SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patient.

OBJECTIVES: Intra-host SARS-CoV-2 evolution during chronic infection in immunocompromised hosts has been suggested as being the possible trigger of the emergence of new variants. METHODS: Using a deep sequencing approach, we investigated the SARS-CoV-2 intra-host genetic evolution in a patient with HIV over a period of 109 days. RESULTS: Sequencing of nasopharyngeal swabs at three time points demonstrated dynamic changes in the viral population, with the emergence of 26 amino acid mutations and two deletions, 57% of them in the Spike protein. Such a combination of mutations has never been observed in other SARS-CoV-2 lineages detected so far. CONCLUSION: Our data confirm that persistent infection in certain immunocompromised individuals for a long time may favor the dangerous emergence of new SARS-CoV-2 variants with immune evasion properties.

Outbreak of SARS-CoV-2 B.1.617.2 (delta) variant in a nursing home 28 weeks after two doses of mRNA anti-COVID-19 vaccines: evidence of a waning immunity.

OBJECTIVES: To describe a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.617.2 (Delta) variant outbreak among residents (n = 69) and health workers (n = 69) of a small nursing home in northeastern Italy, with full vaccination coverage of 91% and 82%, respectively. Evaluation of the anti-Spike IgG titres 28 weeks after the mRNA vaccine booster dose against SARS-CoV-2 infection and severe coronavirus disease 2019 (COVID-19). MATERIALS AND METHODS: Sera were collected within 48 hours from the index case; anti-Spike IgG was determined (expressed as WHO binding antibody units (BAU)/mL) through a commercial quantitative assay; SARS-CoV-2 was diagnosed using RT-PCR, and full-genome sequencing was performed for lineage characterization. Residents were grouped according to anti-Spike IgG titres (≤50, 51-1000 and > 1000 BAU/mL) and the resulting protection against infection and severe disease was measured. RESULTS: None of the health workers and 14 of the 59 (24%) residents fully vaccinated and without a previous SARS-CoV-2 infection showed anti-Spike IgG ≤50 BAU/mL (one-sided Fisher exact test, p 0.011). Among these residents, a level of anti-Spike IgG ≤50 BAU/mL resulted in a higher risk of SARS-CoV-2 infection (relative risk 1.55, 95% CI 1.17-2.05) and severe COVID-19 (relative risk 5.33, 95% CI 1.83-15.57). CONCLUSION: Low levels of SARS-CoV-2 neutralizing anti-Spike IgG in serum 28 weeks after the administration of the second dose parallel the waning of vaccine protection.