Virological evidence of the impact of non-pharmaceutical interventions against COVID-19 in a resource-limited setting
Moreira-Soto, A.; Bruno, A.; de Mora, D.; Paez, M.; Garcez, J.; Wulf, B.; Sander, A.-L.; Olmedo, M.; Basantes Mantilla, M. J.; Gonzalez, M.; Orlando Narvaez, A.; Salgado Cisneros, S. P.; Zevallos, J. C.; Drexler, J.
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Ecuador was an early COVID-19 hotspot with substantial COVID-19-mortality. In developed countries, low socioeconomic status is associated with COVID-19 infection and low compliance with non-pharmaceutical interventions (NPIs). However, if NPI were successful in resource-limited settings with high human mobility and informal labour is still unclear. We performed a retrospective observational molecular and serological study of Ecuadors reference laboratory. We tested 1,950 respiratory samples from COVID-19 surveillance for SARS-CoV-2 and 12 respiratory viruses using RT-PCR, characterized 642 SARS-CoV-2 genomes, and examined SARS-CoV-2 seroprevalence in 1,967 samples from patients with fever in Ecuadors reference laboratory during 2020-2021. Molecular and serological data were compared to NPI stringency in Bayesian, maximum-likelihood and modelling frameworks. SARS-CoV-2 (Pearson correlation test; r=-0.74; p=0.01) and other respiratory viruses (r=-0.68; p=0.02) detection correlated negatively with NPI stringency. SARS-CoV-2 seroprevalence increased from <1% during February-March 2020 to 50% within 6 weeks and plateaued after NPI implementation. Decrease of effective reproduction number <1 and antibody reactivity over time suggested intense SARS-CoV-2 transmission during pandemic onset, subsequently limited by NPIs. Phylogeographic analyses revealed that travel restrictions were implemented late not preventing 100 near-parallel SARS-CoV-2 introductions, and implementation of NPIs modified SARS-CoV-2 geographic spread by restricting recreational activity. NPIs stringency correlated negatively with the number of circulating SARS-CoV-2 lineages (r=-0.69; p=0.02). Virological evidence supports NPIs restricting human movement as an effective public health tool to control the spread of respiratory pathogens in resource-limited settings, providing a template for emerging SARS-CoV-2 variants and future epidemics.
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