Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Abstract

The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.

Keywords: Epidemic-pandemic preparedness; Genomic surveillance; SARS-CoV-2; Viral evolution.

Fig. 1

Timeline of the progression and milestones occurring during the COVID-19 pandemic (December 2019–October 2022). The first COVID-19 case reported is illustrated in blue, the number of reported COVID-19 cases milestones are illustrated in yellow, the total deaths milestones are illustrated in red, the detection of VOCs are illustrated in green. The ring colour indicates different years (2019–2022), as reported in the legend on the top left. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Genomic surveillance framework for the real-time monitoring of emerging and re-emerging viral pathogens. The framework will include 6 steps. The first step will focus on sample collection. In the second step, outbreak isolates are submitted to molecular screening using real-time PCR. Next (iii), positive samples will be submitted to whole genome sequences and subsequently assembled either using de novo or mapped against a reference genome strategy. Next (iv), novel strains will be submitted to phylogenetic and phylodynamic inferences which in turn will make possible the identification of potential genomic differences through the analysis of the mutational pattern profile (v). In the final step (vi), genomic data will be analysed together with epidemiological, clinical, climatic and mobility data for greatly facilitating large-scale genomic epidemiological investigations.

Fig. 3

VOCs world distribution according to their sequenced genomes. The legend on the bottom right indicates the progression and the spread of each VOC through time at the countrywise level.

Fig. 4

Zoonotic transmission chains. Interactions between humans, and different host species (including wild, domestic animals and vectors), which are important drivers for spillover and spillback events. Different colours indicates different epidemic waves.