Volume 28, Supplement—December 2022
SUPPLEMENT ISSUE
Surveillance
Determining Gaps in Publicly Shared SARS-CoV-2 Genomic Surveillance Data by Analysis of Global Submissions
Elizabeth C. Ohlsen
, Anthony W. Hawksworth, Kimberly Wong, Sarah Anne J. Guagliardo, James A. Fuller, Michelle L. Sloan, and Kevin O’Laughlin
, Anthony W. Hawksworth, Kimberly Wong, Sarah Anne J. Guagliardo, James A. Fuller, Michelle L. Sloan, and Kevin O’Laughlin
Table 2
SARS-CoV-2 sequences submitted to GISAID and GenBank with collection dates during 8-week periods of initial global transmission waves of Alpha, Delta, and Omicron variants of concern*
| Category | Alpha, 2020 Dec 6–2021 Jan 30 | Delta, 2021 June 6–Jul 31 | Omicron, 2021 Dec 6–2022 Jan 30 | p value† |
|---|---|---|---|---|
| Sequences collected |
376,637 |
774,534 |
1,877,225 |
|
| Countries submitting sequences |
168 |
164 |
151 |
|
| Median lag time, d |
39 |
23 |
17* |
|
| Mean sequences submitted/1 million population | 48.8 | 100.4 | 243.3 | <0.001 |
| Low income | 2.1 | 3.2 | 1.1 | |
| Lower-middle income | 3.4 | 8.7 | 13.6 | |
| Upper-middle income | 4.7 | 23.7 | 28.3 | |
| High income |
295.6 |
573.2 |
1,476.1 |
|
| Mean sequences/100,000 SARS-CoV-2 reported infections | 981.0 | 2,017.4 | 4,889.6 | <0.001 |
| Low income | 795.8 | 655.1 | 170.4 | |
| Lower-middle income | 302.1 | 319.2 | 378.3 | |
| Upper-middle income | 115.8 | 493.2 | 351.4 | |
| High income |
1,457.2 |
8,899.4 |
2,074.2 |
|
| Sequences collected within 14 d lag time (% total as of 2022 Mar 20) |
81,358 (21.6) |
165,758 (21.4) |
360,022 (19.2) |
|
| Countries submitting sequences within 14 d of sample collection |
118 |
115 |
94 |
|
| Mean sequences submitted/1 million population within 14 d of collection | 10.5 | 21.5 | 46.7 | <0.001 |
| Low income | 0.4 | 0.8 | 0.08 | |
| Lower-middle income | 0.7 | 1.6 | 1.1 | |
| Upper-middle income | 0.6 | 4.9 | 3.5 | |
| High income | 64.7 | 123.5 | 291.6 |
*Mean time during Omicron cannot be accurately compared to mean lag time during Alpha or Delta because data from GISAID and GenBank were retrieved <2 months after the end of the Omicron period examined in this analysis. GISAID, https://www.gisaid.org. †By Kruskal-Wallis test.
Page created: August 12, 2022
Page updated: December 11, 2022
Page reviewed: December 11, 2022
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.