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Coronavirus persistence in human respiratory tract and cell culture: An overview

ABSTRACT

Emerging human coronaviruses, including the recently identified SARS-CoV-2, are relevant respiratory pathogens due to their potential to cause epidemics with high case fatality rates, although endemic coronaviruses are also important for immunocompromised patients. Long-term coronavirus infections had been described mainly in experimental models, but it is currently evident that SARS-CoV-2 genomic-RNA can persist for many weeks in the respiratory tract of some individuals clinically recovered from coronavirus infectious disease-19 (COVID-19), despite a lack of isolation of infectious virus. It is still not clear whether persistence of such viral RNA may be pathogenic for the host and related to long-term sequelae.

In this review, we summarize evidence of SARS-CoV-2 RNA persistence in respiratory samples besides results obtained from cell culture and histopathology describing long-term coronavirus infection. We also comment on potential mechanisms of coronavirus persistence and relevance for pathogenesis.

Keywords:
SARS-CoV-2; Persistence of viral RNA; Viral pathogenesis; Non-productive infection; Cell culture

Introduction

Human coronaviruses (hCoV) were first identified in the 1960s (e.g. strains 229E and OC43) as pathogens associated with upper respiratory tract infections and occasionally with cases of pneumonia in infants and adults.11 Kahn JS, McIntosh K. History and recent advances in coronavirus discovery. Pediatr Infect Dis J. 2005;24:S223-7.,22 Bradburne AF, Tyrrell DAJ. The propagation of "coronaviruses" in tissue-culture. Arch Gesamte Virusforsch. 1969;28:133-50. After 2002, it has been identified five new hCoV including two related to common cold, bronquiolitis and pneumonia (HKU1 and NL63), as well as three etiological agents of severe acute respiratory syndrome (SARS-CoV, MERS-CoV and SARS-CoV-2).33 Chen B, Tian E-K, He B, et al. Overview of lethal human coronaviruses. Sig Transduct Target Ther. 2020;5:89.

4 van der Hoek L, Pyrc K, Jebbink MF, et al. Identification of a new human coronavirus. Nat Med. 2004;10:368-73.
-55 Woo PCY, Lau SKP, Chu C, et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005;79:884-95.

SARS-CoV emerged at the beginning of November 2002 in Guangdong Province, China, and disseminated to 32 countries and regions producing 8437 cases of severe acute respiratory syndrome (SARS), besides 813 deaths by July 2003; no SARSCoV related disease has been reported since January 2004.66 de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016;14:523-34.,77 Zhong N, Zheng B, Li Y, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February 2003. Lancet. 2003;362:1353-8. The Middle East respiratory syndrome (MERS) was described in 2012 in Saudi Arabia, in a man with acute pneumonia and renal failure; the MERS-CoV was isolated as the etiological agent. From June 2012 to May 2019, there have been a total of 2442 confirmed cases of MERS and 843 related deaths in 27 countries.66 de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016;14:523-34.,88 World Health Organization. Middle East Respiratory Syndrome Coronavirus (MERS-CoV)-The Kingdom of Saudi Arabia. 2019 https://www.who.int/csr/don/16-july-2019-merssaudi-arabia/en/
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Surveillance about suspected MERS-CoV infection is currently recommended by WHO to detect early cases and prevent clusters.99 World Health Organization. Surveillance for Human Infectionwith Middle East Respiratory Syndrome Coronavirus (MERS CoV). 2018 https://www.who.int/csr/disease/coronavirus_infections/surveillance-human-infection-mers/en/.
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In late December 2019, cases of pneumonia of unknown etiology were reported in Wuhan, China, and in subsequent weeks, it was identified a novel coronavirus currently named SARS-CoV-2, as the causal agent. Since then, SARS-CoV-2 spread globally causing a pandemic with 147,539,302 cases of coronavirus infectious disease-19 (COVID-19) and 3116,444 deaths (up to April 27, 2021).1010 World Health Organization. WHO Coronavirus (COVID-19) Dashboard. April 2021 https://covid19.who.int/
https://covid19.who.int/...
Besides asymptomatic, COVID19 includes clinical presentations that can be categorized as mild, moderate (no-severe pneumonia), severe (pneumonia), and critical illness.1111 Pongpirul WA, Wiboonchutikul S, Charoenpong L, et al. Clinical course and potential predictive factors for pneumonia of adult patients with Coronavirus Disease 2019 (COVID-19): a retrospective observational analysis of 193 confirmed cases in Thailand. PLoS Negl Trop Dis. 2020;14:e0008806.,1212 World Health Organization. Clinical Management of SevereAcute Respiratory Infection (SARI) When COVID-19 Disease is Suspected: Interim Guidance. 13 March 2020 https://apps.who.int/iris/handle/10665/331446.
https://apps.who.int/iris/handle/10665/3...
Chronic conditions such as hypertension, cardiovascular disease and diabetes influence the severity of COVID-19 and time to recovery. Detection of SARS-CoV2 is usually performed by quantitative RT-PCR and higher viral loads are often associated with severe symptoms1313 Fajnzylber J, Regan J, Coxen K, et al. SARS-CoV-2 viral load is associated with increased disease severity and mortality. Nat Commun. 2020;11:5493.,1414 Walsh KA, Jordan K, Clyne B, et al. SARS-CoV-2 detection, viral load and infectivity over the course of an infection. J Infect. 2020;81:357-71.; although it has also been reported cases of subjects developing mild COVID-19 with high viral loads, achieving clearance of infectious virus and viral RNA within one and three weeks after symptoms onset, respectively.1515 Wolfel R, Corman VM, Guggemos W, et al. Virologica€ l assessment of hospitalized patients with COVID-2019. Nature. 2020;581:465-9.

Long-term viral RNA detection has also been described in patients recovered from COVID-19, despite no identification of infectious viral particles.1616 Sun J, Xiao J, Sun R, et al. Prolonged persistence of SARS-CoV-2 RNA in body fluids. Emerg Infect Dis. 2020;26:1834-8.,1717 Li Q, Zheng X-S, Shen X-R, et al. Prolonged shedding of severe acute respiratory syndrome coronavirus 2 in patients with COVID-19. Emerg Microbes Infect. 2020;9:2571-7. Such observations have supported the criteria for releasing COVID-19 patients from isolation even before obtaining a negative RT-PCR test.1818 World Health Organization. Criteria for Releasing COVID-19 Patients from Isolation. 2020 https://www.who.int/publications/i/item/criteria-for-releasing-covid-19-patientsfrom-isolation.
https://www.who.int/publications/i/item/...
However, it is still not clear whether SARS-CoV-2 RNA persistence might be pathogenic for the host, despite a lack of assembled infectious virus.

Here, we summarize evidence of SARS-CoV-2 RNA persistence in respiratory samples besides results from cell culture and histopathology describing long-term productive and nonproductive coronavirus infection in epithelial, myeloid and neural cells. We also comment on possible mechanisms of coronavirus persistence and relevance for pathogenesis.

Long-term detection of SARS-CoV-2-RNA in clinical samples

Long-term SARS-CoV-2-RNA detection is frequent1919 Rhee C, Kanjilal S, Baker M, Klompas M. Duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity: when is it safe to discontinue isolation? Clin Infect Dis. 2021;72:1467-74.

20 Walsh KA, Spillane S, Comber L, et al. The duration of infectiousness of individuals infected with SARS-CoV-2. J Infect. 2020;81:847-56.
-2121 Widders A, Broom A, Broom J. SARS-CoV-2: the viral shedding vs infectivity dilemma. Infect Dis Health. 2020;25:210-5. in 13 -45% of patients with COVID-19.2222 Hartman WR, Hess AS, Connor JP. Persistent viral RNA shedding after COVID-19 symptom resolution in older convalescent plasma donors. Transfusion. 2020;60:2189-91.

23 Carmo A, Pereira-Vaz J, Mota V, et al. Clearance and persistence of SARS-CoV-2 RNA in patients with COVID-19. J Med Virol. 2020;92:2227-31.

24 Vena A, Taramasso L, Di Biagio A, et al. Prevalence and clinical significance of persistent viral shedding in hospitalized adult patients with SARS-CoV-2 infection: a prospective observational study. Infect Dis Ther. 2021;10:387-98.
-2525 Xiao AT, Tong YX, Zhang S. Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients. Clin Infect Dis. 2020;71:2249-51. In the third week after symptom onset, RT-PCR positive tests can be detected in 43 -66% of patients with mild-to-moderate COVID-19 or in those hospitalized,2525 Xiao AT, Tong YX, Zhang S. Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients. Clin Infect Dis. 2020;71:2249-51.,2626 Corsini Campioli C, Cano Cevallos E, Assi M, Patel R, Binnicker MJ, O’Horo JC. Clinical predictors and timing of cessation of viral RNA shedding in patients with COVID-19. J Clin Virol. 2020;130:104577. and then occurs a progressive reduction to 32% in the fourth week, whereas most of cases display negative tests in the sixth-to-seventh weeks. As negative results are prevalent since the fourth week, virus RNA persistence could be considered after 28 days of symptom onset.2323 Carmo A, Pereira-Vaz J, Mota V, et al. Clearance and persistence of SARS-CoV-2 RNA in patients with COVID-19. J Med Virol. 2020;92:2227-31.,2525 Xiao AT, Tong YX, Zhang S. Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients. Clin Infect Dis. 2020;71:2249-51.,2727 Gombar S, Chang M, Hogan CA, et al. Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19. J Clin Virol. 2020;129:104477.,2828 Rodríguez-Grande C, Adan-Ji menez J, Catalan P, et al . Inference of active viral replication in cases with sustained positive reverse transcription-PCR results for SARS-CoV-2. J Clin Microbiol. 2020;59:e02277.

In a retrospective study (n = 2142), patients with critical COVID-19 were longer positive for viral RNA than non-critically ill patients (median time, 24 days vs. 18 days, respectively), according to analysis of nasopharyngeal swabs (NPS); similarly, serum biomarkers such as IL-6, IL-8, aspartate aminotransferase, IL-2 receptor, D-dimer and C-reactive protein remained higher in the former group, all along virus nucleic acid persistence.2929 Fu Y, Li Y, Guo E, et al. Dynamics and correlation among viral positivity, seroconversion, and disease severity in COVID-19: a retrospective study. Ann Intern Med. 2021;174:453-61. Inside the non-critical group, 20% of subjects with low IgM levels also remained positive for viral RNA up to 73 days after symptom onset, with respect to non-critical COVID-19 patients with higher IgM levels that cleared earlier the viral infection. Convalescent plasma was administered to persistently RNA positive patients resulting in test negativization within two weeks after this passive immunization, supporting that anti-SARS-CoV-2 antibodies are important for viral clearance.2929 Fu Y, Li Y, Guo E, et al. Dynamics and correlation among viral positivity, seroconversion, and disease severity in COVID-19: a retrospective study. Ann Intern Med. 2021;174:453-61. Another study that included 43 patients with mild COVID-19 and six with severe disease reported median time for negative RT-PCR tests of 22.7 days and 33.5 days, respectively.1616 Sun J, Xiao J, Sun R, et al. Prolonged persistence of SARS-CoV-2 RNA in body fluids. Emerg Infect Dis. 2020;26:1834-8. Additional reports have shown that viral load is significantly higher in patients with severe disease than in those with mild COVID-19 and that viral RNA clearance is delayed in subjects with severe symptoms or in patients under corticosteroid treatment.3030 Chen X, Zhu B, Hong W, et al. Associations of clinical characteristics and treatment regimens with the duration of viral RNA shedding in patients with COVID-19. Int J Infect Dis. 2020;98:252-60.,3131 Zheng S, Fan J, Yu F, et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: retrospective cohort study. BMJ. 2020;369:m1443.

By contrast, another study that analyzed upper respiratory samples from patients categorized in groups of moderate-tosevere (hospitalized) and mild disease, reported that the hospitalized group displayed viral RNA for 28.0 ± 10.1 days, whereas patients with mild COVID-19 were positive for 35.3 ± 8.0 days, suggesting this last group was slower to eliminate viral infection. Interestingly, in this same study IgG titers were lower in mild than in hospitalized patients, thus, higher antibody titers are associated with enhanced viral elimination but also could be related to severe forms of COVID-19.2323 Carmo A, Pereira-Vaz J, Mota V, et al. Clearance and persistence of SARS-CoV-2 RNA in patients with COVID-19. J Med Virol. 2020;92:2227-31. In this regard, it has been observed significantly increased serum titers of IgM, IgA and IgG3 antibodies against the receptor-binding domain (RBD) of the spike envelope protein in severe and critically ill COVID-19 patients, compared to patients with mild disease. Similar results have been observed during titration of neutralizing antibodies, which are always higher in hospitalized individuals.3232 Chen W, Zhang J, Qin X. SARS-CoV-2 neutralizing antibody levels are correlated with severity of COVID-19 pneumonia. Biomed Pharmacother. 2020;130:110629.,3333 Bosnjak B, Stein SC, Willenzon S, et al. Low serum neutralizing anti-SARS-CoV-2 S antibody levels in mildly affected COVID19 convalescent patients revealed by two different detection methods. Cell Mol Immunol. 2021;18:936-44. In vitro assays with sera from severe patients revealed high levels of a low-fucosylated IgG1 which, similarly to IgG3, forms immune complexes with SARS-CoV-2 spike pseudotyped VSV viruses, that bind and activate FCgRIIIa signaling to produce high levels of IL-6, TNF and IL-1b in monocytes and natural killer cells, suggesting that the antibody effector function contribute to the “storm of cytokines” observed in severe COVID19.3434 Chakraborty S, Gonzalez J, Edwards K, et al. Proinflammatory IgG Fc structures in patients with severe COVID-19. Nat Immunol. 2021;22:67-73. Thus, quantitative and qualitative characteristics of the antibody response might be determinant in kinetics of viral clearance and the outcome of the disease.

Additionally to clinical status, age is another factor associated to SARS-CoV-2 RNA persistence.2222 Hartman WR, Hess AS, Connor JP. Persistent viral RNA shedding after COVID-19 symptom resolution in older convalescent plasma donors. Transfusion. 2020;60:2189-91. In this respect, analysis by age and disease severity have shown that viral RNA shedding is significantly longer in respiratory samples from subjects older than 60 years that coursed with severe COVID19 than in younger people under similar clinical conditions.3131 Zheng S, Fan J, Yu F, et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: retrospective cohort study. BMJ. 2020;369:m1443. A study with 384 patients of a median age of 58 years reported that elderly was a significant factor associated with prolonged viral RNA detection, with median time of 32 days (range 4 -111 days); patients older than 70 years showed virus genome persistence over 70 days.3535 Zhou C, Zhang T, Ren H, Sun S, Yu X, Sheng J, et al. Impact of age on duration of viral RNA shedding in patients with COVID19. Aging (Albany NY). 2020;12:22399-404.

Despite only some studies have evaluated presence of replication-competent virus, possibly due to infrastructure limitations to handle pathogens at Biosafety Level-3, it is currently clear that RNA detection is of longer duration than isolation-time of infectious virus in cell culture, since samples become negative to viable virus within eight to ten days after symptoms onset.3636 van Kampen JJA, van de Vijver DAMC, Fraaij PLA, et al. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID19). Nat Commun. 2021;12:267.

37 Manzulli V, Scioscia G, Giganti G, et al. Real time PCR and culture-based virus isolation test in clinically recovered patients: is the subject still infectious for SARS-CoV2? J Clin Med. 2021;10:309.
-3838 Bullard J, Dust K, Funk D, et al. Predicting infectious severe acute respiratory syndrome coronavirus 2 from diagnostic samples. Clin Infect Dis. 2020;71:2663-6. Nevertheless, studies that included patients with severe COVID-19 reported isolation of infectious viral particles at day 20.1919 Rhee C, Kanjilal S, Baker M, Klompas M. Duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity: when is it safe to discontinue isolation? Clin Infect Dis. 2021;72:1467-74.,3636 van Kampen JJA, van de Vijver DAMC, Fraaij PLA, et al. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID19). Nat Commun. 2021;12:267. Probability of detection of infectious virus at 15 days post-symptom onset has been estimated lower than 5%,3636 van Kampen JJA, van de Vijver DAMC, Fraaij PLA, et al. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID19). Nat Commun. 2021;12:267. suggesting that even though viral RNA is long-term maintained in convalescent patients, they might not be contagious through respiratory secretions.

Nevertheless, Li et al. described isolation of viable virus in Vero E6 cells from sputum collected at 73 and 102 days after disease onset from two elderly patients clinically recovered, although they still showed persistent lung abnormalities by chest computed tomography. In this study, reinfection was not considered as responsible for longstanding viral shedding, since sequencing of SARS-CoV-2 genome from two consecutive samples (separated by 20 days) collected from two subjects, revealed 100% sequence identity (only one substitution in one paired sample), suggesting no new viral infection had occurred and that few prolonged viral RNA carriers from the aged group might propagate infection longer than expected.1717 Li Q, Zheng X-S, Shen X-R, et al. Prolonged shedding of severe acute respiratory syndrome coronavirus 2 in patients with COVID-19. Emerg Microbes Infect. 2020;9:2571-7.

Furthermore, an immunocompromised state is also associated to high frequency of SARS-CoV-2 persistence, as it has been observed in oncologic patients and transplant recipients.3939 Avanzato VA, Matson MJ, Seifert SN, et al. Case study: prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with cancer. Cell. 2020;183:1901-1912.e9.

40 Wei L, Liu B, Zhao Y, Chen Z. Prolonged shedding of SARSCoV-2 in an elderly liver transplant patient infected by COVID19: a case report. Ann Palliat Med. 2020. apm-20-996.

41 Decker A, Welzel M, Laubner K, et al. Prolonged SARS-CoV-2 shedding and mild course of COVID-19 in a patient after recent heart transplantation. Am J Transplant. 2020;20:3239- 45.

42 Balashov D, Trakhtman P, Livshits A, et al. SARS-CoV-2 convalescent plasma therapy in pediatric patient after hematopoietic stem cell transplantation. Transfus Apher Sci. 2021;60:102983.

43 Nakajima Y, Ogai A, Furukawa K, et al. Prolonged viral shedding of SARS-CoV-2 in an immunocompromised patient. J Infect Chemother. 2021;27:387-9.

44 Schend J, Daniels P, Sanan N, Tcheurekdjian H, Hostoffer R. Clinical observation of COVID-19 in a patient with an acquired humoral deficiency secondary to chemotherapeutic agents. Allergy Rhinol (Providence). 2020;11:2152656720978764.

45 Moore JL, Ganapathiraju PV, Kurtz CP, Wainscoat B. A 63-year-old woman with a history of non-hodgkin lymphoma with persistent SARS-CoV-2 infection who was seronegative and treated with convalescent plasma. Am J Case Rep. 2020;21:e927812.

46 Baang JH, Smith C, Mirabelli C, et al. Prolonged severe acute respiratory syndrome coronavirus 2 replication in an immunocompromised patient. J Infect Dis. 2021;223:23-7.

47 McKie AM, Jones TPW, Sykes C. Prolonged viral shedding in an immunocompetent patient with COVID-19. BMJ Case Rep. 2020;13:e237357.
-4848 Choi B, Choudhary MC, Regan J, et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med. 2020;383:2291-3. Worth mentioning, viral RNA of NL63-CoV has also been detected up to »60 days in cancer patients that develop respiratory symptoms, whereas 229E-CoV was detected over a period of 77 days in a pediatric patient with a brain tumor, indicating coronaviruses are opportunistic pathogens.4949 Ogimi C, Greninger AL, Waghmare AA, et al. Prolonged shedding of human coronavirus in hematopoietic cell transplant recipients: risk factors and viral genome evolution. J Infect Dis. 2017;216:203-9.,5050 Dominguez SR, Robinson CC, Holmes KV. Detection of four human coronaviruses in respiratory infections in children: a one-year study in Colorado. J Med Virol. 2009;81:1597-604. Table 1 displays a summary of case reports for SARS-CoV-2 infected patients that presented immunosuppression.

Interestingly, the longest time for RNA detection was 151 days, in a man with anti-phospholipid syndrome and diffuse alveolar hemorrhage that developed complications and coinfection with Aspergillus fumigatus, leading to fatal outcome.4848 Choi B, Choudhary MC, Regan J, et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med. 2020;383:2291-3. Another case of prolonged SARS-CoV-2 RNA detection and isolation of replication-competent virus showed positivity for 105 and 70 days, respectively, in a woman with chronic lymphocytic leukemia that developed a secondary hypogammaglobulinemia.3939 Avanzato VA, Matson MJ, Seifert SN, et al. Case study: prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with cancer. Cell. 2020;183:1901-1912.e9. Viral infection coursed asymptomatic, similarly to many SARS-CoV-2 infections in immunocompromised patients. Therefore, immunosuppression entails viral RNA persistence, as also occurs in some elderly people (Fig. 1). However, it is still uncertain the biological relevance and mechanisms associated with long-term coronavirus persistence. Therefore, in the following section we comment some findings in cell culture and histopathology that propose coronavirus persistence might contribute to pathogenesis in infected individuals.

Coronavirus persistence in experimental models

Viral persistence

Persistent viral infections are established by concurrence of molecular and immunological events that allow the virus to evade the immune response and acquire a gene expression program to regulate both its own replication (to avoid killing the host cell) and host gene expression, enabling a long-lasting virus-host interaction.5151 Oldstone MBA. Viral persistence: parameters, mechanisms and future predictions. Virology. 2006;344:111-8.,5252 Randall RE, Griffin DE. Within host RNA virus persistence: mechanisms and consequences. CurrOpin Virol. 2017;23:35-42. Persistence can occur as productive or non-productive infection. In the former type of persistence, virions are detected constantly or intermittently, whereas in the latter type, infectious viruses are not produced, regardless of viral genome remaining intracellular and expression of some viral proteins may take place.5353 Reetoo KN, Osman SA, Illavia SJ, Cameron-Wilson CL, Banatvala JE, Muir P. Quantitative analysis of viral RNA kinetics in coxsackievirus B3-induced murine myocarditis: biphasic pattern of clearance following acute infection, with persistence of residual viral RNA throughout and beyond the inflammatory phase of disease. J Gen Virol. 2000;81:2755-62. Under such condition, kinetics of detection of the persistent virus genome might be determined by rates of residual RNA replication and its catabolic degradation, as well as by lysis of viral RNA positive cells through cell-mediated cytotoxicity.5353 Reetoo KN, Osman SA, Illavia SJ, Cameron-Wilson CL, Banatvala JE, Muir P. Quantitative analysis of viral RNA kinetics in coxsackievirus B3-induced murine myocarditis: biphasic pattern of clearance following acute infection, with persistence of residual viral RNA throughout and beyond the inflammatory phase of disease. J Gen Virol. 2000;81:2755-62.

Thus, SARS-CoV-2 possibly establishes a non-productive viral persistence in some individuals, since infection progress from a productive state to a persistent condition with measurable viral RNA but undetectable release of infectious virus; although shedding of viable virus is apparently of longer duration in immunocompromised and elderly patients, than in those immunocompetent.

Contribution of SARS-CoV-2 RNA persistence to COVID-19 pathogenesis is not currently understood but it could not be discarded this viral RNA and possibly some viral proteins still expressed, might be continual stimuli that activate at least innate immune receptors, maintaining an inflammatory condition up to complete viral clearance.5454 Jacobs JJL. Persistent SARS-2 infections contribute to long COVID-19. Med Hypotheses. 2021;149:110538.

Evidence of persistence in epithelial cells

A non-productive infection by hCoV in respiratory epithelium was described by Loo et al. in an in vitro model of infection of human bronchial epithelial cells (HBECs) with 229E-CoV and OC43-CoV.5555 Loo S-L, Wark PAB, Esneau C, Nichol KS, Hsu AC-Y, Bartlett NW. Human coronaviruses 229E and OC43 replicate and induce distinct antiviral responses in differentiated primary human bronchial epithelial cells. Am J Physiol Lung Cell Mol Physiol. 2020;319:L926-31. Kinetics of replication of 229E-CoV was faster than that of OC43-CoV, with viral RNA copies and infectious virus titers peaking at 24 and 96 h post-infection (hpi), respectively. At seven days post-infection, both types of coronavirus-infected HBECs showed similar number of viral RNA copies (»105/ml), despite infectious virus was only isolated from OC43-CoV infected cells (»104 TCID50/ml), suggesting that genomic RNA from 229E-CoV persisted intracellular without virions assembly. Such observation correlates with detection of genomic and subgenomic viral RNA from SARS-CoV-2 in respiratory samples from COVID-19 patients, even in absence of virus isolation.5656 Perera RAPM, Tso E, Tsang OTY, et al. SARS-CoV-2 virus culture and subgenomic RNA for respiratory specimens from patients with mild coronavirus disease. Emerg Infect Dis. 2020;26:2701-4. Of relevance, 229E-CoV induced synthesis of high levels of type-I and type-III interferon in HBECs, contrasting with results by OC43-CoV infection. Also, a productive persistent infection was described at 28 days post-infection in OC43-CoVinfected airway epithelial cells, with viral loads of »107 virus genome copies/sample and undetectable synthesis of IFN-λ.5757 Essaidi-Laziosi M, Brito F, Benaoudia S, et al. Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures. J Allergy Clin Immunol. 2018;141:2074-84. Possibly both, low and slow kinetics of replication of the OC43-CoV contributed to evade its early detection by intracellular innate immune recognition receptors, allowing a prolonged productive persistence.5555 Loo S-L, Wark PAB, Esneau C, Nichol KS, Hsu AC-Y, Bartlett NW. Human coronaviruses 229E and OC43 replicate and induce distinct antiviral responses in differentiated primary human bronchial epithelial cells. Am J Physiol Lung Cell Mol Physiol. 2020;319:L926-31.

A comparative study of infection of SARS-CoV and SARSCoV-2 in lung tissue explants along 48 h showed that both viruses have tropism by type I and type II pneumocytes as well as by alveolar macrophages. However, SARS-CoV-2 generated higher titers of infectious virus than SARS-CoV (3.2fold increase), associated with a lack of induction of IFN-I, IFN-II and IFN-III, but augmented transcription of IL-6, MCP-1, CXCL1, CXCL5 and CXCL10. In this case, SARS-CoV induced mRNA expression of six additional proinflammatory cytokines and chemokines that were not stimulated by SARSCoV-25858 Chu H, Chan JF-W, Wang Y, et al. Comparative replication and immune activation profiles of SARS-CoV-2 and SARS-CoV in human lungs: an ex vivo study with implications for the pathogenesis of COVID-19. Clin Infect Dis. 2020;71:1400-9.; authors suggested that such exacerbated proinflammatory state could be related to the higher fatality rate of SARS-CoV with respect to SARS-CoV-2. This study did not evaluated virus persistence but considered a particular capability of evasion of the innate immune response is characteristic of SARS-CoV-2, allowing early high viral loads and efficient dissemination to new hosts. In this regard, Xia et al. described mechanisms of inhibition of IFN-I synthesis and response exerted by some structural, non-structural and accessory proteins of SARS coronaviruses. Particularly, nonstructural proteins 1 and 6 from SARS-CoV-2 were more potent to inhibit IFN-a signaling than the equivalent proteins from SARS-CoV and MERS-CoV leading to higher viral replication.5959 Xia H, Cao Z, Xie X, et al. Evasion of type I interferon by SARSCoV-2. Cell Rep. 2020;33:108234. Thus, it could be proposed that such poor IFN mediated response might at least partially promote SARS-CoV-2 persistence, (besides a modest antibody response, as considered above), whereas it is stimulated a continuing synthesis of proinflammatory cytokines and chemokines, which contribute to COVID-19 pathogenesis (Fig. 2).

Table 1
Case reports of immunosuppressed patients with long-term SARS-CoV-2 RNA detection.
Fig. 1
Main factors associated with SARS-CoV-2 RNA persistence. *Immunosuppression induced for example, by drug treatment in patients with cancer and transplant recipients.

Analysis of postmortem lung tissue from individuals who died of COVID-19 has shown wide presence of pneumocytes and endothelial cells positive for SARS-CoV-2 RNA by in situ hybridization, even though diagnosis in some patients had occurred 30-40 days earlier, supporting a long-lasting viral infection.6060 Bussani R, Schneider E, Zentilin L, et al. Persistence of viral RNA, pneumocyte syncytia and thrombosis are hallmarks of advanced COVID-19 pathology. EBioMedicine. 2020;61:103104.

Persistence in myeloid cells

Fig. 2
Human coronaviruses (hCoV) infect different types of cells from respiratory and non-respiratory tissues. hCoV can be cleared by the antiviral immune response, although they are also able to persist either in productive or non-productive manner. Persistently infected cells and some cells that cleared the virus (e.g. myeloid cells) show an activation state characterized by a chronic production of cytokines and chemokines, contributing to inflammation. The dashed arrow represents particularly those cells producing cytokines, notwithstanding virus had been eliminated. The different types of hCoV can differentially inhibit type-I, II and III interferon through activity of non-structural proteins, which are key players in evasion of the innate immunity. vRNA, viral RNA.

Epithelial cells might not be the unique reservoir of hCoV since monocytes and macrophages have also been described as permissive cells. Particularly, 229E-CoV infects human peripheral blood monocytes and monocyte-derived macrophages (MDM), although infectious virus are below limit of detection at 72 hpi, even though spike protein remains detectable by immunofluorescence during at least five days,6161 Desforges M, Miletti TC, Gagnon M, Talbot PJ. Activation of human monocytes after infection by human coronavirus 229E. Virus Res. 2007;130:228-40. suggesting myeloid cells enable a non-productive infection. Furthermore, infection of the human monocytic THP-1 cell line with 229E-CoV allows carrier persistence for at least two months, characterized by 1-2% of infected cells and low viral titers (101-102 TCID50/ml). Interestingly, both primary monocytes and THP-1 cells infected by 229E-CoV secreted CCL5, CXCL10, CXCL11 and TNF-a in supernatants6161 Desforges M, Miletti TC, Gagnon M, Talbot PJ. Activation of human monocytes after infection by human coronavirus 229E. Virus Res. 2007;130:228-40.; thus, 229E-CoV persists in monocytes with low to undetectable release of infectious virus and might contribute to inflammation. Notwithstanding, it is still controversial whether myeloid cells are permissive to SARS-CoV-2. Boumaza et al. showed that primary human monocytes and MDM were infected in vitro by SARS-CoV-2, but genome replication was active only during the first 48 hpi in monocytes. Interestingly, viral contact induced expression of IL-6, IL-1b, IL-10, TNF-a and TGF-b1 in both monocytes and macrophages, suggesting an M1/M2 mixed phenotype.6262 Boumaza A, Gay L, Mezouar S, et al. Monocytes and macrophages, targets of SARS-CoV-2: the clue for Covid-19 immunoparalysis. J Infect Dis. 2021. jiab044.,6363 Raggi F, Pelassa S, Pierobon D, et al. Regulation of human macrophage M1-M2 polarization balance by hypoxia and the triggering receptor expressed on myeloid cells-1. Front Immunol. 2017;8:1097. Additionally, peripheral blood monocytes from COVID-19 patients expressed higher levels of CD163 than healthy controls, whereas this M2 macrophage marker has also been observed in histopathology from lung tissue.6262 Boumaza A, Gay L, Mezouar S, et al. Monocytes and macrophages, targets of SARS-CoV-2: the clue for Covid-19 immunoparalysis. J Infect Dis. 2021. jiab044.,6464 Zeng Z, Xu L, Xie X, et al. Pulmonary pathology of early-phase COVID-19 pneumonia in a patient with a benign lung lesion. Histopathology. 2020;77:823-31. On the other hand, a population of large non-classical monocytes CD14+/CD16+ has been identified in peripheral blood mononuclear cells of COVID-19 patients.6565 Zhang D, Guo R, Lei L, et al. Frontline Science: COVID-19 infection induces readily detectable morphologic and inflammation-related phenotypic changes in peripheral blood monocytes. J Leukoc Biol. 2021;109:13-22. This cell population is characterized by altered morphology (e.g. vacuolated) and expression of significantly higher levels of CD80 and CD206 with respect to the peripheral blood monocytes of normal size; IL-6 and TNF-a are also expressed at higher levels in monocytes from COVID19 patients than that from healthy donors. Even though viral infection was not evaluated in such large monocytes, an in vitro assay of pseudovirus entry, coupled to green florescence signal, showed up to 25% of primary monocytes were infected, suggesting that myeloid cells are permissive to SARS-CoV-2 infection.6565 Zhang D, Guo R, Lei L, et al. Frontline Science: COVID-19 infection induces readily detectable morphologic and inflammation-related phenotypic changes in peripheral blood monocytes. J Leukoc Biol. 2021;109:13-22.

Histopathology of postmortem hilar lymph nodes and spleens from COVID-19 subjects, showed peripheral macrophages (CD68+) and tissue-resident macrophages (CD169+) expressing viral nucleocapsid protein, whereas T and B lymphocytes were negative for such viral antigen. Additionally, only macrophages infected by SARS-CoV-2 expressed IL-6.6666 Feng Z, Diao B, Wang R, et al. The novel severe acuterespiratory syndrome coronavirus 2 (SARS-CoV-2) directly decimates human spleens and lymph nodes. MedRxiv. 2020 http://medrxiv.org/lookup/doi/10.1101/2020.03.27.20045427
http://medrxiv.org/lookup/doi/10.1101/20...
Another study in pulmonary tissue showed through electron microscopy SARS-CoV-2 particles localized in cytoplasm of pneumocytes and alveolar macrophages.6767 Carsana L, Sonzogni A, Nasr A, et al. Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study. Lancet Infect Dis. 2020;20:1135- 40.

Such experimental evidence supports the hypothesis that monocytes/macrophages allow at least a transitory productive infection by SARS-CoV-2 (Fig. 2); afterwards, a non-productive infection is set up, whereas myeloid cells sustain synthesis of proinflammatory and immunomodulatory cytokines. Possibly immunomodulatory cytokines reflect an overproduction of proinflammatory factors that contribute to disease severity and possibly to long-term sequelae observed in convalescent COVID-19 patients.6868 Praschan N, Josephy-Hernandez S, Kim DD, et al. Implications of COVID-19 sequelae for health-care personnel. Lancet Respir Med. 2021;9:230-1.,6969 Sibila O, Albacar N, Perea L, et al. Lung function sequelae in COVID-19 patients 3 months after hospital discharge. Arch Bronconeumol. 2021;57:59-61. Further studies are necessary to determine whether myeloid cells may be, not only targets, but also vehicles for viral dissemination to extra pulmonary tissues and long-term viral reservoirs.

Persistence in neural cells

Neurological manifestations have been described in some hCoV individuals infected, including SARS-CoV-2. Central nervous system (CNS) damage may be consequence of neuroinvasion either by hematogenous or transneural routes, although indirect damage such as that produced by immunopathogenesis is also considered (reviewed by Abdelaziz and Waffa,7070 Abdelaziz OS, Waffa Z. Neuropathogenic human coronaviruses: a review. Rev Med Virol. 2020;30:e2118. and by Kumar et al.7171 Kumar S, Veldhuis A, Malhotra T. Neuropsychiatric and cognitive sequelae of COVID-19. Front Psychol. 2021;12:577529.).

Early studies focused on coronavirus neurotropism described susceptibility of human primary astrocytes and microglia to 229E-CoV and OC43-CoV, even though infection with 229E-CoV occurred in absence or at a low-to-undetectable production of viral particles.7272 Bonavia A, Arbour N, Yong VW, Talbot PJ. Infection of primary cultures of human neural cells by human coronaviruses 229E and OC43. J Virol. 1997;71:800-6. Both 229E-CoV and OC43CoV have displayed capability to persist in astrocytoma, neuroblastoma and oligodendrocytic human cell lines for 25-40 passages, with constant levels of viral RNA, whereas viral titers may oscillate between undetectable to 107 TCID50/ ml.7373 Arbour N, Ekandé S, Côté G, et al. Persistent infection of human oligodendrocytic and neuroglial cell lines by human coronavirus 229E. J Virol. 1999;73:3326-37.,7474 Arbour N, Côté G, Lachance C, Tardieu M, Cashman NR, Talbot PJ. Acute and persistent infection of human neural cell lines by human coronavirus OC43. J Virol. 1999;73:3338-50. A mouse model to study neuropathology associated with OC43-CoV infection showed in 30% of surviving mice, after one year of their recovery from acute encephalitis, smaller hippocampi, clusters of activated microglia and persistent viral RNA; all these findings associated with altered limb clasping reflex. Remarkably, viral protein synthesis was undetectable. In the same study, infection of primary neural cell cultures with OC43-CoV induced overproduction of TNF-a and increased death of infected cells. Therefore, long-term neuropathology in mice correlated with persistence of viral RNA and activated microglia, which might be associated with increased cytotoxicity.7575 Jacomy H, Fragoso G, Almazan G, Mushynski WE, Talbot PJ. Human coronavirus OC43 infection induces chronic encephalitis leading to disabilities in BALB/C mice. Virology. 2006;349:335-46.

The characteristic coronavirus persistence in CNS associated with a lack of detection of infectious virus has been partially explained by Liu et al. in an in vitro model of murine oligodendrocytes persistently infected by mouse hepatitis coronavirus. In such oligodendrocytic cell line, subgenomic viral RNAs and viral proteins were produced constantly, although infectious viruses were not detected by titration assays. However, electron microscopy and biochemical techniques revealed assembly of defective viruses with scarce spike protein in the envelope, and consequently, impaired infectivity.7676 Liu Y, Herbst W, Cao J, Zhang X. Deficient incorporation of spike protein into virions contributes to the lack of infectivity following establishment of a persistent, non-productive infection in oligodendroglial cell culture by murine coronavirus. Virology. 2011;409:121-31. Other persistent viral infections are characterized by long-term detection of viral genomic RNA, possibly also mRNA, but in absence of infectious virus, such as respiratory syncytial virus,7777 Ruiz-Gomez X, Vazquez-Perez JA, Flores-Herrera O, et al. Steady-state persistence of respiratory syncytial virus in a macrophage-like cell line and sequence analysis of the persistent viral genome. Virus Res. 2021;297:198367. Zika virus7878 Medina FA, Torres G, Acevedo J, et al. Duration of the presence of infectious Zika virus in semen and serum. J Infect Dis. 2019;219:31-40. and measles virus.7979 Miller KD, Matullo CM, Milora KA, Williams RM, O’Regan KJ, Rall GF. Immune-mediated control of a dormant neurotropic RNA virus infection. J Virol. 2019;93:e00241. In regard to measles, immunocompetent mice surviving acute infection show persistent viral RNA and mRNA up to two years post-infection, despite viral antigens are not detected. However, depletion of CD4+ and CD8+ lymphocytes reactivates viral protein expression, which is associated with development of neuropathology, indicating adaptive immune response controls measles virus replication although without clearance, leading to a long-term “dormancy”, unless a transient immunosuppression occurs, allowing reactivation of viral replication.7979 Miller KD, Matullo CM, Milora KA, Williams RM, O’Regan KJ, Rall GF. Immune-mediated control of a dormant neurotropic RNA virus infection. J Virol. 2019;93:e00241. Interestingly, it has been observed that anti-SARS-CoV-2 specific CD8+ T cells are increased in the respiratory tract of subjects with persistent viral RNA8080 Vibholm LK, Nielsen SSF, Pahus MH, et al. SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses. EBioMedicine. 2021;64:103230.; possibly this immune cells prevent virus transmission or avoid completion of the virus replication cycle, since contact tracing studies have not identified cases of transmission from longterm viral RNA carriers.2020 Walsh KA, Spillane S, Comber L, et al. The duration of infectiousness of individuals infected with SARS-CoV-2. J Infect. 2020;81:847-56.,8080 Vibholm LK, Nielsen SSF, Pahus MH, et al. SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses. EBioMedicine. 2021;64:103230.

Concluding remarks

Here we exposed that SARS-CoV-2 and other coronaviruses potentially establish a long-term, non-productive persistent infection in epithelial, myeloid and neural cells, which might be associated with prolonged synthesis of inflammatory mediators and cytotoxicity, contributing to airway chronic inflammation and/or neurological sequelae, until viral clearance is achieved.

Altered synthesis of IFN-I, IFN-II and IFN-III, besides a deficient production of anti-SARS-CoV-2 IgM and IgG may be determinant events that contribute to long-term infection in some individuals.

Further research is necessary to understand whether coronavirus RNA persistence has impact not only on viral transmission but also in pathogenesis.

  • Funding information
    This work was supported by the grant PAPIIT-UNAM number IA205521.

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Publication Dates

  • Publication in this collection
    29 Nov 2021
  • Date of issue
    2021

History

  • Received
    06 May 2021
  • Accepted
    13 Sept 2021
  • Published
    02 Oct 2021
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