NGS analysis of nasopharyngeal microbiota in SARS-CoV-2 positive patients during the first year of the pandemic in the Campania Region of Italy

Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

“…Similar observations were published by Stewart et al, who reported strong interrelationships between Streptococcus ‐dominant nasal microbiome and symptoms of viral bronchiolitis 7 . Our past studies revealed that COVID‐19 patients with severe outcomes had a nasopharyngeal district with reduced Proteobacteria and increased Rothia mucilaginosa, Streptococcus oralis , and bacterial species belonging to the genera Prevotella and Veillonella 8 . One of the most underestimated aspects of the microbiome is bacteriophages (phages).…”

“…Furthermore, about 54% of the remained reads per sample were mapped on the human reference genome and were excluded from the downstream analysis, resulting in a total of 43 184 475 reads per sample (range 4 610 220–147 612 628 reads) that passed the “Quality Control module.” On the entire data set more than 358 million reads were mapped on a viral database, corresponding to 18% of analyzed reads per sample (mean: 6 510 568; range: 1718–40 900 812). Only sequences that matched on phages have been considered in this paper as virus and bacteria presence have been already described respectively in Giugliano et al 8 and Ferravante et al 14 A total of six phage families that passed filters (phage entities were retained if they had a minimum of three reads associated in at least 50% of samples analyzed), were considered as detected in the 55 nasopharyngeal swabs taken from the patients infected with SARS‐CoV‐2. The RPM mean value of the six phage families detected, related to the three waves, different degrees of severity as well as the age quartile groups are reported in Table 2 .…”

“…Statistical significance was computed by applying a T ‐test followed by Bonferroni correction. Only comparisons with a p value ≤ 0.05 were considered significant, as described in Giugliano et al 8 …”

“…Statistical significance was computed by applying a T-test followed by Bonferroni correction. Only comparisons with a p value ≤ 0.05 were considered significant, as described in Giugliano et al 8 3 | RESULTS AND DISCUSSION Focusing on the three different pandemic waves, Siphoviridae remains to be the most abundant phage family, followed by Myoviridae in the II and III waves of COVID-19. However, in the I pandemic period, the second most abundant phage family is the unclassified Siphoviridae.…”

“… 7 Our past studies revealed that COVID‐19 patients with severe outcomes had a nasopharyngeal district with reduced Proteobacteria and increased Rothia mucilaginosa, Streptococcus oralis , and bacterial species belonging to the genera Prevotella and Veillonella . 8 One of the most underestimated aspects of the microbiome is bacteriophages (phages). Phages are viruses that infect and replicate only in bacterial cells.…”