SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise
Abstract
:1. Introduction
2. Methods
3. Origins of SARS-CoV-2 and HIV-1
4. Operating Principles of SARS-CoV-2 and HIV-1
4.1. Viral Composition
4.2. Viral Replication
4.2.1. Viral Entry
4.2.2. Translation, Transcription, and Reverse Transcription
4.2.3. Virus–Host Interaction and Exploitation of the Cellular Machinery
4.2.4. Proteolytic Processing of Viral Proteins
5. Humoral Immune Responses
5.1. Antibody Binding and Neutralization
5.2. Antibody Fc-Mediated Functions
5.3. Antibody Escape and Mutant Variants
5.3.1. HIV-1’s Rapid and Continuous Escape
5.3.2. SARS-CoV-2 Mutates on a Low but Constant Level, Yielding Mutant Variants over Time
6. Cellular Responses
6.1. T Cells
6.2. B Cells
6.3. Monocytes/Macrophages
7. Cytokines and Innate Immune Response
Interferon Response
8. SARS-CoV-2 and HIV-1 Co-Infection and Mutual Impact
9. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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HIV-1 | SARS-CoV-2 | Refs | |
---|---|---|---|
Demographic features | |||
geographic origin | West-Central Africa (Cameroon, DR Congo) | China (Wuhan) | [5,6] |
first recorded case | HIV-1: 1959 (DR Congo) | SARS-CoV-2: Nov. 17, 2019 (China) | [7,8,9,10] |
AIDS: 1981 (USA) | COVID-19: Dec. 31, 2019 (China) | ||
est. time of origin/cross-species transmission | 1920s | October/November 2019 | [7,11,12,13] |
animal source | non-human primates | primary host: bats, intermediate hosts: small mammals; yet unconfirmed | [5,14,15,16] |
active cases | 38 Mio a | 12 Mio b | [17,18] |
cases since pandemic start | 76 Mio a (1.7 Mio new infections in 2019) | 179 Mio b | [17,18] |
deaths since pandemic start | 33 Mio a (0.7 Mio in 2019) | 3.9 Mio b | [17,18,19] |
Viral features | |||
Baltimore virus classification | Group VI | Group IV | [20,21] |
virus family | Retroviridae | Coronaviridae | |
virus diameter | 100–150 nm | 60–140 nm | [6,22,23] |
number of spikes per virus | 7–14 | 15–40 | [23,24,25] |
spike size (height × width) | 12 × 15 nm | 20 × 13 nm | [26,27,28,29] |
spike amino acids | 856 | 1273 | [30,31] |
potential N-glyco sites per spike monomer | 31 (HxB2) | 22 (Wuhan-Hu-1) | [30,31] |
spike proteolytic cleavage sites | 1 | 2 | [32,33] |
capsid | Conical (many hexagons and 12 pentagons of subunits) | helical | [34,35,36] |
genome | (+)ssRNA, diploid dsDNA genome intermediate | (+)ssRNA, haploid | [37,38] |
genome size | 9.7 kb (one of the smallest viral genomes) | 29.7 kb (one of the largest viral genomes) | [30,31] |
evolution rate | proviral DNA: 4 × 10−3 per base per cell (1 mutation every 250 base pairs) | 1 × 10−3 per base per year (2 mutations per month) | [12,39,40] |
virus in plasma: 2–17 × 10−3 per base per year | |||
within-host diversity (in the absence of superinfection) | <5% (<10% for proviral env) | <0.05% | [41,42,43] |
replication cycle | ~24 h (in vitro)–60 h (in vivo) | ~7–36 h | [44,45,46,47,48] |
Entry and host responses | |||
primary target cells | CD4+ T cells, Macrophages | ACE2+ mucosal and endothelial cells | [49,50] |
primary entry receptors/proteins | CD4, CCR5/CXCR4 | ACE2, TMPRSS2 | [51,52,53] |
antibody response | Ab binding and neutralization response develops in first month | Ab binding and neutralization response develops in 1–2 weeks | [54,55,56,57] |
nAb development associated with viremia and severity | nAb development associated with viremia and severity | ||
bnAb development usually requires 2–3 years of productive infection (observed in ~10% of HIV-1-infected individuals) | nAbs develop within weeks of infection | ||
bnAbs require high rates of somatic hypermutation | Potent nAbs do not require high rates of somatic hypermutation (SHM), but SHM fosters breadth, potency, and resilience to viral escape | ||
cellular response | impaired B cell, T cell and macrophage/monocyte responses | impaired B cell, T cell and macrophage/monocyte responses | [58,59,60,61,62,63] |
cytokine response | delayed and enhanced anti-inflammatory response, impaired IFN response in progressive cases | delayed and enhanced anti-inflammatory response, impaired IFN response in severe cases | [64,65,66,67,68,69,70] |
Disease features, treatment, and vaccines | |||
clinical symptoms | AIDS | COVID-19 | [6,49,71,72,73,74,75,76,77] |
(1) initially mild, common cold-like symptoms | (1) respiratory infection (fever, cough, sore throat, fatigue, loss of smell) | ||
(2) acquired immune deficiency and opportunistic infections and malignancies | (2) systemic dissemination throughout the body (blood vessels, nervous system, inner organs) | ||
type of infection | chronic (HIV-1 integrates as provirus into host genome) | acute | |
duration of infection | life-long | 1–2 months (mild) | |
2–9 months (severe) and possible chronic complications | |||
primary site of infection | lymphatic system of gut and reproductive system | respiratory system | |
primary mode of infection | sexual transmission | droplet infection of airways | |
treatment | >45 FDA-approved drugs, strong viral-suppressive effect but no cure | (emergency use) authorization of a few drugs, limited clinical benefit (dexamethasone, remdesivir, nAb cocktails) | [70,78,79,80] |
drugs mainly target the polymerase region (reverse transcriptase, protease, and integrase) | |||
vaccine | no vaccine | (emergency use) authorization of a few vaccines, up to 95% vaccine efficacy | [81,82,83,84,85] |
7 vaccine efficacy trials completed, best efficacy: 31% (RV144, 2009) | >200 vaccine trials ongoing or completed | ||
correlates of protection | animal models: neutralizing antibodies; | neutralizing antibodies, supported by cellular responses | [81,86,87] |
human vaccine trial (RV144): ADCC, low plasma anti-Env IgA/IgG, poly-functional B cell responses, non-neutralizing V2 antibodies |
Pangolin Lineage | B.1.1.7 | B.1.351 | P.1 (B.1.1.248) | B.1.617 | B.1.1.298 (Cluster 5) | B.1.525 | B.1.160 | B.1.427 B.1.429 | B.1.2 | B.1.620 | B.1.526 |
---|---|---|---|---|---|---|---|---|---|---|---|
Variant origin/first detected | UK | South Africa | Brazil/Japan | India | Denmark (from minks) | Nigeria/UK | Europe | California | Midwest, USA | Cameroon, West-Central Africa/Lithuania, Europe | New York, NY, USA |
GISAID clade | GRY | GH | GR | G | GR | G | GH | GH | GH | G | GH |
VOC/VOI | VOC-20DEC-01 | VOC-20DEC-02 | VOC-21JAN-02 | VOC-21APR-02 (B.1.617.2) | - | VOI VUI-21FEB-03 | - | VOI | - | VOI | under monitoring- |
WHO (VOC/VOI) | Alpha | Beta | Gamma | Delta (B.1.617.2) | - | Eta | - | Epsilon | - | - | Iota |
Other names/Nextstrain | 20I/S:501Y.V1 | 20H/S:501Y.V2 | 20J/S:501Y.V3 | G/452R.V3 21A/S:478K | ΔFVI-Spike 20B | UK1188 20A/S:484K | 20A.EU2- | CAL.20C20C /S:452R | COH.20G.Q677H - | 20A | 20C 20C/S:484K |
Clinical impact | Epidemiological data suggest increased transmissibility and virulence; Little impact on vaccine efficacy | Suggested increased transmissibility but no influence on virulence; In vitro studies suggest partial nAb immune escape and reduced vaccine efficacy | Effect on transmissibility and virulence under investigation; In vitro studies suggest partial nAb immune escape and reduced vaccine efficacy | Epidemiological data suggest increased transmissibility; In vitro studies suggest partial nAb immune escape and reduced vaccine efficacy | Suggested increased transmissibility; no evidence of increased virulence or vaccine immune evasion | Suggested to have partial nAb immune escape and reduced vaccine efficacy | No evidence of increased transmissibility, virulence, or immune evasion | Epidemiological data suggest increased transmissibility; In vivo and pseudovirus data suggest increased virulence and partial immune evasion | No evidence of increased transmissibility, virulence, or immune evasion | Suggested to have partial nAb immune escape and reduced vaccine efficacy | Suggested to have increased transmissibility; no evidence of increased virulence yet; partial nAb immune escape and reduced vaccine efficacy predicted |
Amino acid mutations and deletions | |||||||||||
NSP1 | - | - | - | - | Δ M85 | - | - | - | - | - | - |
NSP2 | - | T85I | - | - | - | - | - | T85I# | T85I | T223I | T85I |
NSP3 (PL-pro) | T183I, A890D, I1412T | K837N | S370L, K977Q | - | Δ N1264 | T1189I | - | - | M1788I | V1173I | - |
NSP4 | - | H36Y, S137L | - | - | - | - | M324I | - | - | - | L438P |
NSP5 (3CL-pro) | - | K90R | - | - | - | - | - | - | L89F | - | - |
NSP6 | ΔS106-G107-F108 | - | ΔS106-G107-F108 | - | - | ΔS106-G107-F108 | - | - | - | ΔS106-G107-F108 | ΔS106-G107-F108 |
NSP9 | - | - | - | - | - | - | - | I65V # | - | - | - |
NSP12 (RdRp) | P323L | D144Y, P323L | P323L | P323L | P323L, T739I | P323F* | A185S, P323L, V776L | P323L | P323L | P323L | P323L |
NSP13 (Helicase) | - | T588I | E341D | P77L #, M429I # | - | - | K218R, E261D | P53L #, D260Y | - | A292S | Q88H |
NSP14 | - | - | - | - | - | - | - | - | N129D | - | - |
NSP15 | - | - | - | K259R # | T112I | - | - | - | - | - | - |
NSP16 | - | - | - | - | - | - | - | - | R216C | - | - |
Spike | ΔH69–V70, ΔY144, N501Y, A570D, D614G, P681H, T716I S982A, D1118H | L18F, D80A D215G, ΔL241-L242-A243, R246I, K417N *, E484K, N501Y D614G, A701V | L18F, T20N, P26S, D138Y, R190S, K417T *, E484K, N501Y, D614G, H655Y, T1027I, V1176F | G142D #, E154K #, L452R, T478K #, E484Q #*, D614G, P681R | ΔH69–V70, Y453F, D614G I692V, M1229I | Q52R, A67V, ΔH69–V70, ΔY144, E484K, D614G, Q677H, F888L | S477N, D614G | S13I, W152C, L452R, D614G | D614G, Q677H | P26S, ΔH69–V70, V126A, ΔY144, ΔL241-L242-A243, H245Y, S477N, E484K, D614G, P681H, T1027I, D1118H | L5F #, T95I, D253G, L452R #, S477N #, E484K #, D614G, A701V #, Q957R # |
ORF3a | - | Q57H, S171L | S253P | S26L # | H182Y | - | Q57H | Q57H | Q57H, G172V | - | P42L, Q57H |
M | - | - | - | I82T/S# | - | I82T | - | - | A85S | - | - |
ORF7a | - | - | - | V82A | - | - | - | - | - | - | - |
ORF8 | Q27stop, R52I, Y73C | - | E92K | - | - | - | - | - | S24L | - | T11I |
ORF9b | - | - | - | - | - | - | - | - | - | I5T | - |
E | - | P71L | - | - | - | L21F | - | - | - | - | |
N | D3L, R203K, G204R, S235F | T205I | P80R, R203K, G204R | R203M * D377Y | S194L, R203K, G204R | A12G, T205I | M234I, A376T | T205I | P67S, P199L, D377Y | A220V | P199L#, M234I# |
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Duerr, R.; Crosse, K.M.; Valero-Jimenez, A.M.; Dittmann, M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021, 9, 1389. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071389
Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms. 2021; 9(7):1389. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071389
Chicago/Turabian StyleDuerr, Ralf, Keaton M. Crosse, Ana M. Valero-Jimenez, and Meike Dittmann. 2021. "SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise" Microorganisms 9, no. 7: 1389. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071389