SARS-CoV-2 viral replication persists in the human lung for several weeks after symptom onset
Authors: Tomasicchio M , Jaumdally S , Wilson L , Kotze A , Semple L , Meier S , Pooran A , Esmail A , Pillay K , Roberts R , Kriel R , Meldau R , Oelofse S , Mandviwala C , Burns J , Londt R , Davids M , van der Merwe C , Roomaney A  , Kühn L , Perumal T , Scott A.J , Hale M.J , Baillie V , Mahtab S , Williamson C , Joseph R , Sigal A , Joubert I , Piercy J , Thomson D , Fredericks DL , Miller MGA , Nunes M.C , Madhi S.A , Dheda K 
Published: March 2023

ABSTRACTRationaleIn the upper respiratory tract replicating (culturable) SARS-CoV-2 is recoverable for ∼ 4 to 8 days after symptom onset, however, there is paucity of data about the frequency or duration of replicating virus in the lower respiratory tract (i.e. the human lung).ObjectivesWe undertook lung tissue sampling (needle biopsy), shortly after death, in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patents served as a control group.MethodsLung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling and immunohistochemistry.Results38% (16/42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 weeks) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (p<0.05). Nasopharyngeal culture was negative in 23.1% (6/26) of decedents despite lung culture positivity. This, hitherto, undescribed bio-phenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary pro-inflammatory response but with concurrent viral culture positivity.ConclusionsConcurrent, rather than sequential active viral replication continues to drive a heightened pro-inflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe COVID-19 disease.At a Glance CommentaryScientific Knowledge on the SubjectInvestigations to understand SARS-CoV-2 viral shedding (determined by PCR or antigen testing) have extensively focused on samples from the upper respiratory tract. The widely accepted view is that acute severe SARS-CoV-2 infection is characterised by a viral replicative phase in the first week of symptomatic illness followed by a pro-inflammatory immunopathologic phase peaking in the second and third weeks of illness. However, it remains unclear whether detection of SARS-CoV-2 beyond 2 weeks after symptom onset in published studies represent active replication competent virus because it may represent residual genomic or antigenic material in the tissue.What This Study Adds to the FieldWe have identified a, hitherto, undescribed bio-phenotype of acute severe COVID-19 characterised by persisting viral replication in the lung for up to 4 weeks after symptom onset. ∼40% of acute severe COVID-19 intensive care unit (ICU) decedents (n=42) had nasopharyngeal swab culture positivity at ∼2 weeks post-symptom onset versus only ∼5% in a group of ambulatory control patients (n=18). There was compartment-specific (nasopharynx versus lung) discordance. The phenotype of lung-specific persisting viral replication was associated with variant-specific accelerated death, an exaggerated inflammatory response, and attenuated T-cell immunity in the lung (based on histopathological and transcriptomic studies). This challenges the traditional view that viral replication occurs during the first 5 to 10 days of illness, which is followed by an effector or hyperinflammatory phase. This is the first study, to our knowledge, to systematically culture virus from the human lung and map out its related clinical determinants, and which describes the human lung transcriptomic profile of culture-positive versus culture-negative patients with severe COVID-19 disease.