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Microbes & Immunity Comprehensive genomic surveillance analysis of SARS-CoV-2

public health. Notably, as of January 17, 2023, the World eight groups: VOC Alpha, VOC Beta, VOC Gamma, VOC
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Health Organization has reported a total of 662,445,150 Delta, VOC Omicron, variant of interest (VOI) Epsilon,
confirmed cases of COVID-19 globally, including VOI Iota, and Others, accounting for 924,692 genomes,
6,704,827 deaths (https://www.who.int/emergencies/ 26,118 genomes, 92,904 genomes, 3,139,228 genomes,
diseases/novel-coronavirus-2019), as well as the 462,017 genomes, 46,290 genomes, 24,238 genomes,
administration of more than 13 billion doses of vaccine. and 814,751 genomes, respectively. Notably, VOC Delta
Now, more than 2 years since its emergence, the Omicron constituted the majority, accounting for over half of the
variant of concern (VOC) continues to define the current total genomes deposited (3,139,228/5,530,238; 56.76%). In
stage of the pandemic, representing a significant evolution terms of geographical representation, 37,568 genomes were
from previous COVID-19 variants. More than 3 years into from Africa, 393,975 genomes were from Asia, 3,026,781
the pandemic, the world is now facing the era of the VOC genomes were from Europe, 1,888,466 genomes were from
Omicron, distinctly different from earlier SARS-CoV-2 North America, 49,263 genomes were from Oceania, and
strains. Enhancing global genomic sequencing capacities, 134,185 genomes were from South America. Notably,
particularly in low- and middle-income countries Europe accounted for over half of the total genomes
(LMICs), is essential for improving public health responses deposited (3,026,781/5,530,238; 54.73%). The number
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to the pandemic, as novel viruses can emerge rapidly of SARS-CoV-2 genomes analyzed in each country is
and unpredictably. Previous research has highlighted the presented in Figure 1. The top 10 leading countries in
importance of wastewater-based genome monitoring, genome sequencing were the United States of America
which, compared to traditional clinical epidemiological (n = 1,636,292), the United Kingdom (n = 1,199,075),
surveillance, can more rapidly detect co-circulating SARS- Denmark (n = 402,422), Germany (n = 314,156), Canada
CoV-2 variants and mutations. Furthermore, studies (n = 197,748), Japan (n = 188,849), France (n = 145,919),
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have also emphasized the importance of identifying the Sweden (n = 117,311), Brazil (n = 90,148), and Switzerland
diversity of SARS-CoV-2 variants, especially regarding (n = 81,393). Notably, nine out of the top 10 countries are
their potential to evade detection and affect post-vaccine developed nations.
immune responses. 4 Interestingly, a trend was observed in the daily numbers
In the present study, all SARS-CoV-2 genomic of SARS-CoV-2 genomes deposited over time, varying
metadata were downloaded from the Global Initiative on across different continents and between VOCs/VOIs
Sharing All Influenza Data (GISAID) platform, spanning (Figure 2A and B, respectively). The predominant VOC/
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submission dates from January 10, 2020, to September VOI genomes in Africa, Asia, Europe, North America,
30, 2022, and collection dates from December 24, 2019, Oceania, and South America were all identified as the VOC
to September 25, 2022. For genome quality analysis, only Delta, accounting for 42.74% (16,056/37,568), 51.94%
complete genomes with high coverage from human hosts (204,624/393,975), 55.89% (1,691,805/3,026,781), 60.87%
were considered (n = 5,530,238). The data extracted from (1,149,602/1,888,466), 46.24% (22,779/49,263), and 40.51%
all entries included accession ID, continent and country of (54,362/134,185), respectively. These findings suggest that
sampling, variant, collection date, and submission date to the VOC Delta may exhibit high geographic homogeneity
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the GISAID platform. SARS-CoV-2 was categorized into across various continents. The dynamic patterns in the

Figure 1. Worldwide distribution of SARS-CoV-2 genomes. Worldwide distribution of SARS-CoV-2 genomes (as of September 30, 2022). Circle size
represents the number of SARS-CoV-2 genomes. Data were obtained from the GISAID platform. 5

Volume 1 Issue 1 (2024) 107 doi: 10.36922/mi.2294