Determining Gaps in Publicly Shared SARS-CoV-2 Genomic Surveillance Data by Analysis of Global Submissions

Abstract

Viral genomic surveillance has been a critical source of information during the COVID-19 pandemic, but publicly available data can be sparse, concentrated in wealthy countries, and often made public weeks or months after collection. We used publicly available viral genomic surveillance data submitted to GISAID and GenBank to examine sequencing coverage and lag time to submission during 2020-2021. We compared publicly submitted sequences by country with reported infection rates and population and also examined data based on country-level World Bank income status and World Health Organization region. We found that as global capacity for viral genomic surveillance increased, international disparities in sequencing capacity and timeliness persisted along economic lines. Our analysis suggests that increasing viral genomic surveillance coverage worldwide and decreasing turnaround times could improve timely availability of sequencing data to inform public health action.

Keywords: COVID-19; SARS-CoV-2; coronavirus disease; pandemic; respiratory infections; severe acute respiratory syndrome coronavirus 2; vaccine-preventable diseases; viral surveillance; viruses; zoonoses.

Figure 1

Weekly volume of SARS-CoV-2 sequences collected per 1 million population by income category of country, GISAID (https://www.gisaid.org) and GenBank, 2020–2021. Data include only populations of countries submitting >1 sequences. Data are truncated at the end of 2021 to avoid lag time artifact impacting comparison of sequencing volume nearer to the date of data access on March 21, 2022, because only collected samples that were also submitted by March 21, 2022, appear in these data.

Figure 2

Total SARS-CoV-2 sequences and sequences submitted within 14 days of collection, by population and income category, GISAID (https://www.gisaid.org) and GenBank, 2020–2021. A) Low-income countries; B) lower-middle-income countries; C) upper-middle-income countries; D) high-income countries. Dates indicate sequence collection dates. Data include only populations of countries submitting >1 sequence.