High viral replication efficiency of SARS-CoV-2 Omicron variant

The emergence of SARS-CoV-2 variants of concern (VOC) with increasingly greater human transmissibility is a global public health threat. The omicron version also avoids protection from natural infections and vaccines, but it's unclear whether this is due to immune evasion or inherent virological features. 

In ex vivo explant cultures of human bronchus and lung, we examined the replication competence and cellular tropism of the wild-type (WT) virus, D614G, Alpha, Beta, Delta, and Omicron variants. The infection's reliance on TMPRSS2 was also investigated. We found that Omicron replicated faster in the bronchus than all other SARS-CoV-2 strains, but not in the lung parenchyma. 

The cellular tropism of all VOCs was similar to that of the WT. Omicron was more cathepsin-dependent than the other VOCs studied, implying that the omicron version reaches cells via a distinct mechanism than the others. Although the factors of severity are multifaceted, the lower replication competency of Omicron in human lung may explain the lowered severity of Omicron that is currently being described in epidemiological research. These discoveries give crucial biological correlations to epidemiological data.

According to researcher "Our findings imply that the Omicron variant has a much higher replication competence in the human bronchus (around 70-fold increase) than both wild-type and Delta viruses at 24 hpi. It's unknown how much faster bronchus replication contributes to transmissibility, but a higher infectious virus load in conducting airways could result in more infectious virus released while breathing or speaking, promoting transmission via the airborne pathway. Recent studies have also found that Omicron virus replicates more efficiently in differentiated human nasal epithelial cultures in vitro than Delta and WT virus. Infectious SARS-CoV-2 has been found in fine aerosol particles in COVID-19 patients' breathed air".

This Research was publish in nature under title " SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo"

The mechanisms behind the higher replication competency in the bronchus are still unknown. The spike protein in the Omicron variation includes 37 amino acid changes, 15 of which are in the receptor binding domain. Infection with Omicron is ACE2 dependent, and the spike of Omicron spike binds to ACE2 more efficiently than the wild-type virus. We discovered that the human bronchus has a higher level of ACE2 expression than the lung, which could explain why SARS-CoV-2 replication is higher in the bronchus. Amino acid changes in the nucleocapsid protein of Omicron (R203K and G204R) have been linked to increased virus multiplication.

According to epidemiological research, the Delta variant was significantly more transmissible than the Alpha variant, which was in turn more transmissible than the previous viral strains. Thus, our findings that the Delta variation possesses higher infectious virus titres in the bronchus than the wild-type virus are consistent with epidemiological findings. Pseudoviruses expressing Delta spike have been demonstrated to be more capable of infecting ACE2 low human bronchial epithelial cells than previous variations. Furthermore, the Delta spike is mostly cleaved, which may help it replicate more efficiently in the human airway. P681R improved furin-cleavage sequence cleavage, which explains why Delta outperformed Alpha in a competition assay in Calu-3 and human airway epithelium in vitro models.

Authors added "Omicron variation showed lower viral replication capability in the lung than in the bronchus. Immunohistochemistry investigations show less virus-infected cells in human lung explant cultures ex vivo, confirming this distinction. The biological drivers of this discrepancy in Omicron and Delta variants' comparative replication competency in the bronchus and lung have yet to be discovered. These findings could imply that Omicron has a lower clinical severity, however such conclusions must be modified because the severity of COVID-19 disease is influenced not only by virus replication but also by dysregulated innate immune responses".

According to epidemiological research conducted in South Africa and the United Kingdom, Omicron causes less hospitalizations than the Delta version. As a result, the results of the ex vivo cultures are consistent with current epidemiological studies, both in terms of disease transmission and severity. Our discovery that Omicron infection is less reliant on TMPRSS2 activities but more sensitive to a cathepsin inhibitor than Delta infection suggests that Omicron enters cells largely through the endocytic pathway, whereas Delta preferentially enters cells via cell surface fusion. The use of a ubiquitous endocytic route may widen the cellular spectrum for Omicron infection, allowing Omicron to infect cells with ACE2 expression even if TMPRSS2 is not present.

Single cell sequencing studies show that cells that co-express ACE2 and cathepsins are more common in the upper airway than cells that co-express ACE2 and TMPRSS2, which could explain Omicron's higher bronchus replication competence. Our findings that Omicron predominantly penetrates cells through the endosomal pathway while Delta relies more on cell surface fusion are consistent with previous findings in alveolar epithelial cells and nasal epithelial cells. The use of pharmacological inhibitors of TMPRSS2 in the treatment of clinical infections caused by the Omicron form may be of limited effect. Although single-cell investigations on the distribution of TMPRSS2 in cell cultures have been conducted, data on the extent of its distribution is limited due to antibody sensitivity and specificity.

The fact that just one virus strain from each lineage was studied is one of the study's shortcomings. Furthermore, all six virus variations were not tested in the same experiment, which would be logistically challenging due to the minimal tissue available to test six viruses with replicates.