes at ++physiological pH++ -> **direct fusion** * 在membrane組裝 ![](https://i.imgur.com/KitL3Ka.jpg =400x) ### Pathogenesis and epidemiology |Virus|Disease|Tansmission| |---|---|---| |<a href="#Measles-virus">Measles virus</a>|Maculopapular rash (rubeola) Complications:   Otitis(耳炎), Croup(哮吼), Encephalitis|呼吸道->淋巴組織散佈 **Life-long immunity**| |<a href="#Parainfluenza-virus">Parainfluenza virus</a>|Mild cold-like symptom|**上呼吸道**感染 鮮少造成viremia| |<a href="#Mump-virus">Mump virus</a>|Parotitis (腮腺炎) Orchitis (睪丸炎) Meningoencephalitis(腦膜腦炎)|呼吸道上皮->腮腺| |<a href="#Respiratory-syncytia-virus">Respiratory syncytia virus</a>|**Fatal acute** respiratory tract infection Common cold -> pneumonia|Highly contagious Lower respiratory tract| --- <h3 id="Measles">Measles virus</h3>(麻疹病毒) |3C & P (cough, conjunctivitis, coryza, and photophobia) -> Koplik’s spots -> SSPE| |---| 1. Inoculation of respiratory tract 2. Cell-associated (monocyte and lymphocytes) viremia (Lmphatic spread) 3. Wide dissemination * **Conjunctivae** * Respiratory tract * Urinary tract * Small blood vessels * Lymphatic system * CNS 5. T-cell response to virus-infected epithelial cells => **Rash** * **Koplik’s spots** (柯氏斑點) 7. Rarly cause Encephalitis (occurs in 3 ways) * **SSPE: Subcute sclerosing Panencephalitis** (亞急性硬化性泛腦炎) * Virus causes ==immunosuppresion==. > Prompt to other infections > Can last after recovery * Highly contagious, transmitted by **respiratory droplets**. --- <h3 id="Parainfluenza">Parainfluenza virus</h3> * ++Limited to respiratory tract++ * **Coldlike sypmtoms, bronchitis (支氣管炎), croup(哮吼)** * Protective immunity is short duration => **會被重複感染** --- <h3 id="Mump">Mump virus</h3>(腮腺炎病毒) * Inoculation of respiratory tract -> Viremia -> Systemic infection * **Parotid gland** (腮腺): Loacl inflammation, swelling (腫脹) * Pancreas (胰臟): Juvenile diabetes * Testes (睾丸): Orchitis (睪丸炎) #### Measles-Mumps-Rubella Vaccine --- <h3 id="Respiratory syncytia">Respiratory syncytia virus</h3> * ++Respiratory tract local infection++, causes common cold to pneumonia. * Pneumonia results from **cytopathologic** spread of virus (including syncytia) * **呼吸道狹窄**(Narrow airways) in ++infants++ : **formation of plugs** of mucus, fibrin, and necrotic materials --- <h2 id="Rhabdovirus">Rhabdovirus</h2> ### Properties * Rhabdo -- Rod * Enveloped helical nucleocapsid (bullet shape), simplest, non-segmented -ssRNA virus * Similar genetic organization, transcription, and replication to those of ++Paramyxoviridae and Filoviridae++. * Contains genera: * ++Vesiculovirus++ (vesicular stomatitis virus, VSV, most intensively studied) * ++Lyssavirus++ (**rabies** (狂犬病), rabieslike viruses in animals) ### Life cycle 1. **Receptor mediated endocytosis**: **G protein (glycoprotein)** > Fusion occurs at **acid pH** (enodsome) => 不會有syncytia現象 2. L (RdRp) and P synthesizes mRNA (five monocistronic fragments). 3. Translation: * G is translated by ++ER-bound ribosomes++ * M (Matrix protein), N(nucleocapsid protein), P, and L (RNA polymerase) L are translated by ++free ribosomes++. 4. **High level of N** blocks polyadeynlation and mRNA cleavage => full length +RNA. * There is ++no early/late division++. ![](https://i.imgur.com/IpXMWX8.png =500x) ### Rabies #### Transmission route * Zoonosis (animal to human) * Animal bite * US: bats * Asia: stray dogs * Taiwan: badgers (鼬獾) #### Disease mechanism 1. Virus raplicates in the muscle, with no symptoms (**Incubation phase**) 2. After weeks to month, the virus infects the peripheral nerves and travels up the CNS to the brain (**Prodrome phase**, 前驅期) > 發燒、頭痛、喉嚨痛、疲倦、噁心 4. Infection of the brain (**Neurologic phase**) > Classic brainstem encephalitis (典型的腦幹腦炎)： > 腦神經異常、咽部肌肉收縮的疼痛 => 恐水症(hydrophobia) #### Treatment * **Post-exposure prophylaxis**(預防): due to ++long incubation time++ * Clean wound * Vaccination * **Human rabies immune globulin (HRIG)** > 在非疫區，原則不必打疫苗或HRIG，但要打破傷風 * Once symptoms develop, treatment virtually always **unsuccessful**. #### Diagnosis * **Negri bodies** (內基小體): aggregation of viral nucleocapside in neurons --- <h2 id="Orthomyxo">Orthomyxovirus</h2> ### Properties * Ortho - standard; myxo - mucus * **Segmented** -ssRNA virus, helical symmetry, enveloped * ==Replicate in the nucleus== * Influenza: * Influenza A: human and other mammalians (**zoonosis**) * Influenza B: **human only** * Influenza C: mainly human, swine in China #### Structure * Hemagglutinin (血球凝集素, HA): **Attachment protein**, **Fusion protien** (binding to ++sialic acid++) * Neuraminidase (神經胺酸, NA): Preventing clumping(結塊) and **facilitating release** ( cleaves the ++sialic acid++) > **Only Influenza A has subtypes**: 18 HA and 11 NA subtypes * M2: Ion channel, important for **uncoating** * RdRP: PA, PB1, and PB2 * RNA: **8 segments** (**helical RNP => RNA+NP**) ### Life cycle #### Transcription * RNA splicing for **M2 and NS2** * Cap snatching(stealing): * Influenza virus RdRP (PA) has intrinsic **cap-dependent endonuclease** => steal host mRNA CAP => as a **primer** * Genome is ++transcribed into mRNA++ in the **nucleus** ![](https://i.imgur.com/Tx7Z6fJ.png =700x) ### Pathogenesis * Systemic symptoms: **interferon** and **cytokine** response * Local symptoms: **epithelial cell damage** (ciliated and mucus-secreting cells) * Reye syndrome (雷氏症候群): 幼兒 + 流感 + **Aspirin** => ++嚴重肝和腦的疾病++ * Complications: Bacterial superinfection ### Epidemiology * Spread by inhalation of **small aerosol droplets** * Virus likes a **cool, less humid atmosphere** => winter * High-risk: **Elderly & immunocompromised people** * Major causes of influenza virus- associated death. * **Bacterial pneumonia** * **Cardiac failure** ### Serology * **Antigenic drift** (抗原漂變) * RNA-dependent RNA polymerase has **no proof-reading activity** -> **mutation prone** * **Antigenic shift** (抗原轉移) * Only for influenza A viruses. * **“New” HA or NA proteins** =>宿主從來沒被這個HA或NA感染過 * May cause **pandemics** * Reassortment (segmented viruses) > 兩種型態的病毒同時感染相同細胞時，RNA片段被錯誤包裹到其他病毒 ### Avian influenza viruses * No/limited human to human transmission * H5N1 / H7N9 * Receptor: * Human influenza viruses: sialic acid–a-2,6-Gal(++上呼吸道++) * Avian influenza viruses: sialic acid-a-2,3-Gal(++下呼吸道++) ### Prevention/Treatment #### Durgs |藥物|藥品名|機制|補充| |---|---|---|---| |Rimantadine Amantadine|Flumadine(R) Symadin(R)|M2 inhibitor|Type A only **抗藥性高**| |Zanamivir Oseltamivir|Relenza(R) Tamiflu(R) (**克流感**)|NA inhibitor|Types A and B 僅能**緩解症狀**| |Baloxavir marboxil|Xofluza(R) (紓伏效)|inhibit **cap-dependent endonuclease** activity|Types A and B| #### Vaccine * ‘Best guess’ of main antigenic type * A型: H1N1, H3N2 * B型: Yamagata, Victoria * 三價流感疫苗：2A+1B；四價流感疫苗：2A+2B * **Sub-unit vaccine** for children **Reassortant live attenuated vaccine** for healthy persons --- <h2 id="Reo">Reovirus</h2>(呼腸孤病毒) * Orthoreovirus (正呼腸孤病毒) * Orbiviruses (球狀病毒) / Coltiviruses (科羅拉多壁蝨熱病毒) * <a href="#Rotavirus">Rotavirus(輪狀病毒)</a> ### Property * **Double-layered capsid** =>對於++環境抗性非常高++ > Virion is resistant to detergents, acidic pH, drying. * Naked icosahedral symmetry * ds-RNA **segmented** genome (10-12 fragments) * Family has members that infect a **broad range of hosts** from fungi to humans ### Structure * ISVP (Intermediate/Infectious subviral particle) * Proteolytic **cleavage of outercapsid** (in GI tract) activates the virus for infection -> produces an **ISVP (infectious)** * DsRNAs are **never exposed to cytoplasm**.(因為dsRNA會引發很強的免疫反應) ![](https://i.imgur.com/X8ATsJX.png =500x) ### Life cycle ### Entry * **Receptor mediated endocytosis** * **Acid-dependent** proteolytic cleavage (ISVP -> core) #### Transcription * Complete transcription system, including **RdRP**, **5’ capping** and **poly (A) addition** #### Replication * Early phase: mRNAs are synthesized and capped **inside intact cores** and **extruded through channels into the cytosol** > by ++virion enzymes++ * Late phase: Synthesis of double-stranded genome RNAs occurs **within core-like subvirion particles** * 病毒複製發生於**細胞質** * Double-stranded RNA **remains in the inner core** * Gene segments can be reassorted during coinfection of cells by different strains ![](https://i.imgur.com/mekGwwV.png =500x) --- <h3 id="Rota">Rotavirus</h3> (諾羅病毒) * The ++most common cause++ of **severe diarrheal disease** in **infants and young children** worldwide. * NSP4 > **Inner capsid protein** > Enterotoxin: **mobilize calcium** and causes **diarrhea** * Reassortment of the 11 gene segments -> **Wide variety** of rotavirus strains * 11 different VP7 antigens (outer capsid) (**G-types**) * 11 different VP4 antigen (outer capsid spike protein) (**P-types**) #### Vaccines * Live, attenuated virus will replicate in the gut #### Epidemiology * Transmitted by **fecal-oral route**. * Rotavirus vaccine is available. * **Live, attenuated virus** will replicate in the gut --- <h2 id="Retro">Retrovirus</h2> ### Classification (based on disease) * Lentiviruses > Slow viruses causing **AIDS** and **neurologic disorders** (**HIV-1, 2**) * Endogenous viruses (HERV) > may take up 1% of human genome ### Property * Enveloped with **two copies (diploid)** of +RNA genome * Have virion associated **RNA-dependent DNA polymerase** (reverse transcriptase) and **integrase** enzymes. * Replicate through a **DNA intermediate** (provirus). * Provirus **integrates randomly into the host genome**. ### Genome structure * Gag (Group-specific antigen) * Capsid protein (CA): icosahedral or conical(圓錐) core * Matrix protein (MP), Nucleocapsid protein(NP) * Pol(DNA polymerase): * **RTase** * RNA-dependent DNA polymerase (**Reverse transcripase**) * DNA-dependent DNA polymerase * **RNase H** * **Integrase** * Protease * Env (Envelope proteins) * Surface protein (SU), Transmembrane protein (TM) * Genome = **mRNA** * ++5'-CAP & 3' poly (A) tail++ * 5’ and 3’ ends: **Repeated sequence** ( R ) * U5 and U3: **Unique regions** ### Life cycle #### Entry * Attach: SU (HIV: **gp120**) * Fusion: TM (HIV: **gp41**) * Receptor: **CD4** * Co-receptor: **CCR5** (M-tropic) or **CXCR4** (T-tropic) #### cDNA synthesis * Primer: **tRNA** * RT: * **RNase H activity** (remove RNA from RNA/DNA) * **DNA polymerase activity**. * Very **error prone** -> variants * LTR (long-terminal repeat) is **duplicated at both ends** of the cDNA: U3, R, U5. ![](https://i.imgur.com/ziuKYAk.png =400x) #### Integration * A copy of cDNA is integrated into the cellular genome at a **random site** #### Transcription * **LTR** contains **promoter** and **enhancer** sequences > U3作為promoter * RNA splicing * Gag/Pol: Polyproteins -> proteolytically by **viral protease** * Env #### Translation (gag-pol fusion) * Gag/Pol polyprotein * Suppression of termination (Gamma retrovirus genus) > About 5-10%, UAG is miss-read as CAG (Gln) * Alternative reading frames (HIV-1) > About 5 % of ribosomes shift #### Assembly * The virus **assembles at the plasma membrane**. * Virus **matures after budding** from the cell after protease (PR) cleaves Gag and Gag-pro precursors. * HIV can also spread from cell to cell through syncytia. ![](https://i.imgur.com/OQzV43E.png =500x) --- <h3 id="HIV">Human immunodeficiency virus (HIV)</h3> ### Property * **Lentivirus** genus * Infect CD4^+^ T cells, macrophages, and dendritic cells. * Receptor: CD4 Coreceptor: CXCR4 (T-tropic), CCR5 (M-Tropic) > **SDF-1** in mucosal membrane blocks **CXCR4** virus infection > People with **CCR5-Δ32** are **resistant** to HIV infection. * AIDS (Acquired Immune Deficiency Syndrome) ### HIV infection 1. HIV binds to **DC-SIGN** 2. Active replication in **lymphoid tissue** 3. Massive **viremia** leads to the wide dissemination of virus 4. Persistent infection (reservoir) 5. Immune response down regulates virus replication (**Asymptomatic**) 6. Large **viremia** 7. **Severe immunodeficiency**, **AIDS dementia** * M-tropic (CCR5, ++non-syncytia-inducing++) **switch to** T-tropic (CXCR4, ++syncytia-inducing++) > due to ++changes in cytokine pattern++ and/or ++mutation of Env gene++ * The infection rapidly destroys CD4 T-cells. * HIV-induced cytolysis * HIV budding * Syncytia (cell-cell fusion) * **Cell permeability ↑** * Apoptosis * **Pyroptosis**: a **highly inflammatory form** of programed cell death, ++caspase 1-dependent++ ### Progression of AIDS-related diseases ![](https://i.imgur.com/Uowv0XH.png =400x) * **AIDS-related complex (ARC)**: Weight loss and malaise, diarrhea, night sweats, and fatigue * **Opportunistic** infection and **recurrent infection** (bacteria, herpes, JC, EBV..) * **Malignancies** (惡性腫瘤) (HHV8-associated **Kaposi’s sarcoma**) * AIDS-related dementia: Infected macrophage and microglial cells **secrete neurotoxic substances** #### Disease mechanism * HIV primary infects **CD4 T cells** & cells of the **myeloid lineage** (包含**微膠細胞(Microglial cells)**) * Virus mutant: CCR5(M-tropic) -> CXCR4(T-tropic) * Lytic infection of virus causes CD4 T cell **apoptosis or pyroptosis** * Causes **syncytia formation** * HIV-1 infecZon leads to increase incidence(發生率) of **malignancy(惡性腫瘤)** > EBV, HHV8 (KSHV), HPV #### Transmission of HIV * Inoculation in blood * Sexual transmission * Perinatal (圍產期) transmission > 分娩前後=>藉由++剖腹產++避免經由產道感染 #### Anti-HIV drugs * Different classed of anti-HIV drugs * Nucleoside analog inhibitor (RTase) * Nonnucleoside RTase inhibitor * Protease inhibitors * Integrase inhibitor * Binding and fusion inhibitor * **No vaccine** and no cure for AIDS. * HAART (highly active antiretrovirus therapy, triple therapy) (雞尾酒療法) * The treatment cannot be discontinued ### Oncogenic retroviruses * 帶有oncogene * 在感染後幾天內便會develop tumor * 不會感染人類 ### Long-latency retrovirus * Caused by virus-encoded regulatory protein controlling transcription * Efficiency of tumor formation is very **low** * Takes **long time** for tumor to develop #### Human T-cell lymphotropic (leukemia) virus (HTLV-1) * Encodes a protein (**tax**) that transactivates gene expression * for growth-stimulating cytokines (IL-2, 3, GMCSF, IL-2 receptor) and LTR-dependent transcription activities. ---