Modeling the evolution of SARS-CoV-2 under non-pharmaceutical interventions and testing

Abstract

Social and behavioral non-pharmaceutical interventions (NPIs), such as mask-wearing, social distancing, and travel restrictions, as well as diagnostic tests, have been broadly implemented in response to the COVID-19 pandemic. Epidemiological models and data analysis affirm that wide adoption of NPIs helps to control the pandemic. However, SARS-CoV-2 has extensively demonstrated its ability to evolve. Therefore, it is crucial to examine how NPIs may affect the evolution of the virus. Such evolution could have important effects on the spread and impact of the pandemic. We used evo-epidemiological models to examine the effect of non-pharmaceutical interventions and testing on two evolutionary trajectories for SARS-CoV-2: attenuation and test evasion. Our results show that when stronger measures are taken, selection may act to reduce disease severity. Additionally, the timely application of NPIs could significantly affect the competition between viral strains, favoring the milder strain. Furthermore, a higher testing rate can select for a test-evasive viral strain, even if that strain is less infectious than the detectable competing strain. Importantly, if a less detectable strain evolves, epidemiological metrics such as confirmed daily cases may distort our assessment of the pandemic. Our results highlight the important implications NPIs can have on the evolution of SARS-CoV-2. LAY SUMMARY We used evo-epidemiological models to examine the effect of non-pharmaceutical interventions and testing on two evolutionary trajectories for SARS-CoV-2: attenuation and test evasion. Our results show that when stronger measures are taken, selection may act to reduce disease severity.

Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses

“…Before vaccines were widely accessible, strategies to control SARS-CoV-2 transmission and cases mainly relied on nonpharmaceutical interventions such as reducing social interactions, using antigenic testing, and imposing travel limits. Studies have shown declining lineage importations and persistence after lockdowns for the UK and Switzerland [5,11], and decreasing case numbers after establishment of NPIs [31][32][33][34]. To prepare for future pandemics and to identify the most effective measures, it is crucial to evaluate how SARS-CoV-2 lineage importations into the country and their subsequent internal dissemination relate to the nonpharmaceutical interventions that were put into effect.…”

“…Before vaccines were widely accessible, strategies to control SARS-CoV-2 transmission and cases mainly relied on nonpharmaceutical interventions such as reducing social interactions, using antigenic testing, and imposing travel limits. Studies have shown declining lineage importations and persistence after lockdowns for the UK and Switzerland [5,11], and decreasing case numbers after establishment of NPIs [31][32][33][34]. To The largest reductions of SARS-CoV-2 lineage importations were seen in Germany after the provision of free rapid tests, and the strengthening of regulations on mask wearing from wearing any kind of mask to obligatory surgical/FFP2 mask wearing in public transport and in stores, and on internal movements and gatherings.…”

Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution

“…NPIs have proven effective in reducing the spread of SARS-CoV-2 in many contexts [20][21][22][23][24][25] . The introduction of strong selection pressure by NPIs and the evolutionary impact of this has been the focus of much attention [26][27][28] , but how viral load dynamics are altered in vivo…”

Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution

“…NPIs have proven effective in reducing the spread of SARS-CoV-2 in many contexts [20][21][22][23][24][25] . The introduction of strong selection pressure by NPIs and the evolutionary impact of this has been the focus of much attention [26][27][28] , but how viral load dynamics are altered in vivo…”

“…NPIs have proven effective in reducing the spread of SARS-CoV-2 in many contexts 20–25 . The introduction of strong selection pressure by NPIs and the evolutionary impact of this has been the focus of much attention 26–28 , but how viral load dynamics are altered in vivo has not yet been explored. We were thus interested in the role of isolation as a strong NPI and explored the possible impact of such human behavioral changes on SARS-CoV-2 evolution.…”