Table 2.
Overview of the most abundant viruses (family and genus) detected in SARS‐COV‐2 positive samples from three different waves in the Campania Region
| Mar–May 2020 (10 genus from 7 families) | Sep–Nov 2020 (6 genus from 4 families) | Jan–Feb 2021 (5 genus from 5 families) | |||
|---|---|---|---|---|---|
| Family (genus) | Reads number (RPM) | Family (genus) | Reads number (RPM) | Family (genus) | Reads number (RPM) |
|
Coronaviridae (Betacoronavirus) |
517.032 516.869 |
Coronaviridae (Betacoronavirus) |
765.266 764.777 |
Coronaviridae (Betacoronavirus) |
867.010 866.518 |
|
Pneumoviridae (Orthopneumovirus) |
694 1.225 |
– | – | – | – |
|
Retroviridae (Lentivirus, human immunodeficiency virus‐1) |
71.339 86 |
Retroviridae Human endogenous retroviruses |
6.532 6.529 |
Retroviridae Human endogenous retroviruses |
6.010 6.009 |
| Human endogenous retroviruses | 71.233 | ||||
|
Herpesviridae (Simplexvirus) (Lymphocryptovirus) |
19.160 18.539 138 |
Herpesviridae (Simplexvirus) (Roseolovirus) (Lymphocryptovirus) |
6.704 6.623 8 36 |
Herpesviridae (Simplexvirus) |
849 815 |
|
Poxviridae Chordopoxvirinae (subfamily) Orthopoxvirus BeAn58058 virus |
7.793 7.793 |
Poxviridae Orthopoxvirus (BeAn58058virus) |
680 680 |
Poxviridae Orthopoxvirus (BeAn58058virus) |
543 543 |
|
Anelloviridae (Alphatorquevirus) |
28 28 |
– | – |
Anelloviridae Alphatorquevirus |
14 14 |
|
Pandoraviridae (Pandoravirus) |
71 | – | – | – | – |
Note: The viral reads (expressed as a mean of the reads/total samples for each period) identified from samples collected during the first, second, and third waves were classified into 7, 4, and 5 families, respectively.
Abbreviations: RPM, reads per million; SARS‐COV‐2, severe acute respiratory syndrome coronavirus 2.