The emergence of novel pathogens presents a major threat to human, animal and plant populations. An additional threat is posed by the emergence of variants of known pathogens (such as highly pathogenic influenza viruses and antibiotic resistant bacteria). This has been acutely evidenced during the SARS-CoV-2 pandemic, where control of transmission was repeatedly thwarted by the emergence of variants of concern and their global spread.
Key ecological questions remain regarding effective means of minimizing the impact of emerging pathogens, in particular the feasibility of preventing spatial dispersal, in light of global interconnectedness. While the early detection and containment of a novel pathogen is an ambitious goal, the benefits are potentially enormous.
Focusing on the emergence of novel SARS-CoV-2 variants, we aim to establish i) the ecological and epidemiological conditions and ii) the monitoring efforts necessary for identifying and containing a variant at source. To accomplish this, we formulate a spatial model of SARS-CoV-2 transmission that can accommodate the emergence of novel variants as well as multiple approaches to monitoring. Our model is a continuous-time Markov jump process that captures the competition between variant exportation and case detection (e.g. via random case sequencing) as incidence in the source population grows.
Results/Conclusions
We derive mathematical expressions for the probability of identifying a novel pathogen before infections are exported, enabling us to quantify the monitoring requirements for successful containment, and their dependence on ecological and epidemiological parameters (such as spatial connectivity and pathogen transmissibility). We study two types of monitoring scheme: i) genomic surveillance based on the detection of atypical genetic sequences and ii) epidemiological surveillance based on clusters of excess mortality.
Our findings suggest that epidemiological factors make identification of a SARS-CoV-2 variant through mortality data unlikely prior to pathogen dispersal. In contrast, we find that successfully identifying and containing variants via genomic surveillance is realistic, provided sequence processing and dissemination is prompt. We show that a crucial factor in determining the prospects of containing a variant is the ratio of detection delay to variant doubling time — increases in the timeliness of sequence dissemination can result in equivalent gains to substantial improvements in sequencing coverage.
We compare the results of our mathematical calculations with ongoing monitoring efforts. Our findings suggest that genomic surveillance in multiple countries, including Denmark and the United Kingdom, make containment of an omicron-like variant probable, provided ≲50 sequences are needed before identification.
