Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021

Abstract

The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), informing evidence-based public health decision making. Ukraine has experienced four waves of the Coronavirus Disease 2019 (COVID-19) between spring 2020 and spring 2022. However, insufficient capacity for local genetic sequencing limited the potential application of SARS-CoV-2 genomic surveillance for public health response in the country. Herein, we report local sequencing of 103 SARS-CoV-2 genomes from patient samples collected in Kyiv in July-December 2021 using Oxford Nanopore technology. Together with other published Ukrainian SARS-CoV-2 genomes, our data suggest that the third wave of the epidemic in Ukraine (June-December 2021) was dominated by the Delta Variant of Concern (VOC). Our phylogeographic analysis revealed that in summer 2021 Delta VOC was introduced into Ukraine from multiple locations worldwide, with most introductions coming from Central and Eastern European countries. The wide geographic range of Delta introductions coincides with increased volume of travel to Ukraine particularly from locations outside of Europe in summer 2021. This study highlights the need to urgently integrate affordable and easily scaled pathogen sequencing technologies in locations with less developed genomic infrastructure, in order to support local public health decision making.

Discovery of Avian Paramyxoviruses APMV-1 and APMV-6 in Shorebirds and Waterfowl in Southern Ukraine

“…As a mainstay of capacity-building projects, a tiling primer approach combined with nanopore technology has proven successful in low-resourced laboratories. For example, this approach has been used to generate highly accurate sequences of Ebola and Zika viruses in outbreak settings and SARS-CoV-2 and other pathogens in Ukraine [ 29 , 30 , 45 ]. This study was the first report of the genome of an APMV-6 isolate from wild birds in Ukraine and the first use of our tiling and nanopore technology for APMV-1 and APMV-6 sequencing in sentinel veterinary labs in Ukraine.…”

An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations

“…Of note, ONT MinION sequencers have been employed to track numerous outbreaks, including the Ebola virus [ 113 ] and influenza in 2015 [ 114 ] and the Zika virus in 2016 [ 115 ]. Notably, MinION sequencers were recently used to track the SARS-CoV-2 Alpha and Delta variants in Ukraine, utilizing reverse transcription-driven cDNA sequencing [ 116 ]. Similarly, a group successfully sequenced a full monkeypox viral genome—including ITR sequences previously missed by other short read platforms—within 8 h, obtaining sequencing depths of ~12–57x genome coverage [ 117 ].…”

Healthcare Challenges due to Global Conflict Escalation Amid the Pandemic, Climate, and Economic Dilemmas

“…The correlation between low vaccination and Russian aggression is still a question, as Ukraine was the second lowest (15%) vaccinated country after Armenia in Europe until the end of October, 2021 (AP, 2021). With a population of 42 million people, Ukraine has reported more than 10% cases of COVID-19 and over 0.1 million deaths from March 2020 through February 2022 (Yakovleva et al, 2022). Among deaths from COVID-19, close to 60% were teenagers aged 10-19 years, and more than 40% were children aged 0-9 years (Seriakova et al, 2022).…”