Here, we report the complete genome sequence of an African swine fever (ASF) virus (ASFV/Kyiv/2016/131) isolated from the spleen of a domestic pig in Ukraine with a lethal case of African swine fever. Using only long-read Nanopore sequences, we assembled a full-length genome of 191,911 base pairs in a single contig.
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.
The complete genome of Salmonella enterica subsp. enterica serovar Kottbus strain Kharkiv (serogroup C2-C3), which was isolated from a commercial pork production facility in Kharkiv, Ukraine, was assembled using long-read Nanopore sequences. A single circular contig (4,799,045 bp) comprised a complete chromosome encoding antibiotic resistance, highlighting the risk of cross-species livestock and human infection.
Alaska is the largest geographic state in the United States with the lowest population density and a mix of urban centers and isolated rural communities. The differences in population dynamics in Alaska from the contiguous United States may have contributed to a unique pattern of emergence and spread of SARS-CoV-2 variants observed in early 2021. Here we examined 2,323 virus genomes from Alaska and 278,635 virus genomes from the contiguous United States collected between the first week of December 2020 through the last week of June 2021. We focused on this timeframe because of the notable emergence and spread of the SARS-CoV-2 lineage B.1.1.519 observed in Alaska. We found that this variant was consistently detected in Alaska from the end of January through June of 2021 with a peak prevalence in April of 77.9% unlike the rest of the United States with a peak prevalence of 4.6%. In Alaska, the earlier emergence of B.1.1.519 coincided with a later peak of Alpha (B.1.1.7) when compared to the rest of the United States. We also observed differences in the composition of lineages and variants over time between the two most populated regions of Alaska. Although there was a modest increase in COVID-19 cases during the peak incidence of B.1.1.519, 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, and a founder effect likely contributed to the unique spread of B.1.1.519 in Alaska.
Since spring 2020, Ukraine has experienced at least two COVID-19 waves and has just entered a third wave in autumn 2021. The use of real-time genomic epidemiology has enabled the tracking of SARS-CoV-2 circulation patterns worldwide, thus informing evidence-based public health decision making, including implementation of travel restrictions and vaccine rollout strategies. However, insufficient capacity for local genetic sequencing in Ukraine and other Lower and Middle-Income countries limit opportunities for similar analyses. Herein, we report local sequencing of 24 SARS-CoV-2 genomes from patient samples collected in Kyiv in July 2021 using Oxford Nanopore MinION technology. Together with other published Ukrainian SARS-COV-2 genomes sequenced mostly abroad, our data suggest that the second wave of the epidemic in Ukraine (February-April 2021) was dominated by the Alpha variant of concern (VOC), while the beginning of the third wave has been dominated by the Delta VOC. Furthermore, our phylogeographic analysis revealed that the Delta variant was introduced into Ukraine in summer 2021 from multiple locations worldwide, with most introductions coming from Central and Eastern European countries. 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.
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.
Unoccupied aerial system (UAS) technologies applied to health assessments of large whales can have positive implications for progressive management. We focused on the collection of cetacean respiratory blow samples for endocrine, DNA profiling, microbial metabarcoding, and metagenomics analyses, with the goal of improving management of large whale populations. Blow samples were collected from humpback (Megaptera novaeangliae, n = 109 samples analyzed), blue (Balaenoptera musculus, n = 21 samples analyzed), and killer whale (Orcinus orca, n = 1 sample analyzed) species, as well as the responses of the whales to the collection of their blow by UAS. Endocrine analyses were validated for 5 steroid hormones in humpback whales and 4 hormones in blue whales. For DNA profiling, we attempted to extract and amplify nuclear and mitochondrial DNA, resulting in sequencing of mtDNA haplotypes for 54% of samples, identification of sex for 39%, and individual identification by microsatellite genotyping for 17%. The DNA profiles of 2 of the blow samples from humpback whales were matched to a DNA register for this regional population. Metagenomic and microbial metabarcoding classifications found a diverse number of bacteria, eukaryotes, and viruses in humpback whale blow. Although a significant portion of classifications were found in both seawater and blow, several of the most abundant organisms were present only in blow samples, suggesting they are true members of the respiratory microbiome. A comprehensive integration of laboratory‐based approaches using noninvasive UAS collection technologies could become an important management tool for health assessments of large cetaceans, especially for species listed as endangered. The addition of individual and population‐level health assessments to currently practiced stewardship of large whales, renders them as excellent sentinels of ocean health. © 2021 The Wildlife Society.
BackgroundDue to practical challenges associated with genetic sequencing in low resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people is understudied. We examined the use of field-applicable HCV sequencing methods and phylogenetic analysis to determine HCV transmission dynamics in internally displaced people who inject drugs (IDPWID) due to war in eastern Ukraine.MethodsIn this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who have settled in Odessa, Ukraine. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships.FindingsBetween June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID. Rapid testing identified an HIV, anti-HCV, and HIV/HCV co-infection prevalence of 39%, 67.7%, and 31.1%, respectively. We generated 57 partial or NFLG HCV sequences and identified eight transmission clusters, of which at least two originated within a year and a half post-migration. Unstable housing post-migration was associated with more reports of injection drug use in the past 30 days (p=0.048).InterpretationLocal generation of viral sequencing data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can inform timely adaptation of prevention and treatment.FundingOxford University John Fell Fund, ISS Wellcome Trust, Branco Weiss Fellowship.
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