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BACKGROUND: Due 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) in Ukraine. METHODS: In this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who were displaced to Odesa, Ukraine, before 2020. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore Technology (ONT) MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships. RESULTS: Between June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID (PNAS Nexus.2023;2(3):pgad008). Rapid testing (Wondfo® One Step HCV; Wondfo® One Step HIV1/2) identified an anti-HCV seroprevalence of 67.7%, and 31.1% of participants tested positive for both anti-HCV and HIV. 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-displacement. CONCLUSIONS: Locally generated genomic data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can help inform effective public health strategies. For example, evidence of HCV transmission clusters originating soon after displacement highlights the importance of implementing urgent preventive interventions in ongoing situations of forced displacement.
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Infecciones por VIH , Hepatitis C , Abuso de Sustancias por Vía Intravenosa , Humanos , Hepacivirus/genética , Ucrania/epidemiología , Estudios Transversales , Filogenia , Estudios Seroepidemiológicos , Teorema de Bayes , Infecciones por VIH/complicaciones , Abuso de Sustancias por Vía Intravenosa/complicaciones , Abuso de Sustancias por Vía Intravenosa/epidemiología , PrevalenciaRESUMEN
BACKGROUND: The essential role of copper in eukaryotic cellular physiology is known, but has not been recognized as important in the context of influenza A virus infection. In this study, we investigated the effect of cellular copper on influenza A virus replication. METHODS: Influenza A/WSN/33 (H1N1) virus growth and macromolecule syntheses were assessed in cultured human lung cells (A549) where the copper concentration of the growth medium was modified, or expression of host genes involved in copper homeostasis was targeted by RNA interference. RESULTS: Exogenously increasing copper concentration, or chelating copper, resulted in moderate defects in viral growth. Nucleoprotein (NP) localization, neuraminidase activity assays and transmission electron microscopy did not reveal significant defects in virion assembly, morphology or release under these conditions. However, RNAi knockdown of the high-affinity copper importer CTR1 resulted in significant viral growth defects (7.3-fold reduced titer at 24 hours post-infection, p = 0.04). Knockdown of CTR1 or the trans-Golgi copper transporter ATP7A significantly reduced polymerase activity in a minigenome assay. Both copper transporters were required for authentic viral RNA synthesis and NP and matrix (M1) protein accumulation in the infected cell. CONCLUSIONS: These results demonstrate that intracellular copper regulates the influenza virus life cycle, with potentially distinct mechanisms in specific cellular compartments. These observations provide a new avenue for drug development and studies of influenza virus pathogenesis.
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Adenosina Trifosfatasas/metabolismo , Proteínas de Transporte de Catión/metabolismo , Cobre/metabolismo , Células Epiteliales/virología , Interacciones Huésped-Patógeno , Subtipo H1N1 del Virus de la Influenza A/fisiología , Replicación Viral , Línea Celular , Transportador de Cobre 1 , ATPasas Transportadoras de Cobre , Medios de Cultivo/química , Células Epiteliales/metabolismo , HumanosRESUMEN
Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are etiologically associated with several types of human malignancies. However, as these two human gammaherpesviruses do not replicate efficiently in cultured cells, the morphogenesis of gammaherpesvirus virions is poorly understood. Murine gammaherpesvirus 68 (MHV-68) provides a tractable model to define common, conserved features of gammaherpesvirus biology. ORF52 of MHV-68 is conserved among gammaherpesviruses. We have previously shown that this tegument protein is essential for the envelopment and egress of viral particles and solved the crystal structure of ORF52 dimers. To more closely examine its role in virion maturation, we performed immunoelectron microscopy of MHV-68-infected cells and found that ORF52 localized to both mature, extracellular virions and immature viral particles in the cytoplasm. ORF52 consists of three α-helices followed by one ß-strand. To understand the structural requirements for ORF52 function, we constructed mutants of ORF52 and examined their ability to complement an ORF52-null MHV-68 virus. Mutations in conserved residues in the N-terminal α1-helix and C terminus, or deletion of the α2-helix, resulted in a loss-of-function phenotype. Furthermore, the α1-helix was crucial for the predominantly punctate cytoplasmic localization of ORF52, while the α2-helix was a key domain for ORF52 dimerization. Immunoprecipitation experiments demonstrated that ORF52 interacts with another MHV-68 tegument protein, ORF42; however, a single point mutation in R95 in the C terminus of ORF52 led to the loss of this interaction. Moreover, the homologues of MHV-68 ORF52 in Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus complement the defect in ORF52-null MHV-68 and interact with MHV-68 ORF52. Taken together, these data uncover the relationship between the α-helical structure and the molecular basis for ORF52 function. This is the first structure-based functional domain mapping study for an essential gammaherpesvirus tegument protein.
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Gammaherpesvirinae/metabolismo , Proteínas Virales/metabolismo , Virión/metabolismo , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Línea Celular , Cricetinae , Cartilla de ADN , Gammaherpesvirinae/fisiología , Humanos , Datos de Secuencia Molecular , Sistemas de Lectura Abierta , Mutación Puntual , Unión Proteica , Reacción en Cadena en Tiempo Real de la Polimerasa , Homología de Secuencia de Aminoácido , Proteínas Virales/química , Proteínas Virales/genética , Replicación ViralRESUMEN
From 2011-2018, we conducted surveillance in marine mammals along the California coast for influenza A virus (IAV), frequently detecting anti-influenza antibodies and intermittently detecting IAV. In spring 2019, this pattern changed. Despite no change in surveillance intensity, we detected IAV RNA in 10 samples in March and April, mostly in nasal and rectal swabs from northern elephant seals (Mirounga angustirostris). Although virus isolation was unsuccessful, IAV sequenced from one northern elephant seal nasal swab showed close genetic identity with pandemic H1N1 IAV subclade 6B.1A.1 that was concurrently circulating in humans in the 2018/19 influenza season. This represents the first report of human A(H1N1)pdm09 IAV in northern elephant seals since 2010, suggesting IAV continues to spill over from humans to pinnipeds.
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Caniformia , Subtipo H1N1 del Virus de la Influenza A , Virus de la Influenza A , Gripe Humana , Phocidae , Animales , Humanos , Gripe Humana/epidemiología , California/epidemiologíaRESUMEN
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.
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COVID-19 , Dermatitis , Humanos , Alaska/epidemiología , SARS-CoV-2/genética , COVID-19/epidemiologíaRESUMEN
Internally displaced persons are often excluded from HIV molecular epidemiology surveillance due to structural, behavioral, and social barriers in access to treatment. We test a field-based molecular epidemiology framework to study HIV transmission dynamics in a hard-to-reach and highly stigmatized group, internally displaced people who inject drugs (IDPWIDs). We inform the framework by Nanopore generated HIV pol sequences and IDPWID migration history. In June-September 2020, we recruited 164 IDPWID in Odesa, Ukraine, and obtained 34 HIV sequences from HIV-infected participants. We aligned them to publicly available sequences (N = 359) from Odesa and IDPWID regions of origin and identified 7 phylogenetic clusters with at least 1 IDPWID. Using times to the most recent common ancestors of the identified clusters and times of IDPWID relocation to Odesa, we infer potential post-displacement transmission window when infections likely to happen to be between 10 and 21 months, not exceeding 4 years. Phylogeographic analysis of the sequence data shows that local people in Odesa disproportionally transmit HIV to the IDPWID community. Rapid transmissions post-displacement in the IDPWID community might be associated with slow progression along the HIV continuum of care: only 63% of IDPWID were aware of their status, 40% of those were in antiviral treatment, and 43% of those were virally suppressed. Such HIV molecular epidemiology investigations are feasible in transient and hard-to-reach communities and can help indicate best times for HIV preventive interventions. Our findings highlight the need to rapidly integrate Ukrainian IDPWID into prevention and treatment services following the dramatic escalation of the war in 2022.
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African swine fever (ASF) is a viral disease, endemic to Africa, that causes high mortality when introduced into domestic pig populations. Since the emergence of p72-genotype II African swine fever virus (ASFV) in Georgia in 2007, an ASF epidemic has been spreading across Europe and many countries in Asia. The epidemic first reached Ukraine in 2012. To better understand the dynamics of spread of ASF in Ukraine, we analyzed spatial and temporal outbreak data reported in Ukraine between 2012 and mid-2023. The highest numbers of outbreaks were reported in 2017 (N = 163) and 2018 (N = 145), with overall peak numbers of ASF outbreaks reported in August (domestic pigs) and January (wild boars). While cases were reported from most of Ukraine, we found a directional spread from the eastern and northern borders towards the western and southern regions of Ukraine. Many of the early outbreaks (before 2016) were adjacent to the border, which is again true for more recent outbreaks in wild boar, but not for recent outbreaks in domestic pigs. Outbreaks prior to 2016 also occurred predominantly in areas with a below average domestic pig density. This new analysis suggests that wild boars may have played an important role in the introduction and early spread of ASF in Ukraine. However, in later years, the dynamic suggests human activity as the predominant driver of spread and a separation of ASF epizootics between domestic pigs and in wild boars. The decline in outbreaks since 2019 suggests that the implemented mitigation strategies are effective, even though long-term control or eradication remain challenging and will require continued intensive surveillance of ASF outbreak patterns.
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Emerging RNA virus infections are a growing concern among domestic poultry industries due to the severe impact they can have on flock health and economic livelihoods. Avian paramyxoviruses (APMV; avulaviruses, AaV) are pathogenic, negative-sense RNA viruses that cause serious infections in the respiratory and central nervous systems. APMV was detected in multiple avian species during the 2017 wild bird migration season in Ukraine and studied using PCR, virus isolation, and sequencing. Of 4090 wild bird samples collected, mostly from southern Ukraine, eleven isolates were grown in ovo and identified for APMV serotype by hemagglutinin inhibition test as: APMV-1, APMV-4, APMV-6, and APMV-7. To build One Health's capacity to characterize APMV virulence and analyze the potential risks of spillover to immunologically naïve populations, we sequenced virus genomes in veterinary research labs in Ukraine using a nanopore (MinION) platform. RNA was extracted and amplified using a multiplex tiling primer approach to specifically capture full-length APMV-1 (n = 5) and APMV-6 (n = 2) genomes at high read depth. All APMV-1 and APMV-6 fusion (F) proteins possessed a monobasic cleavage site, suggesting these APMVs were likely low virulence, annually circulating strains. Utilization of this low-cost method will identify gaps in viral evolution and circulation in this understudied but important critical region for Eurasia.
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Avulavirus , Virus de la Enfermedad de Newcastle , Animales , Ucrania/epidemiología , Filogenia , Animales Salvajes , AvesRESUMEN
The complete genome of Erysipelothrix sp. strain Poltava, isolated from fatal acute septic erysipelas of swine in Ukraine, was assembled using Nanopore sequences. One circular chromosome of 1,794,858 bp (N50, 1,794,858 bp) encodes 16 putative antibiotic resistance genes and secreted virulence factors, highlighting the risk of cross-species livestock and human infection.
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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.
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COVID-19 , Secuenciación de Nanoporos , COVID-19/epidemiología , Humanos , SARS-CoV-2/genética , Ucrania/epidemiologíaRESUMEN
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.
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COVID-19 , Virus , Calefacción , Humanos , SARS-CoV-2 , Ventiladores MecánicosRESUMEN
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 2022-02-27, 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 Alaskaâ™s unique dynamics influence the emergence of SARS-CoV-2 variants.
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Porcine circovirus type 2 (PCV2) is responsible for a number of porcine circovirus-associated diseases (PCVAD) that can severely impact domestic pig herds. For a non-enveloped virus with a small genome (1.7 kb ssDNA), PCV2 is remarkably diverse, with eight genotypes (a-h). New genotypes of PCV2 can spread through the migration of wild boar, which are thought to infect domestic pigs and spread further through the domestic pig trade. Despite a large swine population, the diversity of PCV2 genotypes in Ukraine has been under-sampled, with few PCV2 genome sequences reported in the past decade. To gain a deeper understanding of PCV2 genotype diversity in Ukraine, samples of blood serum were collected from wild boars (n = 107) that were hunted in Ukraine during the November-December 2012 hunting season. We found 34/107 (31.8%) prevalence of PCV2 by diagnostic PCR. For domestic pigs, liver samples (n = 16) were collected from a commercial market near Kharkiv in 2019, of which 6 out of 16 (37%) samples were positive for PCV2. We sequenced the genotyping locus ORF2, a gene encoding the PCV2 viral capsid (Cap), for 11 wild boar and six domestic pig samples in Ukraine using an Oxford Nanopore MinION device. Of 17 samples with resolved genotypes, the PCV2 genotype b was the most common in wild boar samples (10 out of 11, 91%), while the domestic pigs were infected with genotypes b and d. We also detected genotype b/d and b/a co-infections in wild boars and domestic pigs, respectively, and for the first time in Ukraine we detected genotype f in a wild boar from Poltava. Building a maximum-likelihood phylogeny, we identified a sublineage of PCV2 genotype b infections in both wild and domestic swine, suggesting a possible epizootic cluster and an ecological interaction between wild boar and domestic pig populations in northeastern Ukraine.
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Circovirus , Enfermedades de los Porcinos , Animales , Circovirus/genética , Variación Genética , Sus scrofa , Porcinos , Enfermedades de los Porcinos/epidemiología , Ucrania/epidemiologíaRESUMEN
Teschen disease is an acute fatal enterovirus encephalomyelitis of pigs, characterized by a range of central nervous system disorders. The cause of porcine enterovirus encephalomyelitis is the picornavirus porcine teschovirus-1 (PTV-1). There are at least 12 disctinct serotypes of PTVs, where PTV-2 to PTV-12 serogroups are associated with other forms of disease (Talfan disease or poliomyelitis suum) or benign enzootic paresis. Combined, PTVs have been found to have a high seroprevalence, up to 65%, in healthy pig populations in Europe. PTVs have also been detected in wild boar, including the divergent PTV-13 serogroup; wild suids may represent a sylvatic reservoir capable of carrying the virus long distances. In Ukraine, Teschen disease is widespread and causes lethal disease in domestic pigs. To understand temporal and geographical distribution of Teschen disease virus (PTV-1) in wild boar in Ukraine (2001-2013), we analyzed seroprevalence of 6840 blood serum samples from hunted suids using a virus microneutralization assay. A total of 1364 samples (19.9%) were seropositive, with average antibody titer ratios 5.89 ± 0.03 log2 (range 5-12 log2). Teschen seroprevalence was temporally and geographically concentrated in the northern and western regions of Ukraine, corresponding to forested regions (polissya) and overlapping with wild boar populations and habitats, suggesting endemicity in wild boar. The virus sporadically emerged in central, southern, and eastern forested regions, suggesting long-distance movement of infected wild suids. Thus, wild boar should be monitored for potential transboundary spread in forested and mountain regions and spillover of PTVs to domestic swine populations.
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Encefalomielitis Enzoótica Porcina , Enfermedades de los Porcinos , Animales , Estudios Seroepidemiológicos , Sus scrofa , Porcinos , Enfermedades de los Porcinos/epidemiología , Ucrania/epidemiologíaRESUMEN
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.
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , Alaska/epidemiología , COVID-19/epidemiología , Sustitución de AminoácidosRESUMEN
Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.
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Conflictos Armados , Ciencia , Humanos , UcraniaRESUMEN
Human type A influenza viruses A(H1N1)pdm09 have caused seasonal epidemics of influenza since the 2009-2010 pandemic. A(H1N1)pdm09 viruses had a leading role in the severe epidemic season of 2015/16 in the Northern Hemisphere and caused a high incidence of acute respiratory infection (ARI) in Ukraine. Serious complications of influenza-associated severe ARI (SARI) were observed in the very young and individuals at increased risk, and 391 fatal cases occurred in the 2015/16 epidemic season. We analyzed the genetic changes in the genomes of A(H1N1)pdm09 influenza viruses isolated from SARI cases in Ukraine during the 2015/16 season. The viral hemagglutinin (HA) fell in H1 group 6B.1 for all but four isolates, with known mutations affecting glycosylation, the Sa antigenic site (S162N in all 6B.1 isolates), or virulence (D222G/N in two isolates). Other mutations occurred in antigenic site Ca (A141P and S236P), and a subgroup of four strains were in group 6B.2, with potential alterations to antigenicity in A(H1N1)pdm09 viruses circulating in 2015/16 in Ukraine. A cluster of Ukrainian isolates exhibited novel D2E and N48S mutations in the RNA binding domain, and E125D in the effector domain, of immune evasion nonstructural protein 1 (NS1). The diverse spectrum of amino-acid substitutions in HA, NS1, and other viral proteins including nucleoprotein (NP) and the polymerase complex suggested the concurrent circulation of multiple lineages of A(H1N1)pdm09 influenza viruses in the human population in Ukraine, a country with low vaccination coverage, complicating public health measures against influenza.
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Subtipo H1N1 del Virus de la Influenza A/genética , Gripe Humana/virología , Infecciones del Sistema Respiratorio/virología , Sustitución de Aminoácidos , Variación Genética , Genotipo , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética , Humanos , Subtipo H1N1 del Virus de la Influenza A/clasificación , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Gripe Humana/epidemiología , Filogenia , Infecciones del Sistema Respiratorio/epidemiología , Estaciones del Año , Ucrania/epidemiología , Proteínas no Estructurales Virales/genéticaRESUMEN
The complete genome sequence of Brucella abortus 68, isolated from an aborted sheep fetus in Luhansk, Ukraine, was assembled using Nanopore sequences. Two circular chromosomes totaling 3,281,317 bp (N 50, 2,124,943 bp) comprised the complete genome sequence. The strain encodes the fosfomycin antibiotic resistance gene fosX, highlighting the risk of cross-species livestock and human infection.
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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.