Several viral diseases have challenged humanity since the beginning of the 21^st century, presenting new obstacles to the global public health services. In December 2019, a beta coronavirus (CoV) was identified, now known as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is currently greatly threatening the lives of people all over the globe. The current pandemic demands an urgent call for the discovery of new potential molecules or vaccines to fight SARS-CoV-2. In this review, we present a detailed perspective of SARS-CoV-2, from its origin, related viruses, with special emphasis on transmission from environment to human, host-virus interaction, and mechanism of action. We also summarize the status of currently available pharmaceuticals for the treatment of COVID-19 and vaccines, which are being under various stages of clinical trials.

CoVs are microscopic (65-125 nm in diameter), enveloped, single stranded positive sense RNA viruses, with a genome size of 26 to 32kb ( Figure 1 ). Based on the phylogenetic analyses, the CoVs can be classified into subfamily Orthocoronavirinae, subdivided into four genera; BetaCoV, DeltaCoV, AlphaCoV and GammaCoV (1). The Alpha- and BetaCoVs can infect mammals whereas the Gamma and DeltaCoVs mostly infect birds (2). Examples of Alpha- and BetaCoVs which have severe implications on livestock include porcine enteric diarrhea virus (PEDV), porcine transmissible gastroenteritis virus and swine acute diarrhea syndrome CoV (SADS- CoV). CoVs are also known to induce respiratory burden in dogs [canine respiratory CoV (CRCoV)], progressive demyelinating encephalitis in mice [mouse hepatitis virus (MHV)] and gastrointestinal symptoms in various animals [bovine CoV (BCV), canine CoV (CCoV), feline CoV (FCoV), transmissible gastroenteritis CoV (TGEV), and turkey CoV (TCV)] (3). Interestingly, all CoVs responsible for virally induced pandemic in humans belong to the BetaCoVs. Since most of the CoVs are capable of infecting animals it is believed that wild animals are the natural reservoirs of CoVs. However, many CoV species also inhabit commercial and domestic animals.

The first CoV infectious bronchitis virus (IBV) was discovered in 1930, which caused acute respiratory infection in chicken. Two additional animals CoVs were isolated during 1940 and were characterized as TGEV and MHV (4). In 1960, the first human CoVs, namely human CoV OC43 and human CoV 229E were isolated from humans. SARS-CoV (5, 6), HCoV-NL63 (7)and HCoV-HKU1 were identified in 2004 in China, Netherlands and Hong Kong, respectively (8, 9). Moreover, MERS-CoV (Middle East respiratory syndrome CoV) or MERS-CoV CoVEMC/2012 (MERS CoV Erasmus Medical Center/2012) was first detected in Saudi Arabia (10), and SARS-CoV-2 was reported in 2019 in China (11). Furthermore, a detailed study of SARS-CoV-2 genomic sequence ( Figure 2 ) revealed that it is very closely associated with the 2003 pandemic related SARS-CoV (11, 12).

In general, domestic animals serve as the intermediate host for transmitting these viruses to humans (13). Notably, all the HCoVs which originated in animals were detected in bats; thus, bats likely represent a major reservoir of Alpha- and BetaCoVs (13). SARS-CoV-2 is predicted to have a bat origin due to the high sequence homology of RNA dependent RNA polymerase (RdRp) and S (spike) gene with bat CoVs (RaTG13) (14). The presence of an intact single ORF8 in the genome is yet another indicator of its bat origin. Though bats are considered the natural host, no direct progenitor of the virus has thus far been detected, therefore, it is likely that SARS-CoV and SARS-CoV-2 were newly produced viruses as a result of recombination of already existing bats species (15). Cui et al. showed that SARS-CoV progenitors originated as a result of recombination in bat CoVs which eventually infected the palm civets and humans (13). Furthermore, a genomic recombination study stated that bats possessed several CoV subclades which consistently participated in recombination with HCoVs. Thus, the diverse genetic pool presented by bats may have contributed to SARS-CoV-2 origin (16). Additionally, bats, the only flying mammals, have several advantages like the ability to fly long distances, stay in a clustered habitat, longevity, apt body temperatures, etc., which makes them a suitable incubation host for these RNA viruses (17). In the case of SARS-CoV, masked palm civets (Paguma larvata) sold widely at Guangdong’s wet markets were investigated to be the intermediate host (18). Variation in the receptor binding domain (RBD) of S gene and open reading frame 8 (ORF8) essential for angiotensin-converting enzyme 2 (ACE2)-mediated interaction of the virus and crucial for transmission of the virus from civets to humans were identified (19, 20).

Dromedary camels serve as an intermediate host for MERS-CoV (21). Importantly, camels from the Middle East, Africa, and Asia had MERS-CoV-specific antibodies (22–24). Also, Tylonycteris bat CoV HKU4 and Pipistrellus bat CoV HKU5 are phylogenetically related to MERS-CoV (25, 26). Furthermore, the recently identified human infecting SARS-CoV-2 (27) shared greater than 80% and 50% resemblance with SARS-CoV and MERS-CoV, respectively. Intriguingly, the RBD of the S protein is similar in amino acid sequence to that of SARS-CoV, thus implicating that these viruses share a similarity in receptor binding (28). A phylogenetic study revealed that SARS-CoV-2 shared similarities to Malayan pangolin (Manis javanica) CoV (pangolin-CoV-2020). The CoV from pangolin is also known to share homology with the bat CoV (29). Thus, pangolins are predicted to be the SARS-CoV-2 intermediate host However, one study supports the possibility of rodents or squirrels acting as possible intermediate hosts (30).

The initial cases of SARS-CoV-2 infection represented by severe pneumonia appeared in December 2019 (31). Human-to-human transmission of SARS-CoV-2 was first reported and confirmed by a group of clinicians and scientists from the University of Hong Kong (12). CoVs are known to cause respiratory illnesses which may vary from mild to severe manifestations and gastrointestinal tract infections in humans (32). The wide spectrum of COVID-19 extends from benign respiratory distress, self-resolving, to extreme progressive pneumonia, multiple organ failure, and death (33). The first known infected individuals were related to the wet markets of Huanan South China (34). The illness caused by the virus was termed CoV disease of 2019 (COVID-19), and declared a pandemic on 11 March 2020 by the World Health Organization (WHO) (https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19—11-march-2020). The disease rapidly spread from China to several countries across the globe (35). Since then, several countries have adopted serious measures to provide effective disease prevention and surveillance strategies for their population (12, 36). Based on the CoV Resource Center at Center for Systems Science and Engineering, Johns Hopkins University, United States (US), as of 27 March 2021 (9:27 AM), the total number of confirmed SARS-CoV-2 cases worldwide were 126,134,596 of which 2,767,547 (2.19%) were fatal (https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6). Figure 3 shows an overview on how severe the infection has spread globally. On the top of the list, US recorded more than 30 million cases, followed by Brazil (> 12 million), India (> 11 million), France (> 4.5 million), Russia (> 4.4 million), United Kingdom (UK) (> 4.3 million), Italy (> 3.4 million), Spain (> 3.2 million), Turkey (> 3.1 million), Germany (> 2.7 million), and Colombia (> 2.3 million).

Elderly individuals, mostly in the age group of 25 and 89 years, especially with a comorbid condition or a compromised immune status, were associated with SARS-CoV-2 infection (38). The cases of COVID-19 were least among infants and children (38). In addition, studies reported the susceptibility of male individuals to COVID-19; however still controversies exist (39). The epidemiological features and clinical manifestations resulting from COVID-19 are poorly characterized, as they are primarily dependent on case reports from vivid regions.

SARS-CoV-2 can be transmitted by being in direct contact with an infected individual or indirect contact through virus-contaminated premises or surfaces (40, 41) ( Figure 4A ). Domestic animals live close to the human environment and can act as carriers of a variety of pathogens (44). Recent reports have demonstrated that SARS-CoV-2 has potential to infect cats, ferrets, Syrian hamsters and dogs (43–46). The cats are susceptible to airborne transmission. These animals may act as carriers and source of transmission of the disease within the animal or human population.

Climatic factors play an essential role in the spread and evolution of any pathogen and disease. Like influenza viruses, CoVs display a seasonal infectivity pattern, most prevalent from December to April (47). In particular, 229E and OC43 are responsible for 15–29% of the overall cases of common colds (3).

A study reported time series analysis for the impact of temperature and humidity on COVID-19 transmission focused on the area of Hubei province from where the pandemic originated (48). A temperature rises of 1°C daily and humidity ranging from 67% to 86% caused reduction in cases by 36-57%. Additionally, when the temperature was between 5-8.2°C and relative humidity was increased by 1% daily, confirmed cases were reduced by 11% to 22%. Thus, an increase in temperature and humidity was correlated to lower levels of COVID-19. Another study with cases from China and USA, also stated that higher temperature and humidity was associated with lower transmission rates (49). The study also depicted that, post lockdown in the included countries, temperature and humidity was still affecting the transmission but with lesser intensity. Contrary to this, another study from China does not support the hypothesis that high temperature or UV radiation can reduce COVID-19 transmission (50).

Another investigation, for 166 countries (excluding China) suffering from the COVID-19 outbreak, by Wu et al. (51), concluded that temperature and humidity are inversely proportional to daily new COVID-19 cases and deaths. A 1°C rise in temperature reduced the appearance of new cases and deaths by 3.1% and 1.2% respectively. While 1% rise in relative humidity reduced new cases and deaths by 0.9% and 0.51% respectively. A temperature, humidity and latitude analysis study were performed by Sajdi et al to predict COVID-19 spread and seasonality (52). It depicted that meteorological status was stable prior to the month of disease outbreak and hence aided in the droplet stabilization and enhanced viral propagation. The spread of COVID-19 was significant in the 30-50° N’ longitude corridor with similar weather patterns of temperature 5-11°C, and low specific (3-6 g/kg) and absolute humidity (4-7 g/m³).

A study performed by Juni et al, capturing the initial period of the pandemic in March 2020, focused on the effect of social factors like school closures, restrictions of mass gatherings, measures of social distancing and geographical factors like latitude, temperature and humidity on COVID-19 transmission (53). Restrictions in mass gatherings, school closures and measures of social distancing led to a 35%, 37%, 38% relative reduction in epidemic growth respectively. While there was 9% relative reduction in epidemic growth when relative humidity was increased by 10% and 8% relative decrease was observed with increased absolute humidity per 5 g/m³. In this study, there was no correlation found either with temperature or latitude. A report conducted on EU-15 countries also states that 1°C rise in temperature slightly reduced the transmission rate (54). A few other reports have also demonstrated that there is a negative correlation in temperature and COVID-19 transmission and/or associated deaths (55–57).

In the case of African regions, Meo et al. conducted a study to analyze implications of weather conditions on incidence and mortality of COVID-19 pandemic in 16 highly populated countries. The output of the study suggested an increase in relative humidity and temperature decreases rise in new COVID-19 cases and death (58). Another study focusing 52 African states also suggested a similar scheme as Meo et al., 2020, that the mean temperature and relative humidity are inversely related to COVID-19 growth in African region (59). As per rapid expert consultation provided by National Academies of Science, Medicine, Engineering, which reviewed some published and unpublished studies, decreased transmission was seen in excessive ambient temperatures and humidity (National Academies of Sciences, Engineering, and Medicine 2020). However, there are various limitations to the studies conducted so far. It has been 16 months since the pandemic has started and the studies conducted so far considers only a short. Hence, it is difficult to assess the long-term trend accounting for the different seasons for particular areas under study. Also, different countries implemented various strategies to control the COVID-19 transmission which actually could have impacted the reduction or increase in cases instead of meteorological reasons (60). Conclusively, based on current evidence, the higher temperature, relative humidity and absolute humidity were associated with fewer COVID-19 cases. However, more studies are required in the future to decode the relation of temperature, humidity and various other environmental factors in worldwide COVID-19 transmission.

SARS-CoV-2 has a high transmission rate within the human population throughout the globe. In general, CoVs undergo modification at a rate of 10⁴ substitutions in a year per site. The mutation rates for SARS-CoV and MERS-CoV whole genome is assessed to be 0.80 – 2.38 × 10³ and 1.12×10³ nucleotide substitutions per year at a site (61, 62). HCoVs recognize different host receptors to enter the hosts; for example, HCoV-OC43 and HCoV-HKU1 recognize various O-acetylated sialic acid moieties (63), HCoV-229E interact through the human aminopeptidase N (hAPN), MERS-CoV uses dipeptidyl peptidase-4 (DPP4) (64), and HCoV-NL63 and SARS-CoV binds to the ACE2 receptor (65, 66). ACE2 and Transmembrane Serine Protease 2 (TMPRSS2) on the host cells function as entry receptors for SARS-CoV-2 (67). Noticeable mutations in SARS-CoV-2, which help the virus distinguish from the rest of the beta CoVs, include multiple mutations in the RBD of the S protein, a furin-like protease site at the S1/S2 interface, and the presence of 3 O-linked glycans encompassing the protease site (68–70).

It is predicted that SARS-CoV-2 evolves within the host after infection, thereby modulating its transmissibility and infectivity potential (71). Recent research studies showed that the new SARS-CoV-2 has evolved with many mutations and developed the ability to cross species. One such variant is the SARS-CoV-2 VUI 202012/01 (Variant under Investigation, year 2020, month 12, and variant 01) detected in the United Kingdom. The variant is known to have 14 mutations and three deletions in its sequence. In particular, two of the identified mutations, N501Y and P681H, result in altered RBD and are predicted to influence virus transmissibility (https://www.who.int/csr/don/21-december-2020-sars-cov2-variant-united-kingdom/en/). Mutations at Tyr442, Leu472, Asn479, Asp480, Thr487, and Tyr491 of SARS-CoV S-protein Coveney are considered crucial for its function (72). Notably, the RBD of SARS-CoV-2 differed at 5/6 residues compared to SARS-CoV, which may have promoted the binding of the virus to host ACE2 (73). Specific mutations in the RBD of SARS-CoV-2 enabled the virus to evade the neutralizing antibody response. D614G mutation was predominant in most strains of the SARS-CoV-2 and is predicted to have influenced the spread of the virus (74, 75). This mutation first identified in China and Germany is widely spread in various areas of Europe. Besides, variation, i.e., a 382-nucleotide deletion, in the virus ORF8 resulted in milder infection (76). A study involving glycan profiling investigation indicated that the SARS-CoV-2 S protein is known to possess heterogenous N-linked glycans. Finally, glycan profiling and a detailed understanding of virus evolution are necessary to develop an effective drug and vaccine strategy.

Recently, several new SARS-CoV-2 variants have been identified resulting in clusters of outbreaks and, in some cases, global dissemination. Any of these variants contains a range of mutations, some of which are essential to the viral genome’s function. The majority of these mutations are detrimental to the virus and hence disappear by natural selection. However, some SARS-CoV-2 variants can be more transmissible, may affect its ability to be identified by diagnostic tests, have resistance to therapeutic agents, may evade natural and vaccine-induced immunity, and may have an effect on COVID-19 morbidity and mortality (77). This viral evolution is a well-characterized phenomenon observed in seasonal coronaviruses (78–80) and has been recently replicated in vitro (81).

Viral mutations and variants are regularly monitored by sequence-based analysis, experimental studies, and epidemiological data. They are categorized generally as variants of interest, variants of concern, and variants of significance. The SARS-CoV-2 variants of concern spread at least 20% to 50% more easily from person to person. This enables them to infect a greater number of individuals and evolve more rapidly and extensively, gradually establishing themselves as the dominant strain.

Recently, the initial optimism about the development of COVID-19 vaccines has been dashed by the appearance of new SARS-CoV-2 variants (82). Current coronavirus vaccines were developed for older versions of the virus, but scientists say they the immune response could be weaker and less long-lasting. Currently there are five variants of concern:

The B.1.1.7, lineage, originated in the U.K, it soon spread to other countries after its discovery in December 2020 and grew at an exponential pace. B.1.1.7 tends to be more contagious due to many mutations in the coronavirus’s spike protein. Mutations include N501Y, which makes the virus latch on to human cells more closely, but is unlikely to aid the virus in evading existing vaccinations; P681H, which may aid infected cells in the production of new spike proteins more efficiently; and the deletions H69–V70 and Y144/145, which change the form of the spike and can help evade certain antibodies (83).

The B.1.351 Lineage, first reported in South Africa in December 2020, this variant, also known as 20H/501Y.V2 carries a mutation (N501Y) in the spike protein’s RBD, which lead to increased transmission, with estimates ranging between 40% and 70%; K417N, which also aids the virus in binding to human cells more closely; and E484K, a mutation that may aid the virus in evading certain types of antibodies (84).

After spreading from South Africa into neighboring countries, it has expanded to at least 68 nations. Scientists are worried about the variant because clinical trials have shown that individuals who recover from other variants may not be protected against B.1.351 (84).

The P.1 lineage was discovered in four people in Japan who contracted P.1 while on vacation in Brazil. The lineage first appeared in late 2020 in Manaus, Brazil’s largest city in the Amazon region. It quickly became the dominant variant in that city, and it has now spread to at least 37 countries.

P.1 is a close relative of the B.1.351 lineage, and it shares some of the same coronavirus spike protein mutations. The spike protein’s critical mutations are identical to those seen in the B.1.351 lineage, but may have occurred independently: N501Y and K417T, which could facilitate the virus adherence to its host; and E484K, a mutation that may aid the virus in evading certain types of antibodies (85).

The CAL.20C variant was originated in California, in late 2020, from the B.1.427 and B.1.429 lineages. This variant shows the L452R mutation and may give the coronavirus an advantage in spreading over other variants, but the results of experiments to prove this have yet to be published. About 45% of existing samples in California contain this mutation. Two reports indicate that CAL.20C is more infectious than older strains of the coronavirus, but it does not seem to be circulating as rapidly as variants such as B.1.1.7 (86).

The B.1.617 variant, also known as G/452.V3, was first detected in Maharashtra, India, in October 2020. This variant has been described as a super-spreader, prompting the closure of five cities (Lautoka, Nadi, Suva, Lami, and Nausori), accounting for nearly two-thirds of the country’s population. The variant was first observed in other countries in late February 2021, including the United Kingdom on 22 February, the United States on 23 February, and Singapore on 26 February 2021. The B.1.617 variant shows the E484Q and L452R mutations, which confers a higher binding capacity to the human ACE2 receptor, as well as a greater ability to escape host immune systems. Recent studies shows that B.1.617.2 is at least as transmissible as the B.1.1.7 variant. A research conducted by the Centre for Cellular and Molecular Biology (CCMB), in Hyderabad, discovered that sera from Covishield-vaccinated people protected against the B.1.617 variant (87).

Further research is required about the protection against infection and disease provided by the current generation of SARS-CoV-2 vaccines in respect of existing and possibly evolving viral variants of concern. Additional research is required on the role of T cell-mediated immunity against SARS-CoV-2 and its role in viral variant selection. Another critical concern is whether updated vaccines can be developed and implemented relatively soon (82).

The overall lifecycle of all the CoVs shows a similar pattern of viral entry inside the cell till the viral egress from the infected cell ( Figure 4B ). The life cycle of the CoV begins upon (i) interaction of its S protein with the host receptor, followed by (ii) virus entry into the host cell, (iii) intracellular viral replication and transcription, (iv) protein production, assembly, and release of new virions (88). The virus can attack the epithelial lining of the exposed part of a person who has encountered the virus through any of the transmission routes. After entering into the cells, the virus multiplies and produces several copies for further spread inside the body. SARS-CoV-2 utilizes the ACE2, similar to SARS-CoV, to gain entry inside the cells. ACE2 is expressed by a variety of body cells including the lung epithelia where SARS-CoV-2 predominantly attacks. However, recent reports suggest various other targets where SARS-CoV-2 can possibly attack (38, 89, 90). The various aspects regarding SARS-CoV-2 entry are still under study. Recently, Neuropilin-1 has been shown to facilitate SARS-CoV-2 entry and infectivity (91). Some other reports propose that integrin can also aid in the entry of SARS-CoV-2 inside the cells (92, 93). The involvement of neuropilin and integrins in SARS-CoV-2 entry may strengthen the virus to enter in various cells where these receptors are prominently expressed as compared to ACE-2. Additionally, various signaling pathways other than those involved in ACE-2 mediated entry can also get triggered leading to changes in canonical cellular response (94).

SARS-CoV-2 utilizes a three-step method for its fusion with the cell membrane, which involves receptor binding followed by the change in S protein conformation and subsequent cathepsin proteolysis by cytoplasmic proteases and induction of membrane fusion in endosome (95–97). Further, the endosome opens and the virus is released. The host proteases which generally hydrolyze the endogenous protein, can facilitate in the degradation of viral N protein leading to viral RNA uncoating (98). Another suggested mechanism for entry into the cytoplasm is that the S protein binds to ACE2 and then cleaved proteolytically by host serine protease TMPRSS2 (99, 100). Interestingly the host-pathogen membrane fusions occur at low pH via S2 subunit of S protein. SARS-CoV-2 possess a site for furin-mediated cleavage which is absent in SARS-CoV (67). Recently it has been revealed that inhibitor of a serine protease and cathepsin halts entry and growth of SARS-CoV-2 in human airway epithelial cells in vitro (67). By either way, the viral genomic RNA is released into the infected cell cytoplasm. The replication and transcription of the viral genome are carried out by different non-structural proteins (nsps) encoded by the viral genome. The generated positive RNA genome is translated to replicases from ORF1a/b of the virus. This then works to produce more RNA viral genome copies. The viral structural proteins, translated from positive RNA strands, like E, M, S proteins get integrated to the endoplasmic reticulum membrane and continue to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) (101, 102). The viral genome RNA coated with N proteins then gets encircled by vesicles from the ERGIC compartment to form virions. These are further exocytosed out of the cell to infect nearby cells and establish the infection in the microenvironment (103).

When the virus enters the host cells and starts propagating inside the system, the host immune system tries to tackle the infection in all possible ways. The host system uses swords and shields of cellular machinery involving immune cells and molecular machinery like cytokines, chemokines including various cell signaling factors against the invader. During or post viral entry, the virus may get recognized by host cells using pattern recognition receptors (PRRs). Further, the cellular defense system secrets a variety of signaling molecules to invite immune cells at the site of infection. The immune cells process the viral antigens post endocytosis and are then processed inside these cells. Additionally, the processed viral peptides are displayed to the cell surface through major histocompatibility complex (MHC) class I proteins and presented to cytotoxic T lymphocytes (CD8+). These further become activated, demonstrating clonal expansion leading to virus-specific effector and memory T lymphocytes. These T lymphocytes lyse the virus-infected tissue cells. Also, by another way, the virus particles or peptides can be processed by antigen-presenting cells for displaying through MHC II molecules to CD4+ T lymphocytes. The CD4+ cells get activated to release cytokines and drive CD8+ T cell expansion. Further, the CD8+ T cell can kill other infected host cells. On the other hand, the B cells can also interact with CD4+ T lymphocytes or can recognize the virus directly. Post interaction, the cytokines released from with CD4+ T cells accelerate the B cell activation leading to clonal expansion and specific antibody production to neutralize the virus and ultimately control the spread of infection.

Post viral entry inside the cell, the major PRR involved in recognizing the viral material that is pathogen-associated molecular patterns (PAMPs) are RIG-I, MDA-5, TLRs (TLR3 and TLR7) which recognizes cytosolic RNAs. These PRRs further drive immune molecule signaling. In vitro studies have shown that SARS-CoV-2 induces RIG-I pathway (104). Another pathway induced by SARS-CoV-2 inside cells includes NOD-like receptor (NLR) activation and tumor necrosis factor (TNF)-α production (104). The inborn genetic error in TLR3 signaling pathways result in altered type I interferon (IFN) response and are shown to be associated with lethal COVID-19 (105). IFNs are considered as primary antiviral cytokines. In the case of SARS-CoV-2 infection a decreased IFN responses has been observed in vitro and in animal model (106). In SARS-CoV-2 infected human lung tissues as well, the IFNs were not significantly induced (107). The low secretion of IFN post SARS-CoV-2 is correlated to immune evasion strategy of the virus (108, 109). Recent studies have shown that the SARS-CoV-2 proteins like Nsp13 (a helicase– triphosphatase), Nsp15 (an endonuclease), and ORF-9b targets IFN pathway by interacting with TBK1, RNF41 and TOMM70 respectively (110, 111).

The subsequent immune activation post infection makes alteration in the balance of acute phase reactants in the peripheral system. In case of SARS-CoV-2 infection, higher levels of D-dimer, c-reactive protein (CRP), and procalcitonin (PCT) were associated with severe disease compared to non-severe disease (105). Various reports have observed a correlation between COVID-19 severity and the elevated levels of IL-6, alanine aminotransferase (ALT), lactate dehydrogenase (LDH), high-sensitivity cardiac troponin I, creatinine, creatine kinase, D-dimer, serum ferritin, prothrombin time (PT), CRP etc. (36, 112). Once SARS-CoV-2 establishes its infection in the lung microenvironment, COVID-19 development is accelerated due to increased load of viral infection as well as host response produced against the infection. Just like SARS and MERS, the severe COVID-19 cases have shown a common manifestation of cytokine storms (113, 114) Particularly, COVID-19 severity and cytokine syndrome observed in the disease is clinically associated with older patients i.e., above the age of 65 yes compared to those under 65 (115, 116). It’s uncertain why older people are more vulnerable to cytokine storms, although one explanation is that it’s due to NLRP3 activation which is an inflammasome component. During aging, the gradual elevation in abundance and activity of NLPR3 is observed in immune cells including alveolar macrophages. Age dependent increase of NLPR3 in alveolar macrophages have been shown to contribute in pulmonary fibrosis (115–117). In a two-phase model suggested by Mueller et al, NLRP3 basal overactivation may be the first step, followed by SARS-CoV-2 antigen-mediated hyperactivation, which causes the cytokine storm. Also, in elderly people, due to age progression, the capacity of immune response declines leading to reduced protection against pathogens, this is referred as immunosenescence (118). During onset of infection, immunosenescence drives more active innate immune response leading to chronic and low-grade inflammation (118). This may further be correlated to increased cytokine storm in elderly patients and subsequent COVID-19 severity. Post-infection driven inflammasome activation in immune cells, epithelial cells and endothelial cells release cytokines, interleukin (IL)-1β and IL-18 which is proportional to the severity of COVID-19 symptoms (100). The toll-like receptors (TLR) displayed on the host cells acts as viral RNA sensing machinery and induce NF-kB pathway which activate a plethora of pro-inflammatory cytokines leading to virus-induced inflammation (119).

Reports suggest that SARS-CoV-2 viral protein targets several innate-immune signaling proteins (110, 111). As stated earlier in this section, Nsp13, Nsp15, and ORF-9b targets IFN pathway. The Nsp13 also interacts with TLE1, TLE3 and TLE5 while the Orf9c interacts with NLRX1, F2RL1 and NDFIP2, which are involved in NF-κB pathway. ORF6 may hinder IFN signaling by targeting NUP98–RAE1 (110, 111). A study exploring transcriptional changes in immune cells and samples of bronchoalveolar washing of COVID-19 patients analyzed the different cytokine expression modulations. In a bronchoalveolar lavage fluid (BALF) sample the expression of CCL2, CCL8, CCL3L1, CXCL2, CXCL1, IL33 was upregulated. While in peripheral blood mononuclear cells (PBMC) CXCL-10, TNFSF10, TIMP1, C5, IL18, amphiregulin, neuregulin1, and IL10 were found to be induced post-COVID-19, which denotes the cytokine storm in patients (120). The overall exaggerated immune response, subsequent cytokine storm, the viral infection leads to the development of acute respiratory distress syndrome in COVID-19 patients. Various comorbidities associated with COVID-19 add up in severity of the disease can be correlated to mortality in many cases (121).

To control spread of infection inside the body, the adaptive immune response plays a crucial role. Post the first week of symptoms onset, virus-specific antibodies of IgM isotype are observed in the patients. Subsequently, IgG response is also observed that may retain long term immune memory (122). IgM and IgG responses against N protein and RBD of S protein were observed in non-severe as well as severe patients in the middle age group (with IQR, 34–56 years) after 10 days of first symptom generation (122). Wajnberg et al. studied more than 30,000 COVID-19 patients with mild to moderate symptoms and concluded that the neutralizing antibodies persisted at least 5 months (123). Some other reports also state that these antibodies may persist up to four months while other reports have presented the alleviation of neutralizing antibodies before four months itself in COVID-19 patients (post 4-12 weeks of symptoms onset) (124). A recent report analyzing neutralizing antibody response dynamics in patients who have recovered from COVID-19 states that it may vary greatly, and prediction of immune longevity can only be accurately determined at the individual level (125). Various geographical regions and age groups are necessary to understand more in this context.

There exists heterogeneity in CD4+ and CD8+ T cell response in non-severe and severe COVID-19 (126–128). Some studies have shown decreased cytokine response while others report aggressive CD8+ response with high cytotoxic effect (126). An increased CD8+ response against the proteins of SARS-CoV-2 was observed in patients with mild COVID-19 as compared to severe cases, thus indicating a protective role against the virus (129). The CD4+ cells showed impaired function as well as alleviated IFN-γ secretion in severe COVID-19 patients with higher age and comorbidity index (127). Grifoni et al. conducted a study to analyze T cell response against SARS-CoV-2 proteins and focused on non-hospitalized, recovered COVID-19 patients after 20-35 days of symptom onset (130). The report demonstrated the presence of virus specific CD4+ cells in 100% and CD8+ cells in 70% of recovered COVID-19 patients (130). This indicates virus specific T cell memory. However, the efficacy of these cells to protect from re-infection is not explored further. Interestingly, the T cell responses were against internal viral proteins instead of surface glycoprotein (130). In another report considering mild as well as severe COVID-19 patients post recovery, compared to other viral proteins the CD4+ response was more against spike protein of SARS-CoV-2 (129). SARS-CoV-2-reactive CD4+ T cells were also detected in ∼40%–60% of unexposed individuals (130). This hints towards the cross-reactive T cell recognition between circulating “common cold” coronaviruses and SARS-CoV-2 (130).

There are some other important subtypes of CD4+ T cells which include regulatory T cells (T-reg cells) and Th-17 cells. T-reg cells play a crucial role in maintaining overactive immune response while Th-17 cells promotes inflammatory cytokine production (131). The balance between these two plays important role in response to infection. In severe COVID-19 patients, increased Th17 cytokines while decreased T-reg numbers has been observed (131). Moreover, in these patients the increased IL-6 could promote Th-17 activation and T-reg inhibition (131). Such a mechanism during COVID-19 favors imbalance of Th-17 and T-reg cells ratio and may aid up in severity (131). Further exploration is yet required to decode precise roles of CD4+ and CD8+ T cells against acute SARS-CoV-2 infection as well as in protection from future infection.

Till date, no potential therapeutic agents (antivirals) have been discovered to treat specifically this global disease. Currently, researchers all over the world are working aggressively to discover a potential drug. Drug discovery and development is a tedious/challenging task, takes several years, and involves billions of dollars. Numerous experiments and techniques have been aimed at preventing further spread of COVID-19 and to improve successful and secure therapeutics. Depending on the target, possible anti-CoV therapies can be classified into two categories: (1) those acting on the CoV itself and (2) those acting on the human immune system or cells (132). The production of therapeutic methods is accelerated by elucidating immune responses caused by SARS-CoV-2 (133).

Various pharmacological interventions have been implemented by countries to cure the disease, including currently proven antivirals, various oxygen therapy types, or mechanical ventilation. COVID-19 pandemic demands a rapid development of successful and efficacious therapeutics/pharmaceuticals that can be achieved through application of three principles: (i) the first approach includes investigating and testing the therapeutic efficacy of currently available antivirals (134–136). (ii) Molecular databases and repositories/libraries that can aid in high processing capacity and continuous evaluation of millions of potential therapeutics (135, 137). (iii) Targeted treatment designed to interrupt the virus signaling (cellular and molecular pathways), and immunological response (135, 138–141). The safest and easiest way to produce pharmaceutical products for treatment of SARS-CoV-2 is the first strategy, to find potential molecules from manufactured medicines. It may be accepted by the Green Channel or approved by the hospital ethics committee for accelerated clinical care of patients once effectiveness has been assessed (142). The approaches to drug repurposing can be performed by in vitro and in vivo studies using a conventional approach, or it can be achieved by a statistical approach, which relies on bioinformatics methods, ‘Big Data’ and ‘Artificial Intelligence’ (AI) to find new indications for drugs already in use, and subsequent validation in vitro and in vivo (143).

Broad-spectrum antivirals, such as IFNs, ribavirin, and cyclophilin inhibitors have been used to treat CoV pneumonia. The benefit of these therapies is that, since they have been approved for the treatment of other viral infections, their metabolic properties, dosages used, possible effectiveness and side effects are known. However, because these therapies are broad-spectrum, they are unable to directly kill CoVs, and potential side effects should be considered (144). Unfortunately, due to differences in pharmacokinetic (PK) and pharmacodynamic (PD) properties, in vitro analysis seldom translates to in vivo, posing a significant barrier to clinical translation of a therapeutic candidate (145). Already approved pharmaceuticals, including antimalarials, antiviral, lysosomotropic drugs; and then selected broad spectrum antibiotics, and immunotherapeutic drugs, are the key classes of therapeutic agents that seem effective in COVID-19 therapy and are currently being recommended in various countries (146–154).

Ribavirin is used in the management of many viral infections, including chronic hepatitis C virus, viral hemorrhagic fever, and respiratory syncytial virus, in conjunction with other antiviral medications and, in certain instances, IFN-α. Ribavirin was first commercialized in the early 1980s for the treatment of respiratory syncytial virus in infants, making it the most well-known and widely used antiviral agent. Aside from being regarded as a broad-spectrum antiviral agent against DNA and RNA, which can obstruct viral messenger RNA binding RNA-dependent RNA polymerase production (RpRd), it is also a prodrug that metabolizes into nucleoside analogues that block viral RNA and capping viral mRNA. The combination of nitazoxanide, ribavirin, and ivermectin, as well as zinc supplementation, removed SARS-CoV-2 from the nasopharynx faster than symptomatic treatment (155).

Remdesivir is one of the most effective antiviral medicines for managing coronavirus infection that has been studied. It is an adenosine nucleotide phosphoramidite prodrug with broad-spectrum in-vitro antiviral activity against a variety of RNA viruses. Remdesivir, while being a nucleotide precursor, has been shown to prevent viral RNA replication and to prematurely terminate viral RNA transcription by targeting viral RNA-dependent RNA polymerase. For individuals at high risk of hyperinflammation who are diagnosed early during illness (≤10 days) and require supplemental oxygen, the Remdesivir therapy reduced the period to rehabilitation by four days, which is significant improvement for patients and healthcare systems. However, for patients with mild or moderately severe COVID-19 and no need for respiratory support, Remdesivir does not offer significant benefit at day 28. Therefore, Remdesivir is considered as an important COVID-19 treatment option only in selected patient (76).

Ivermectin is an anti-parasitic broad-spectrum drug that has been shown to prevent HIV-1 replication. In-vitro analysis performed in Australia, Ivermectin’s antiviral activity on SARS-CoV-2 infected cells showed a 93 percent reduction in viral RNA present in the supernatant and a 99.80 percent reduction in cell-associated viral RNA. A randomized, double-blind, placebo-controlled study of adult SARS-CoV-2 patients revealed that adult patients with mild COVID-19 treated with 12 mg of Ivermectin resulted in an earlier clearance of the virus with a 5-day course. The treatment was found to be both safe and successful. However, to validate these preliminary results, larger studies would be needed (156).

Interestingly, plant based natural products such as plant metabolites are also extensively in use to fight CoV infection (157). Furthermore, various research groups revealed that lipid metabolism (158, 159), RNA-dependent RNA polymerase (16), many virus structural proteins can act as potential drug targets (160) for the management of COVID-19. However, clinical trials are undergoing to screen and translate a potential therapeutic candidate for the management of COVID-19 (132).

The technique of high-throughput screening, which for instance, contributed to the discovery of the anti-HIV infection drug lopinavir/ritonavir, may identify many drug molecules. Through a strategy focused on genomic knowledge and pathological characteristics of various CoVs, the drugs detected would show stronger anti-CoV effects, but the new drug discovery phase could take many years or even more than 10 years to complete (161).

Vaccines is one of the most significant advances in human medicine for reducing the spread and effects of infectious disease. Vaccines have been used to contain epidemics and are a useful strategy in reducing pandemic mortality (219). The development of a COVID-19 vaccine has been even more rapid than that of any other vaccine. Within less than 12 months after the beginning of the COVID-19 pandemic, teams had developed vaccines that could be deployed for protection of the population from SARS-CoV-2 (220). Each vaccine that has been granted or is being considered for temporary licensing has been validated in trials involving over 20,000 patients, with months of safety evidence collected. Approximately 270 COVID-19 vaccines are presently in varying phases of production, with others using similar technology to already used vaccines and some using novel approaches (221).

An “ideal” COVID-19 vaccine should:

Developing a safe and reliable vaccine usually takes several years since it must undergo clinical trials. However, the unexpected spread of the SARS-CoV-2/COVID-19 pandemic prompted an extraordinary attempt to develop a vaccine against this virus in a relatively limited period of time. While clinical trials have been conducted more rapidly since the pandemic, this has been accomplished by overlapping the various phases of clinical testing (phase 1, 2, and 3) rather than sequentially completing them. The safety assessment process was not affected, and the experiments adhered to the same stringent legal standards as other vaccine tests (222).

Before being formulated and marketed, vaccines must obtain stringent regulatory approval in the country of manufacture by a national regulatory authority (NRA). As of May 2021, about 1.3 billion vaccine doses have been distributed globally, an average of 17 doses per 100 individuals (https://www.nytimes.com/interactive/2021/world/covid-vaccinations-tracker.html). There is also a significant disparity between vaccine systems in various nations, with several countries unable to record even a single dose ( Figure 7 ).

Israel was the first country to demonstrate that the COVID-19 vaccines had an effect on viral transmission of SARS-CoV-2 in society. By February 2021, more than 84 percent of people aged 70 and over had received two doses, making the country the global leader in vaccines. The number of severe COVID cases and deaths dropped dramatically (223). Related findings were seen in a separate study conducted in the United Kingdom (224).

Although vaccines still remain scarce worldwide, the majority of countries have concentrated their early vaccination programs on high-risk populations such as the clinically vulnerable; people in their 60s, 70s, and older; and front-line staff such as doctors and nurses (222).

At this stage, few adverse effects have been recorded from SARS-CoV-2 vaccine clinical trials, and the efficacy of vaccines that have been extensively tested seems to be encouraging. The duration of vaccine immunity is vital to maintaining herd immunity, estimated at 50% to 67%, without population immunity, in the absence of intervention and considering all individuals similarly vulnerable and contagious (225). In the event that COVID-19 vaccinations become more widely available, vaccination programs could expand to include younger people in order to address asymptomatic transmission, which contributes significantly to the dissemination of SARS-CoV-2 and is more prevalent in younger age groups, thus restricting the virus’s dissemination and potentially protecting the most vulnerable people (222, 225).

Another significant issue with vaccines is manufacturing capability. Given that billions of people will be vaccinated, it appears that only 2-3 companies will be able to satisfy this demand. In addition to the vaccine supply problem, logistical issues have also evolved significantly. In terms of logistics, the optimal vaccine for COVID-19 should:

COVID-19 triggered by SARS-CoV-2 is a serious danger to public health. The positive cases of COVID-19 are rising at an unprecedented pace worldwide and is a matter of international concern. It is anticipated that the COVID-19 pandemic would greatly threaten to inflict immense mortality and morbidity burdens while significantly affecting populations and economies globally. In an attempt to secure billions of vulnerable individuals globally, innovative scientific research efforts are undertaken in parallel to drive forward preventive modalities. The elucidation of the SARS-CoV-2 immune defense will accelerate the development of therapeutic strategies. Particularly, the repurposing of anti-CoV and antiviral drugs with peptides already clinically approved could serve as an example for the creation of new effective and safe drugs. The urgent demand for an effective anti-SARS-CoV-2 drug could reshape the drug development landscape. As such, cocktail therapy using a selected mixture of antiviral peptides, antibodies in combination with other groups of antiviral agents could be a potential therapeutic approach that merits further clinical testing. Peptides have been formed as effective keys to viral disease. When aided with computational biology, the design of peptide therapies against SARS-CoV-2 could be accelerated more efficiently.

Following a year of global initiatives, significant progress has been made in the development of COVID-19 vaccines, and several vaccine candidates based on mRNA technology or a virus vector platform have been developed and demonstrated protective efficacy against SARS-CoV-2. To date, the manufacture of mRNA vaccines for the prevention of infection with the SARS-CoV-2 coronavirus has been a success story. However, due to manufacturing and transportation restrictions in many remote regions, vaccines produced so far are unable to fulfill global vaccination criteria. The long-term effectiveness of these vaccines, as well as associated safety issues, are being investigated. Governments, public health sector authorities and advocacy groups must be prepared to ensure access to and delivery of COVID-19 vaccines on a massive scale, in a reasonable manner. Since the leading candidates are administered intramuscularly, the emphasis is on immune responses in the blood rather than on mucosal surfaces. However, mucosal immunity plays an important role, and many intranasal vaccine formulations are being developed. An important question to be addressed is how long defensive immunity can persist after vaccination. The “long defensive immunity” post vaccination is more likely related to the emergence of new viral variants as opposed to the duration of vaccine efficacy. As is also the case for influenza.

Increased viral replication provides further chances for SARS-CoV-2 variants to evolve. As a result, vaccine production may be hampered if the virus later develops resistance to the spike glycoprotein used to create the vaccine. Vaccinations may be engineered to attack multiple viral locations, minimizing the chance of a mutated virus evading existing immunity. Despite these limitations, we will now have a completely different vaccination strategies that can be implemented rapidly the next time we are threatened with a zoonotic epidemic.

UA: Conceptualization, Literature survey, Writing major original draft, Figure designing, References collection, Review structure. SJ: Literature survey, Writing- review and editing, Figure designing. OI: Literature survey, Writing- review and editing, Figures designing. HC: Reviewing and editing, Supervision. Z-SC: Review and editing, Response. VT: Conceptualization, Critical review and editing, Review structure, Response, Supervision. JMPL: Conceptualization, Literature survey, Writing, Figures designing, Table preparation, Critical review and editing, Response. All authors contributed to the article and approved the submitted version.

This work was funded by “Agencia Canaria de Investigación, Innovación y Sociedad de la Información (ACIISI) del Gobierno de Canarias”, project ProID2020010134 “Bioprospección y biotecnología en el descubrimiento de péptidos antimicrobianos contra patógenos resistentes” and CajaCanarias, project 2019SP43. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.