A Repeat Pattern of Founder Events for SARS-CoV-2 Variants in Alaska.

Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found that in Alaska, the Omicron sublineage BA.2.3 overtook BA.1.1 by the week of 27 February 2022, reaching 48.5% of sequenced cases. On the contrary, in the contiguous United States, BA.1.1 dominated cases for longer, eventually being displaced by BA.2 sublineages other than BA.2.3. BA.2.3 only reached a prevalence of 10.9% in the contiguous United States. Using phylogenetics, we found evidence of potential origins of the two major clades of BA.2.3 in Alaska and with logistic regression estimated how it emerged and spread throughout the state. The combined evidence is suggestive of founder events in Alaska and is reflective of how Alaska's unique dynamics influence the emergence of SARS-CoV-2 variants.

Pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska.

Alaska has the lowest population density in the United States (US) with a mix of urban centers and isolated rural communities. Alaska's distinct population dynamics compared to the contiguous US may have contributed to unique patterns of SARS-CoV-2 variants observed in early 2021. Here we examined 2323 SARS-CoV-2 genomes from Alaska and 278,635 from the contiguous US collected from December 2020 through June 2021 because of the notable emergence and spread of lineage B.1.1.519 in Alaska. We found that B.1.1.519 was consistently detected from late January through June of 2021 in Alaska with a peak prevalence in April of 77.9% unlike the rest of the US at 4.6%. The earlier emergence of B.1.1.519 coincided with a later peak of Alpha (B.1.1.7) compared to the contiguous US. We also observed differences in variant composition over time between the two most populated regions of Alaska and a modest increase in COVID-19 cases during the peak incidence of B.1.1.519. However, it is difficult to disentangle how social dynamics conflated changes in COVID-19 during this time. We suggest that the viral characteristics, such as amino acid substitutions in the spike protein, likely contributed to the unique spread of B.1.1.519 in Alaska.

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

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.

Testing of a mobile heating facility to sanitize N-95 respirators against an enveloped respiratory virus.

In the spring of 2020, the Alaska Native Tribal Health Consortium (ANTHC) designed and built a sanitizing treatment system to address shortages of filtering facepiece respirators (FFRs). The design criteria included sanitizing large numbers of FFRs, repeatedly achieving FFR fit test requirements, and deactivating enveloped respiratory viruses, such as SARS-CoV-2. The outcome was the Mobile Sanitizing Trailer (MST), a 20 by 8-foot modified trailer designed to process up to 1,000 FFRs during a standard heat cycle. This paper reports on the MST's ability to: (1) sustain a target temperature, (2) produce tolerable conditions for FFRs as measured by fit factor and (3) successfully deactivate an infectious model virus. We found that the MST reliably and uniformly produced 75 degrees Celsius in the treatment chamber for the prescribed periods. Quantitative analysis showed that the FFRs achieved acceptable post-treatment fit factor even after 18, 60-minute heat cycles. Finally, the treated FFR materials had at least a log 3.0 reduction in viral RNA and no viable virus after 30, 60 or 90 minutes of heat treatment. As a sanitizing treatment during supply shortages, we found the MST a viable option for deactivation of virus and extending the usable life of FFRs.

Implications of Inadequate Water and Sanitation Infrastructure for Community Spread of COVID-19 in Remote Alaskan Communities

The novel coronavirus SARS-CoV-2, the causative agent of COVID-19, emerged in the human population in December 2019 and spread worldwide within a few short months. Much of the public health focus for preventing and mitigating the spread of COVID-19 has been on individual and collective behaviors, such as social distancing, mask-wearing, and hygiene. It is important to recognize that these behaviors and health outcomes occur within broader social and environmental contexts, and factors within local communities such as regional policy, historical context, cultural beliefs, and natural- and built environmental characteristics affect underlying population health and the spread of disease. For example, the COVID-19 pandemic has renewed attention to the importance of secure water and sanitation services in protecting human health;many remote Alaskan communities are particularly vulnerable to infectious disease transmission because of inadequate water and sanitation services. In addition, there are a number of socio-economic, physical, and infrastructure factors in rural Alaska (e.g., remoteness, household overcrowding, climate change impacts, limited medical facilities, and high prevalence of chronic diseases) that contribute to the potential for more severe COVID-19 disease outcomes in these predominantly Alaska Native communities.