A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention
Abstract
:1. Introduction
2. Invasion of SARS-CoV-2
3. Origin of SARS-CoV-2
4. Classification of Coronavirus
5. Structure of SARS-CoV-2
6. Life Cycle of SARS-CoV-2
6.1. Early Stage
6.1.1. Entry and Initiation
6.1.2. S Protein Cleavage
6.1.3. Membrane Fusion
6.2. Advanced Stage
6.2.1. Translation and RNA Replication
6.2.2. Virion Packing and Release
7. Genome Organization of SARS-CoV-2
8. Mutation in SARS-CoV-2
9. Epidemiology of COVID-19
10. Fatality Rate of the Pandemic
11. Pathogenesis Process
11.1. Transmission
11.2. Pathological Process
11.3. Host Response
12. Post-Infection Outcomes
12.1. Clinical Features
12.2. Disease Prognosis
13. Diagnostic Strategies for COVID-19
14. Prevention against COVID-19
14.1. Preventive Measures
- Optimizing infection control protocols, self-isolation, and isolated accommodation for patients.
- Immunocompromised, aged persons must take special care; health care personnel must use PPE such as N95, FFP3 mask, gowns, face shield, etc.
- Frequent handwashing with soap and water, with hand sanitizer as an alternative disinfection process; alcohol can also be used.
- Avoid public gatherings and maintain social distancing of at least 1 m. Must wear face masks and cover coughs and sneezes to help prevent aerosol transmission.
- All of us should put on face masks and maintain respiratory and hand hygiene.
- Staying home during sickness.
- Covering mouth and nose with bent elbow or tissue at the time of sneezing or coughing. Used tissue should be disposed of instantly.
- Washing hands regularly with soap and water. Hand hygiene refers to the use of alcohol-based hand sanitizers before and after each patient’s contact as well as after touching any surface, transport, money, etc. Washing hands with soapy water for 20 s is also very effective and essential for everyone. It is also advised to maintain hand hygiene before and after cooking, before eating, before and after removing gloves and face masks, and after using the toilet. Distinct reusable utensils can be used by the patient after proper cleaning.
- Avoiding handshaking is also advised for the time being for your protection.
- Cleaning regularly touched surfaces and objects. Disinfecting the surrounding environment of the patient, including toilet and furniture [152]. Clean and disinfect bathroom and toilet surfaces at least once every day. Regular household soap or detergent should be used first for cleaning and rinsing purposes; regular household disinfectant and germ killer containing 0.5% sodium hypochlorite (NaOCl) should be applied [153].
- Provisionally, prevention is the best way to stop the spread of infection. WHO has boldly recommended hand and respiratory hygiene for cases, contacts, and health care workers [154].
- The doctors and health workers are particularly advised to wear personal protective equipment (PPE), including an N95 respirator mask and eye shield, while collecting respiratory samples. Avoiding contact with body fluids is mandatory [156].
- The duration of quarantine is 14 days from the last contact with PCR confirmed COVID-19 case. They should be checked daily for fever and other symptoms associated with COVID-19 [157].
- Children’s health monitoring is necessary during this time. Children with a history of close contact with infected patients need to be routinely observed for body temperature and clinical features. When presenting with doubtful symptoms, children should be taken to a delegated hospital for screening. Newborns delivered by COVID-19 infected mothers must complete a pathogen test and be isolated in a single cabin room or at home according to their medical conditions [150].
14.2. Treatment
Vaccination
14.3. Boosting Immunity
15. Infection Associated Factors
15.1. Gender Biases
15.2. Ethnic Differences
15.3. Environmental Effect
15.4. Blood Group and Coronavirus
16. Conclusions and Future Directions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Virus | Source of Virus | Transitional Host | Final Host |
---|---|---|---|
SARS-CoV-1 (SARS-2002) | SARS-like Bat-CoV | Civet cat | Human |
MERS-CoV (MERS 2012) | SARS-like Bat-CoV | Camel | Human |
SARS-CoV-2 (COVID-2019) | Bat-CoV RaTG13 | Pangolin (Pangolin-CoV) | Human |
Country | Total Cases | New Cases | Total Deaths | New Deaths | Total Recovered | Active Cases | Critical Cases |
---|---|---|---|---|---|---|---|
Worldwide | 194,669,939 | +296,849 | 4,172,559 | +4552 | 176,662,440 | 13,834,940 | 84,074 |
USA | 35,185,064 | +393 | 626,717 | +4 | 29,507,148 | 5,051,199 | 7771 |
India | 31,396,300 | +24,814 | 420,758 | +173 | 30,555,315 | 420,227 | 8944 |
Brazil | 19,670,534 | 549,500 | - | 18,340,760 | 780,274 | 8318 | |
Russia | 6,126,541 | +24,072 | 153,874 | +779 | 5,490,634 | 482,033 | 2300 |
France | 5,697,912 | - | 111,616 | - | 5,674,587 | 192,492 | 878 |
UK | 5,978,695 | +29,173 | 129,158 | +28 | 4,450,204 | 1,118,550 | 699 |
Turkey | 5,587,378 | - | 50,879 | - | 5,415,937 | 120,562 | 543 |
Argentina | 4,839,109 | - | 103,584 | - | 4,480,336 | 255,189 | 4318 |
Colombia | 4,716,798 | - | 118,538 | - | 4,477,155 | 121,105 | 8155 |
Italy | 4,317,415 | +4,743 | 127,949 | +7 | 4,123,209 | 66,257 | 178 |
Outcomes | Percentage (%) | |
---|---|---|
Common signs and symptoms | Fever | 77.4–98.6% |
Cough | 59.4–81.8% | |
Fatigue | 38.1–69.6% | |
Dyspnea | 3.2–55.0% | |
Myalgia | 11.1–34.8% | |
Sputum production | 28.2–56.5% | |
Headache | 6.5–33.9% | |
Underlying diseases | 25.2–50.5% | |
Laboratory outcomes | Lymphopenia | 35.3–82.1% |
Thrombocytopenia | 5.0–36.2% | |
Leukopenia | 9.1–33.7% | |
Increased CRP | 60.7–86.3% | |
Increased D-dimer | 36.4–46.4% | |
Increased LDH | 27.4–75.8% | |
Increased CK | 8.0–32.5% | |
Prolonged prothrombin time | 58.0% | |
Increased ALT | 16.1–28.3% | |
Increased AST | 22.2–36.7% | |
Increased interleukin-6 | 51.5% | |
Increased serum ferritin | 62.6% | |
Increased ESR | 84.8% | |
Increased procalcitonin | 5.5–11.3% | |
Increased troponin I | 12.2% | |
Increased creatinine | 1.9–9.8% | |
Complications and fatality | ARDS | 3.4–29.3% |
Shock | 1.0–8.7% | |
Acute renal injury | 0.5–7.3% | |
Acute cardiac injury | 7.2–12.2% | |
Secondary infections | 9.8% |
Risk Factors | Aftermath |
---|---|
Age | Adults (65–84) years make up estimated COVID-19 deaths of (4–11%) in the U.S, while adults ages 85 and above make up 10–27%. |
Diabetes (type 1 and type 2) | People with diabetes were nearly 3.7 times more likely to have a critical case of COVID-19 or die from the disease. |
Heart disease and hypertension | People with conditions that affect the cardiovascular system, such as heart disease and hypertension, generally suffer worse complications of COVID-19. |
Smoking | Smokers face a heightened risk of developing pneumonia, suffering organ damage, and requiring breathing support. |
Blood group type | People with blood types of A group (A-positive, A-negative, and AB-positive, AB-negative) were at a higher risk of contracting the disease compared with non-A-group types. |
Obesity | Obese COVID-19 patients were more than twice as likely to develop severe pneumonia as compared to patients who were of normal weight. |
Genetic factors | Genes for ACE2 receptors in patient’s body make it easier getting infected by COVID-19. |
Treatment | Drugs | Function | Dose | Host | Ref. |
---|---|---|---|---|---|
Anti-viral | Oseltamivir | No activity | 75 mg every 12 h (orally) | Human | [160,166,167] |
Ganciclovir | - | 0.25 g every 12 h (IV) | Human | ||
Remdesivir | Inhibits coronavirus replication including SARS-CoV-2. | 0.77 µM 48 h | Vero E6 cells | ||
Lopinavir/Ritonavir | Blocks the main protease of SARS-CoV-1 and inhibits viral replication | 400/100 mg twice daily | Human | ||
Arbidol (Umifenovir) | No clinical data are available | 200 mg Orally 3 times | Human | ||
Interferon-α (IFN-α) | Reduces infection rate | 500 mg ribavirin combined (2–3) times a day | Human | ||
Anti-malarial | Chloroquine | 1. Anti-viral and anti-inflammatory activities and 2. Post translation alteration by glycosylation inhibition. | 1.13 µM 48 h | Vero E6 cells | [166,168] |
Hydroxyl chloroquine | 200 mg every 8 h (orally) | Human | |||
Cortico steroids | Methyl prednisolone | - | 1–2 mg/kg·d For 3 days (IV) | Human | [159] |
Immune therapy | Convalescent Plasma therapy (CPT) | - | 200–500 mL | Human | [169,170,171,172] |
Tocilizumab (Atlizumap) mAb | Anti-interleukin-6 receptor activity | 400 mg (For body weight < 75 kg) Or 600 mg (For body weight ≥ 75 kg)max dose 800 mg Repeat after 12 h if required (IV) | |||
Anakinra | Anti-interleukin-1β neutralizing | 100 mg twice a day for 72 h and later on single dose per day for 7 days |
Vaccine Name | Developer | Technology | Dose | Phase | Efficacy | Approved in Countries |
---|---|---|---|---|---|---|
Comirnaty or Tozinameran or BNT162b2 | Pfizer and BioNTech | mRNA | 2 doses (Three-weeks apart) | 2/3 | 91.3% | Bahrain, Brazil, New Zealand, Saudi Arabia, Switzerland |
mRNA1273 or Spikevax | Moderna | mRNA | 2 doses (Four-weeks apart) | 3 | Over 90% | Switzerland |
Sputnik V or Gam-Covid-Vac) | Gamaleya Research Institute | Ad5, Ad26 (Adenovirus) | 2 doses (Three-weeks apart) | 3 | 91.6% | Russia (Emergency use) |
Vaxzevria or AZD1222 (also known as Covishield in India) | University of Oxford and the British-Swedish company AstraZeneca | ChAdOx1 | 2 doses | 2/3 | 76% | Brazil |
Convidecia (also known as Ad5-nCoV) | CanSino Biologics and Institute of Biology, Academy of Military Medical Sciences | Ad5(Adenovirus) | Single dose | 3 | 65.28% | China |
Ad26.COV2.S | Johnson & Johnson Beth Israel Deaconess Medical Center | Ad26(Adenovirus) | Single dose | 3 | 72% (U.S.A.); 68% (Brazil); 64% (South Africa) | USA (Emergency use) |
EpiVacCorona | Vector Institute | Protein | 2 doses (Three-weeks apart) | 3 | Unknown | Turkmenistan |
NVX-CoV2373 | Novavax | protein | 2 doses (Three-weeks apart) | 3 | 89.7% | N/A |
BBIBP-CorV | Sinopharm. | Inactivated | 2 doses (Three-weeks apart) | 3 | 78.1% | Bahrain, UAE, China |
CoronaVac (formerly PiCoVacc) | Sinovac Biotech | Inactivated | 2 doses (Two-weeks apart) | 3 | 50.65% (Brazil trial) 83.5% (Turkey trial) | China |
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Sarker, M.T.; Hasan, A.Q.F.; Rafi, M.O.; Hossain, M.J.; El-Mageed, H.R.A.; Elsapagh, R.M.; Capasso, R.; Emran, T.B. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. Biologics 2021, 1, 357-383. https://doi.org/10.3390/biologics1030021
Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. Biologics. 2021; 1(3):357-383. https://doi.org/10.3390/biologics1030021
Chicago/Turabian StyleSarker, Md. Takim, A. Q. Fuad Hasan, Md. Oliullah Rafi, Md. Jamal Hossain, H. R. Abd El-Mageed, Reem M. Elsapagh, Raffaele Capasso, and Talha Bin Emran. 2021. "A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention" Biologics 1, no. 3: 357-383. https://doi.org/10.3390/biologics1030021