Evaluating Data Sharing of SARS-CoV-2 Genomes for Molecular Epidemiology across the COVID-19 Pandemic

Abstract

Following the emergence of COVID-19 in December 2019, caused by the coronavirus SARS-CoV-2, the disease spread dramatically worldwide. The use of genomics to trace the dissemination of the virus and the identification of novel variants was essential in defining measures for containing the disease. We aim to evaluate the global effort to genomically characterize the circulating lineages of SARS-CoV-2, considering the data deposited in GISAID, the major platform for data sharing in a massive worldwide collaborative undertaking. We contextualize data for nearly three years (January 2020-October 2022) for the major contributing countries, percentage of characterized isolates and time for data processing in the context of the global pandemic. Within this collaborative effort, we also evaluated the early detection of seven major SARS-CoV-2 lineages, G, GR, GH, GK, GV, GRY and GRA. While Europe and the USA, following an initial period, showed positive results across time in terms of cases sequenced and time for data deposition, this effort is heterogeneous worldwide. Given the current immunization the major threat is the appearance of variants that evade the acquired immunity. In that scenario, the monitoring of those hypothetical variants will still play an essential role.

Keywords: COVID-19; SARS-CoV-2 molecular epidemiology; genetic variants; genomics; phylogeography; worldwide collaboration.

Figure 1

Major contributions to the deposited data in the GISAID platform in terms of submitting country (A) and month of submission from February 2020 until July 2022 (B). In both graphics, the continent of submission is indicated in the color code. In (A) only countries that contributed to at least 0.5% of the data are indicated individually.

Figure 2

Percentage of sequenced genomes of SARS-CoV-2 given the reported incidence in different countries. Values displayed include months from March 2020 until July 2022.

Figure 3

Estimated time elapsed between SARS-CoV-2 isolate collection and the deposit of the genome in the GISAID dataset for each continent; ((A) Africa, (B) Asia, (C) Europe, (D) North America, (E) Oceania, and (F) South America), between February 2020 and July 2022.

Figure 4

Heat map contextualizing the relative percentage of sequenced genomes in each country against the average percentages worldwide. Red points indicate that the percentage in that country/month was higher than the average worldwide, white represents a similar average, while tones of blue indicate that the average of sequenced genomes was lower than the worldwide average.

Figure 5

Heat map representing the percentage of hypothetical uncharacterized genomes present in each country against the hypothetical global values. A scale from white to blue to black indicates an increasing percentage. Black indicates that in that month, that country accounts for 2.4% or over of genetically uncharacterized SARS-CoV-2 genomes in the world.

Figure 6

Geographic interpolation results of the first appearance of global clades as deposited in GISAID using the Kriging algorithm. Results were obtained for clades G (A), GH (B), GR (C), GK (D), GV (E), GRY (F) and GRA (G).

Figure 7

Median networks of the earliest deposited data of global SARS-CoV-2 lineages. The reference sequence was used as an outgroup in each. Networks are colored according to their geography and also according to time of collection. Networks were performed for clades G (A), GH (B), GR (C), GK (D), GV (E), GRY (F) and GRA (G).