Basic Virology and Immunology

Basic Virology


In December 2019, a series of cases of pneumonia of unknown origin were reported in Wuhan, the capital city of Hubei province in China. The causative virus was isolated and characterized in January 2020 (Zhou et al., Nature 2020, Zhu et al., NEJM 2020). On January 12, 2020 the World Health Organization (WHO) tentatively named the virus as the 2019 novel coronavirus (2019-nCoV). On January 30, 2020 WHO issued a public health emergency of international concern (PHEIC) and on February 11, 2020, the WHO formally named the disease caused by the novel coronavirus as coronavirus disease 2019 (COVID-19). At that time, based on its genetic relatedness to known coronaviruses and established classification system, the International Committee on Taxonomy of Viruses classified and renamed 2019-nCoV as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On March 11, 2020, the WHO formally characterized the global spread of COVID-19 as a pandemic, the first to be caused by a coronavirus.


Coronaviruses are positive-sense, single-stranded enveloped RNA viruses with helical capsids that infect a wide range of hosts including humans, bats, other mammals, and birds. As shown in the schematic taxonomy below, coronaviruses are classified within the order Nidovirales and are further subclassified into four genera: alpha, beta, delta, and gamma coronaviruses, of which alpha and beta coronaviruses are known to infect humans. As a family, coronaviruses most prominently include several human coronaviruses (HCoV) that are associated with lower pathogenicity (HCoV-229E, -NL63, -OC43, -HKU-1), contributing to seasonal cases of the ‘common cold’ and sometimes linked to more severe respiratory illness (Bradburne et al., BMJ 1967; Lieberman et al., Chest 2010). Two betacoronaviruses have previously been identified to cause more severe disease and outbreaks: severe acute respiratory syndrome coronavirus (SARS-CoV), responsible for the SARS worldwide outbreak in 2002-3 with 8,096 cases and 774 deaths reported, and Middle East respiratory syndrome coronavirus (MERS-CoV), responsible for 2,102 cases and 780 deaths reported during the 2012 MERS outbreak. SARS-CoV-2 falls within the Sarbecovirus subgenus of the Betacoronavirus genus along with SARS-CoV, and is the seventh coronavirus identified to infect humans (Zhou et al., Nature 2020, Zhu et al., NEJM 2020).

Schematic of the taxonomy of Coronaviridae family of viruses as per ICTV classification, highlighting coronaviruses known to infect humans. From Pillaiyar et al., Drug Discovery Today, 2020.
Schematic of Baltimore classification scheme based on type of genome and replication for virus families (text in blue), highlighting SARS-CoV-2 and select virus families with viruses (influenza virus, rhinovirus) known to cause common human respiratory infections. Adapted from Collier, Oxford, Kellam, Human Virology 5e 2016.


Coronaviruses have the largest genome of all ribonucleic acid (RNA) viruses infecting humans, consisting of a positive-sense single-stranded RNA roughly 30 kb in size that is 5’-capped and 3’-polyadenylated. Shown in the figure below, the virus genome is non-segmented with as many as 14 open reading frames (Zhu et al., NEJM 2020). The genome is organized with non-structural polyproteins, which are then cleaved to be enzymes such as proteases and a RNA-dependent RNA polymerase, encoded at the 5’ end and structural proteins encoded toward the 3’ end.

SARS-CoV-2 genomic organization and encoded proteins (Lu et al., Lancet 2020; genome assembly data). Figure from Gordon et al., Nature 2020.

Genetic analyses: relatedness to other viruses, suspected origins, and continued surveillance

The majority of new coronaviruses have been isolated from bats, which serve as a natural reservoir, though other animal species have been linked as intermediate hosts in the transmission to humans, such as the civet cat for SARS-CoV (Guan et al., Science 2003) and dromedary camel for MERS-CoV (Chu et al., Emerg Infect Dis 2014). Currently, the closest identified relative to SARS-CoV-2 is a virus isolated in bats with 96% sequence identity (Zhou et al., Nature 2020). It is suspected that an intermediate host may have facilitated the zoonotic event, given both overall limited interactions between bats and humans and also the initial cluster of cases which were epidemiologically linked to a live animal and seafood market in Wuhan. Among a large variety of animals present, the pangolin, a scaly anteater and commonly trafficked mammal, has been implicated as a potential intermediate host, based on high levels of similarity of pangolin coronaviruses to SARS-CoV-2 at the protein level (Lam et al., Nature 2020). However, full genome analysis of pangolin coronaviruses have appeared more distinct (Liu et al., bioRXiv preprint 2020), suggesting that other market animals, such as civets or pigs, may have been the intermediate host between bats and humans (Lu et al., Lancet 2020; Zhang et al. Clin Infect Dis 2020). High levels of recombination among Sarbecoviruses and the large, unsampled diversity of coronaviruses in bats and other animals contribute to the challenge of identifying the origins of SARS-CoV-2 (Boni et al., bioRxiv preprint 2020). Continued sequencing and real-time analysis of SARS-CoV-2 genomes from samples around the world have helped track global spread, monitor local outbreaks and transmission chains, and provide insights into the epidemiology of COVID-19 ( For more information about how to read phylogenetic trees, see here.

Phylogeny showing the genetic relationship of betacoronaviruses, including novel coronavirus SARS-CoV-2 isolates from Wuhan (red) to SARS-CoV and MERS-CoV (blue). The closest related virus to SARS-CoV-2 was isolated from bats (Lu et al., Lancet 2020).
Phylogeny showing relatedness of ‘SARS-like’ betacoronaviruses (‘Sarbecovirus’ subgenus from previous figure) to select SARS-CoV-2 samples isolated from China, USA, and Japan. Each circle ‘tip’ of the phylogenetic tree represents a virus sample, color coded by type of host. From nextstrain.

Thought questions:

  • Based on the phylogeny, would you expect SARS-CoV-2 to behave more like SARS-CoV or MERS-CoV?

  • What are some benefits and drawbacks of analyzing specific genes compared to the whole genome of a virus?

  • How might understanding the origin and intermediate hosts of a virus influence human practices and policies to prevent zoonotic viruses from seeding new epidemics?

Virus structure

Microscopically and as seen in the schematic figure below, coronaviruses have club-shaped trimeric surface spike glycoproteins that give the virions the appearance of a crown, hence their name (from the Latin corona meaning “crown”). Summarized in the table below, coronaviruses contain four major structural proteins: the spike (S), hemagglutinin-esterase (HE) in some betacoronaviruses, membrane (M), and envelope (E) all located on the membrane envelope, and the nucleocapsid (N) protein found in the core. The N proteins associate with the RNA genome to form a long helical ribonucleoprotein (RNP) packaged within the enveloped virus particle. The M protein, the most abundant of the structural proteins, is a transmembrane glycoprotein that gives the envelope its shape. The E protein is thought to be critical for coronavirus infectivity.

Structural proteins of coronaviruses and their functions. Summarized from Fields, Knipe, Howley, Fields Virology 6e 2013.
Coronavirus structure. Schematic showing major structural proteins of the coronavirus virion. From AMBOSS.

The S surface protein plays key roles in the viral life cycle and in host defense: it is responsible for receptor binding, host range, membrane fusion, hemagglutinin activity, and is a target for eliciting host neutralizing antibodies (Millet & Whittaker, Virus Res 2015). SARS-CoV-2 has genetic polymorphisms in the S protein that distinguish it from SARS- and MERS-CoV. This different spike protein structure has been suggested to allow activation by furin, a host-cell enzyme found in many human tissues including lungs, liver, and small intestines (Andersen et al., Nature 2020). Thus, the potential for furin activation in SARS-CoV-2 may explain its expanded cellular tropism (Walls et al., Cell 2020), which may contribute to the manifestation of liver injury with COVID-19 (Zhang et al., The Lancet 2020).

Alignment of amino acid sequences highlights differences between SARS-CoV-2 to SARS-like coronaviruses and SARS-CoV in spike protein residues important for (a) receptor-binding and (b) polybasic cleavage site for potential furin activation. Figure modified from Andersen et al., Nature 2020.

Thought questions:

  • How could the specific proteins (S, E, M, and N) on SARS-CoV-2 be useful targets for diagnosis? For treatment? What technologies or molecular diagnostics/therapeutics would be useful?

Pathogenesis of COVID-19 Infection

Research is ongoing to characterize the pathogenesis of how SARS-CoV-2 results in COVID-19 disease in humans. Below is our current understanding of the literature.

Viral entry

SARS-CoV-2 enters host cells through interacting with ACE2, an interferon-induced gene expressed on type 2 pneumocytes, intestinal epithelial cells, nasal goblet secretory cells (Ziegler et al., Cell preprint 2020), olfactory epithelial support cells and stem cells, and nasal respiratory epithelium (Brann et al. Biorxiv Preprint 2020). Although SARS-CoV-2 has been found inside GI epithelial cells (Xiao et al., Gastroenterology 2020), the virus mainly infects type 2 pneumocytes in the lung (Zhu et al., NEJM 2020). Comprising 3% of the alveolar epithelium, type 2 pneumocytes secrete pulmonary surfactant (dipalmitoyl phosphatidylcholine), which decreases the surface tension of the lungs, and also act as stem cells for the alveolar epithelium.

ACE2 is a transmembrane protein implicated in the renin-angiotensin-aldosterone system (RAAS) and hypertension pathogenesis. Note that ACE2 is a distinct enzyme from ACE: ACE converts angiotensin I to angiotensin II, a potent vasoconstrictor that drives the synthesis of aldosterone, whereas ACE2 converts active angiotensin II to angiotensin 1-7, a primary vasodilatory agent. This functions as negative regulation of RAAS. ACE2 has a protective effect in mouse models of ARDS (Imai et al., Nature, 2005). ACE2 levels in the nasal epithelium increase with age (Bunyavanich et al., JAMA 2020), which may contribute to the differential susceptibility of older individuals to COVID-19. SARS-CoV-2 binds to ACE2 via its S protein. Binding triggers a conformational change in the S protein, allowing it to be cleaved by a host cell serine protease called TMPRSS2 (Zhou et al., Nature 2020). Cleavage of the S protein between its S1 and S2 domains allows fusion of the viral and host cell membranes and viral entry to the cell.

SARS-CoV-2 can enter by two pathways: through endocytosis, and through non-endocytic cell surface entry (Zumla et al., Nat Rev Drug Discovery 2016). The endocytic pathway is a potential target of drugs like chloroquine and hydroxychloroquine (Liu et al., Cell Discovery 2020). Upon entering in a membrane vesicle, the virion fuses with the vesicle and releases its single-segmented RNA genome into the cytosol. Since the virus is positive-sense, it can essentially serve as mRNA and be translated immediately into non-structural viral proteins by the endogenous cell machinery. Some of these proteins form a replication complex to produce more RNA with a viral RNA-based RNA polymerase, including subgenomic RNAs which are used to translate structural proteins, and full-length transcripts to be incorporated into SARS-CoV-2 virions. The nucleocapsid (N) protein binds to the full-length positive sense viral RNA and associates with the matrix glycoprotein in the ER-Golgi intermediate compartment (ERGIC) to form a virion. The M protein associates with S and the virion virion buds into the Golgi lumen, thus gaining an envelope and exocytic vesicles from the Golgi containing the enveloped virus fuse with the cell membrane and releases viruses to infect other cells (Masters and Perlman, “Chapter 28: Coronaviridae”, Fields Virology).

Demonstration of how SARS-CoV-2 infects type 2 pneumocytes, propagates its own mRNA and viral proteins with host machinery, and then releases newly formed SARS-CoV-2 virions. From The Economist.

Systematic studies of possible interactions between SARS-CoV-2 and human proteins have been reported, with aims of investigating host factors mediating virus infection to identify new antiviral drug targets and repurposing of previous drugs (Zhou et al., Cell Discovery 2020; Gordon et al., bioRxiv 2020 preprint).

Thought question:

  • What are the pros and cons of targeting human proteins compared to viral proteins to treat a viral disease?

Transmission dynamics

Transmission of SARS-CoV-2 is thought to occur mainly through respiratory droplets (Aylward et al., Report of the WHO-China Joint Mission 2020). Other routes of transmission such as virus contamination of common objects, aerosolization in a confined space, or spread from asymptomatic infected persons have been suggested, though the significance of their role in contributing to overall transmission have yet to be fully elucidated (Cai et al., Emerg Inf Dis 2020; Rothe et al., NEJM 2020). Respiratory droplets can be generated by sneezing (40,000 droplets), coughing (3,000 droplets), or talking (about 600 droplets per minute). They can also be produced by medical procedures like intubation and bronchoscopy or by use of oxygen masks and nebulizers (Tang et al., Journal of Hospital Science 2006). Larger droplets (>60 microns) tend to spread about 1 meter (3 feet) and require droplet precautions, while smaller ones spread further and require stricter airborne precautions. So far, it seems likely that SARS-CoV-2, like SARS-CoV, is mainly spread through larger droplets,, although the medical procedures mentioned above risk making it airborne with a larger radius of spread (Tang et al., Journal of Hospital Science 2006; Aylward et al., Report of the WHO-China Joint Mission 2020). However, this remains an area of active investigation.

A flash photo of a human sneeze. Source: Tang et al., Journal of Hospital Science 2006

Early reports indicate that SARS-CoV-2 has the potential to be transmitted through fomites, or objects with virus on their surface. SARS-CoV-2 appears to have similar viability in aerosols and on surfaces when compared to that of SARS-CoV. When aerosolized, SARS-CoV-2 remains viable for up to 3 hours, a critical consideration for hospital infection control, particularly when undergoing aerosolizing procedures. Viable SARS-CoV-2 was measured from surfaces up to 4 hours on copper, 24 hours on cardboard, and 72 hours on plastic and stainless steel (van Doremalen et al., NEJM 2020). While these results do not fully evaluate the infectivity of the virus on different surfaces, in general this data supports the notion that maintaining good hygiene (washing hands often, especially after touching public surfaces, and avoiding touching face and mouth) could help mitigate the spread of SARS-CoV-2. Moreover, this data suggests that other viral properties must explain the infectivity differences between SARS-CoV-2 and SARS-CoV. Previous work studying other coronaviruses have also suggested that surface disinfection such as with 62-71% ethanol or 0.5% hydrogen peroxide, commonly found in household cleaning products, can inactivate coronaviruses that persist on surfaces (Kampf et al., J Hosp Infect 2020).

The literature on mask efficacy is still developing, although it is important to lessen transmission from asymptomatic, presymptomatic and symptomatic individuals alike. Surgical masks have shown efficacy in hospitalized patients with seasonal coronaviruses (Leung et al., Nat Med 2020), and homemade cloth masks can block large droplets produced during speech (Anfinrud et al., MedRXiv 2020). However, a small study of 4 patients with COVID-19 did not show efficacy of cloth or surgical masks in decreasing detectable virus near coughing patients (Bae et al., Ann Int Med 2020). Current CDC recommendations are for the lay public to wear cloth masks in public and to reserve N95 masks for people with high levels of exposure (

In concordance with the ability of SARS-CoV-2 to infect intestinal epithelial cells, viral RNA has been detected in 29–55% of stool samples from COVID-19 patients (Xiao et al., Gastroenterology 2020; Wang et al., JAMA 2020; Wu et al., Lancet Gastroenterol Hepatol 2020), as well as environmental samples from the toilet (Ong et al., JAMA 2020). Live virus has also been isolated from stool specimens (Wang et al., JAMA 2020; Zhang et al., CCDC Weekly 2020). Viral RNA can be detected in the stool or on rectal swabs even after oro-/nasopharyngeal swabs turn negative (Xiao et al., Gastroenterology 2020; Xu et al., Nat Med 2020). These data raise the possibility of fecal–oral transmission of SARS-CoV-2 (Yeo et al., Lancet Gastroenterol Hepatol 2020), as was suspected with the SARS outbreak of 2002–2003 (Abdullah et al., Emerg Inf Dis 2003). Live SARS-CoV-2 has also been isolated from blood but only from rare patients, and RNA has been isolated from the conjunctiva of the eyes; no RNA has been isolated to date from urine (Wang et al., JAMA 2020; Liang & Wu, Acta Opthalm 2020; Richterman and Meyerowitz, Partners ID Grand Rounds 3/25/20).

Whether COVID-19 can be spread by vertical transmission, passed from mother to fetus or neonate during pregnancy or during the perinatal period, is not well understood. In a number of limited case series of pregnant women with lab-confirmed COVID-19, none of the infants were found to have COVID-19 and SARS-CoV-2 was not detected in samples including amniotic fluid, cord blood, neonatal throat swab, or breastmilk (Chen et al., Lancet 2020, Li et al., Emerg Infect Dis 2020, Schwartz, Arch Path Lab Med 2020). Previous limited case series have found infants born to mothers with SARS were negative for SARS-CoV (Wong et al., Am J Ob Gyn 2004; Shek et al., Pediatrics 2003) and vertical transmission with SARS or MERS infection have not been documented in the past (Schwartz & Graham, Viruses 2020). Cases of COVID-19 have been reported in neonates and infants; however, these were complicated by close contact history with confirmed infected persons following birth (Qiao, Lancet 2020; Wei et al., JAMA 2020). There is currently little evidence to suggest risk of intrauterine transmission for COVID-19. In contrast, neonates born to COVID-positive mothers can acquire IgG (transplacentally) and IgM (mechanism unknown, possibly imperfect assay) antibodies against the disease (Zeng et al., JAMA 2020).

A feature of COVID-19 is its ability to be transmitted by asymptomatic individuals, whether before symptoms start or by individuals who do not have symptoms. Virus shedding can occur at least 24-48 hours before symptoms start (Aylward et al., Report of the WHO-China Joint Mission 2020; He et al. medRxiv 2020 preprint), and has been shown in asymptomatic individuals (Zhou et al., NEJM 2020). Viral load can be positive multiple (1 to 7) days before symptom onset (Wang et al., JID 2020), and peaks around the time of symptom onset, suggesting significant viral load before someone knows they may be infected (To et al., Lancet ID 2020). Modeling of transmission events in China prior to the January 23rd travel restrictions estimated that undocumented cases, which experienced no to mild symptoms that did not warrant hospitalization, were responsible for 79% of new cases (Li et al., Science 2020); another study found that 12% of cases were transmitted from pre-symptomatic individuals (Du et al., Emerging Inf Dis, 2020). Current estimates of the COVID-19 incubation period, which refers to the time period from initial exposure to symptom onset, range from 1-14 days with a median of 5 days and 95th percentile of 12 days, similar to SARS (Lauer et al., Ann Intern Med 2020; Li et al., NEJM 2020). The detection of SARS-CoV-2 RNA in patients at 20 days and as long as 37 days in one patient also suggests the potential of prolonged virus shedding (Zhou et al., Lancet 2020; He et al. medRxiv 2020 preprint). Increased severity of cases have been suggested to be associated with higher viral loads and longer duration of viral shedding (Liu et al., Lancet Inf Dis 2020). Because they may shed virus for a period of time after symptoms have resolved, it is still unknown how long someone in remission from COVID-19 remains infectious. However, for people who become symptomatic, a recent study was not able to isolate infectious virus after 8 days after symptom onset, suggesting a limited time period for infectious viral shedding (Bullard et al., Clin Inf Dis 2020). The delay between exposure and showing symptoms combined with transmission from asymptomatic hosts have made SARS-CoV-2 particularly difficult to contain.

Thought questions:

  • How would you predict that a difference in infected cell types might change the presentation and transmission of COVID-19?

  • Imagine a few real-life scenarios that you may soon encounter or may have already encountered:

    • Diane wants to order food from a delivery service, but is worried about getting sick. What advice would you give her about touching packages, meeting the delivery person, and ordering premade food?

    • Brian has a friend who had low fevers, fatigue, and a dry cough, but was never tested for COVID-19. His friend self-quarantined at home and now has not had any symptoms for the past day. Brian wants to hang out with this friend today. What would you tell him about his risk of exposure?

  • How do estimates of incubation periods and viral shedding inform public health efforts?

Immune Response in COVID-19

(Prompetchara et al., APJAI 2020)

Innate immune response

In milder cases of SARS, a robust type I interferon response may lead to appropriate adaptive immune responses and viral clearance (Channappanavar et al., JCI Insight, 2019). In severe cases of COVID-19, as in SARS and MERS, decreased viral control of SARS-CoV and MERS-CoV is associated with a delayed or absent type I interferon response; instead, the initial response recruits neutrophils, monocytes and macrophages to the lung, which is associated with increased immunopathology (Blanco-Melo et al., Cell 2020; Hadjadj et al., MedRXiv preprint 2020). The influx of myeloid cells into the lungs is accompanied by a cytokine storm, with increases in levels of serum pro-inflammatory cytokines, such as IL-1, IL-6, IL-12 and TNFɑ, that increase vascular permeability and decrease lung function. IL-6 can signal through direct binding to the IL-6 receptor on lymphocytes; it can also bind to soluble IL-6 receptor and bind to endothelial cells to stimulate vascular effects of the disease, and finally it can change expression of inflammatory mediators in the liver (Moore and June, Science 2020). In COVID-19, both increases in monocytes and neutrophils in the lungs (Prompetchara et al., Asian Pacific Journal of Allergy and Immunology 2020) and higher serum pro-inflammatory responses (cytokine storm) are associated with severe disease (Huang et al., Lancet 2020). Antibodies against the IL-6 receptor, such as tocilizumab and sarilumab and antibodies against IL-6 itself, such as siltuximab, are in clinical trials; the goal is to decrease effects of the cytokine storm in more advanced disease.

(Moore and June, Science 2020)

Thought question:

  • How might the integrity of the lung and ability of immune cells to migrate to the site of infection affect the immune response to SARS-CoV-2?

Adaptive immune response

The adaptive immune response generally consists of humoral immunity, most prominently antibodies produced by B cells, and cellular immunity, including CD4+ and CD8+ T cells and NK cells. These cells are primed by antigen presentation from cells including dendritic cells, macrophages, and B cells. Because SARS-CoV-2 is a new virus, the world population has no pre-existing immunity to it, which is one of the reasons it has been so quick to spread. One study using serological methods found low to no detection of SARS-CoV-2 specific antibodies in samples banked prior to SARS-CoV-2 exposure with negligible cross-reactivity from other human coronaviruses, suggesting humans may be completely immunologically naive to SARS-CoV-2 prior to the emergence of COVID-19 (Amanat et al. Nature Medicine 2020). Once exposed, people can form a detectable humoral immune response to SARS-CoV-2. IgM antibodies to SARS-CoV-2 were found at a median of 12 days after illness onset and IgG after a median of 14 days; the timing of antibody production was not associated with disease severity, but higher antibody titer was associated with worse disease (Zhao et al., Clinical Infectious Diseases 2020). The presence of an antibody response that protects from reinfection has been established in animal models (Bao et al., BioRXiv preprint 2020), but not yet in humans. However, neutralizing human monoclonal antibodies have been cloned and could represent a future therapeutic. While preliminary reports indicate that convalescent plasma appears to positively influence outcomes (suggesting that antibodies might be protective) (Shen et al., JAMA, 2020; Duan et al., PNAS, 2020), more data is awaited. A recent report on COVID-19 in a small number of patients with immunodeficiencies has raised some issues. Patients with agammaglobulinemia had very mild disease while patients with common variable immunodeficiency (CVID) had severe disease. These studies raise the possibility that a humoral immune response may not be protective against severe disease and that atypical B cells (which are a known source of IL-6 in many diseases including granulomatous interstitial lung disease linked to CVID, that respond to B cell depletion) may contribute to severe COVID-19 disease (Quinti, et al. J Allergy Clin Immun, 2020). The numbers are small but these data are provocative. A recent study on patients with Waldenstrom’s macroglobulinemia suggests that a Btk inhibitor (Ibrutinib) may be protective, though Ibrutinib inhibits not only B cell activation but also attenuates immune receptor signaling in myeloid cells (Treon et al., Blood 2020).

When it comes to T cells, CD4+ T cell responses against SARS-CoV-2 peptides are seen in 100% of COVID-19 patients, and CD8+ T cell responses are seen in 70% of these patients (Grifoni et al., Cell 2020). Interestingly, CD4+ T cells that react against SARS-CoV-2 were also seen in 40-60% of patient cells collected in 2015-2018, which correlated with the presence of antibodies against seasonal coronaviruses, suggesting pre-existing cross-immunity from other coronavirus infections (Grifoni et al., Cell 2020). A Th1-type CD4+ T cell response is important in successful control of SARS-CoV and MERS-CoV (Li et al., J Imm 2008; Shin et al., Clin Inf Dis 2019). In mouse models of SARS, loss of CD4+ T cells reduced viral clearance, decreased antibody responses and led to increased mortality, while depletion of CD8+ T cells had no effect (Shen et al., J Virol 2009). In mice, CD4+ T resident memory cells in the lung are particularly important for vaccine-mediated protection against SARS (Zhao et al., Immunity 2016). CD8+ T cell responses are also important to control infection, but may be associated with increased lung pathology in SARS and MERS when overabundant, making it difficult to discern cause from consequence (Shin et al., Clin Inf Dis 2019; Prompetchara et al., As Pac J of All and Imm 2020). MERS-CoV has been shown to decrease antigen presentation on dendritic cells and macrophages, delaying activation of the adaptive immune system (Shokri et al., J Cell Physiol, 2019). So far, this has not been studied in SARS-CoV-2.

Lymphopenia is a hallmark of in COVID-19, is associated with IL-6 and IL-8 levels (Zhang et al., Nature 2020), and is a predictor of disease severity (Tan et al., Signal Transduction and Targeted Therapy 2020). CD4+ and CD8+ T cells are depleted to a greater extent than B cells or NK cells (Zhang et al., Nature 2020), which may be partially explained by recruitment to infected tissue. This may be due to bone marrow suppression by the antiviral response, destruction of lymphatic tissue (Chen et al., MedRXiv 2020), or perhaps by direct viral infection and depletion of lymphocytes (Wang et al., Cellular and Mol Immunol, 2020). It is not yet known whether individual with mild disease recover in part because of vigorous protective cytotoxic CD8+ T cell based elimination of infected cells, and whether the progression of illness in more seriously ill patients reflects a relative absence of such a response. These differences, if established, could in part help explain the clinical spectrum of the disease.

A key question for understanding the dynamics of the pandemic and whether a vaccine will be protective is whether previously infected individuals can be re-infected. In macaque models of infection, one study suggests macaques are protected from subsequent SARS-CoV-2 infection (Bao et al., bioRxiv 2020). Another study shows that some monkeys become infected again after rechallenge, but this infection only lasted a short period of time and no infectious virus was recovered, suggesting that they had developed an effective immune response (Chandrashekar et al., Science 2020). Cases of human reinfection (people testing positive for SARS-CoV-2 RNA after testing negative) have been reported, although this may be due to long-lasting viral loads hovering around the limit of detection (LiveScience, 4/30/20); a study of 790 contacts of 285 re-positive cases in South Korea found no cases of transmission from re-positive individuals, so they are very unlikely to be infectious (Korean CDC, 5/21/20). Immunity to seasonal coronaviruses wanes over several years, permitting reinfection with very similar strains of the same virus, and antibody titers to SARS and MERS decrease after infection, raising questions about the durability of protection against COVID-19 (Lipsitch, M, “Who is immune to the coronavirus?”, NYTimes 4/13/20). For more detailed information on vaccine development, see the below section. For more information about how this affects epidemiological modeling, see Module 2.For more details on immune responses to SARS-CoV-2, please see an expanded version in the supplementary materials.

Thought question:

  • How might the initial mild presentation and later severe disease seen in COVID-19 be explained by the immune response to the virus?

Immune factors involved in infection outcome

Many of the inflammatory markers discussed above have been investigated as possible predictors of disease mortality. See laboratory diagnostics for more information.

Additional Readings:

Prompetchara et al., Asian Pacific Journal of Allergy and Immunology, 2020 de Wit et al., Nat Rev Microbiol 2016