Independent Introductions Research Articles

A new cluster of West Nile virus lineage 1 isolated from a northern goshawk in Spain

West Nile Virus (WNV; family Flaviviridae, genus flavivirus) is a zoonotic arbovirus worldwide spread. Its genetic diversity has allowed the definition of at least seven lineages, being lineages 1 and 2 the most widely distributed. Western Mediterranean region has been affected by WNV since decades. In Spain, WNV is actively circulating, provoking annual outbreaks in birds, horses and lately in humans. Lineage 1 is responsible for outbreaks that occurred in central and southern regions, while lineage 2 has been recently described in wild birds in north-eastern part of the country. During 2017 season, a disease outbreak in captive raptors was reported in southern Spain and WNV was isolated from a dead northern goshawk. Full genome sequencing was followed by phylogenetic analyses and analyses of the amino acidic substitutions. This strain, named Spain/2017/NG-b, highly differs from those which have been circulating both in Spain and in the neighbouring Mediterranean countries, constituting a new distinct group, tentatively classified in a newly defined cluster 7 within the WNV clade 1a, supporting a new, independent introduction of the virus in the Western Mediterranean region from an unknown origin. Besides, circumstantial evidence indicates that this emerging WNV strain could be behind the subsequent outbreak occurred nearby in horses. Overall, the reinforcement of surveillance programs, especially in wild birds, is essential to early detect the circulation of WNV and other related flaviviruses that could cause outbreaks in wild or domestic birds, equine and human populations.

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil

The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all alpha VOC strains obtained between February and August 2021 from the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants. The performed phylogenetic analysis showed that most of the alpha VOC genomes were interspersed with viral strains sampled from different Brazilian states and other countries suggesting that multiple independent Alpha VOC introductions from Brazil and overseas have occurred in the São Paulo State over time. Nevertheless, large monophyletic clusters were also observed especially from the Central-West part of the São Paulo State (the city of Bauru) and the metropolitan region of the São Paulo city. Our results highlight the Alpha VOC molecular epidemiology in the São Paulo state and reinforce the need for continued genomic surveillance strategies for the real-time monitoring of potential emerging SARS-CoV-2 variants during the ever-growing vaccination process.

Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak

SummaryBackgroundA characteristic feature of SARS-CoV-2 is its ability to transmit from pre- or asymptomatic patients, complicating the tracing of infection pathways and causing outbreaks. Despite several reports that whole genome sequencing (WGS) and haplotype networks are useful for epidemiologic analysis, little is known about their use in nosocomial infections.AimWe aimed to demonstrate the advantages of genetic epidemiology in identifying the link in nosocomial infection by comparing single nucleotide variations (SNVs) of isolates from patients associated with an outbreak in Showa University Hospital.MethodsWe used specimens from 32 patients in whom COVID-19 had been diagnosed using clinical reverse transcription-polymerase chain reaction tests. RNA of SARS-CoV-2 from specimens was reverse-transcribed and analysed using WGS. SNVs were extracted and used for lineage determination, phylogenetic tree analysis, and median-joining analysis.FindingsThe lineage of SARS-CoV-2 that was associated with outbreak in Showa University Hospital was B.1.1.214, which was consistent with that found in the Kanto metropolitan area during the same period. Consistent with canonical epidemiological observations, haplotype network analysis was successful for the classification of patients. Additionally, phylogenetic tree analysis revealed three independent introductions of the virus into the hospital during the outbreak. Further, median-joining analysis indicated that four patients were directly infected by any of the others in the same cluster.ConclusionGenetic epidemiology with WGS and haplotype networks is useful for tracing transmission and optimizing prevention strategies in nosocomial outbreaks.

Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave

The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5’UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.

Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom\u2019s first national lockdown

Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.

How do the physiological traits of a lizard change during its invasion of an oceanic island?

Physiology is crucial for the survival of invasive species in new environments. Yet, new climatic conditions and the limited genetic variation found within many invasive populations may influence physiological responses to new environmental conditions. Here, we studied the case of the delicate skinks (Lampropholis delicata) invading Lord Howe Island (LHI), Australia. On LHI, the climate is different from the mainland source of the skinks, and independent introduction events generated invasive populations with distinct genetic backgrounds. To understand how climate and genetic background may shape physiological responses along biological invasions, we compared the physiological traits of a source and two invasive (single-haplotype and multi-haplotype) populations of the delicate skink. For each population, we quantified physiological traits related to metabolism, sprint speed, and thermal physiology. We found that, for most physiological traits analysed, population history did not influence the ecophysiology of delicate skinks. However, invasive populations showed higher maximum speed than the source population, which indicates that locomotor performance might be a trait under selection during biological invasions. As well, the invasive population with a single haplotype was less cold-tolerant than the multi-haplotype and source populations. Our results suggestthat limited genetic variability and climate may influence physiological responses of invasive organisms in novel environments. Incorporating the interplay between genetic and physiological responses into models predicting species invasions can result in more accurate understanding of the potential habitats those species can occupy.

Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay.

We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARS-CoV-2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of the SARS-CoV-2 P.1 VOC in Uruguay.

Using Background Sequencing Data to Anticipate DENV-1 Circulation in the Lao PDR.

Since its first detection in 1979, dengue fever has been considered a major public health issue in the Lao People’s Democratic Republic (PDR). Dengue virus (DENV) serotype 1 was the cause of an epidemic in 2010–2011. Between 2012 and 2020, major outbreaks due successively to DENV-3, DENV-4 and recently DENV-2 have been recorded. However, DENV-1 still co-circulated in the country over this period. Here, we summarize epidemiological and molecular data of DENV-1 between 2016 and 2020 in the Lao PDR. Our data highlight the continuous circulation of DENV-1 in the country at levels ranging from 16% to 22% among serotyping tests. In addition, the phylogenetic analysis has revealed the circulation of DENV-1 genotype I at least since 2008 with a co-circulation of different clusters. Sequence data support independent DENV-1 introductions in the Lao PDR correlated with an active circulation of this serotype at the regional level in Southeast Asia. The maintenance of DENV-1 circulation over the last ten years supports a low level of immunity against this serotype within the Lao population. Thereby, the risk of a DENV-1 epidemic cannot be ruled out in the future, and this emphasizes the importance of maintaining an integrated surveillance approach to prevent major outbreaks.

A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Qu\xe9bec, Canada

BackgroundQuébec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province.MethodsUsing genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus.ResultsConservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and “snowbird” destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7–12 led to the largest transmission lineages of the first wave (accounting for 52–75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order.ConclusionsCombined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020.

BackgroundIn the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data.AimWe applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata.MethodsWe investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission.ResultsWe identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions.ConclusionsEarly spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.

Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data

BackgroundAdvances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe.MethodsWe performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods.FindingsOf 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak.InterpretationInitial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies.FundingWHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.

Detection of Vehicle Smuggling by the Border Guard on the Podkarpackie Section of the Polish-Ukrainian Border in 2014-2020

The purpose of this article is to present the role of the Border Guard in detecting vehicle smuggling on the Podkarpackie section of the Polish-Ukrainian border in 2014-2020. Organized transfer of stolen cars from the European Union to the territory of the Commonwealth of Independent States and introduction of cars to the Polish customs territory excluding customs and tax duties is one of the most important threats to the security of Poland and the European Union. Uncontrolled smuggling of stolen vehicles is concentrated mainly in larger border crossing points, and the disclosed attempts show with considerable professionalism, specialization and organization of criminal groups, often with international connections.

Population genetic structure of raccoons as a consequence of multiple introductions and range expansion in the Boso Peninsula, Japan

The raccoon (Procyon lotor) is an invasive carnivore that invaded various areas of the world. Although controlling feral raccoon populations is important to reduce serious threats to local ecosystems, raccoons are not under rigid population control in Europe and Japan. We examined the D-loop and nuclear microsatellite regions to identify spatially explicit and feasible management units for effective population control and further range expansion retardation. Through the identification of five mitochondrial DNA haplotypes and three nuclear genetic groups, we identified at least three independent introductions, range expansion, and subsequent genetic admixture in the Boso Peninsula. The management unit considered that two were appropriate because two populations have already genetic exchange. Furthermore, when taking management, we think that it is important to monitor DNA at the same time as capture measures for feasible management. This makes it possible to determine whether there is a invasion that has a significant impact on population growth from out of the unit, and enables adaptive management.

Molecular analysis of an increase in trimethoprim/sulfamethoxazole-resistant MRSA reveals multiple introductions into a tertiary care hospital, Germany 2012-19.

Increasing spread of resistance could jeopardize the use of antifolates against MRSA infections. We compared the prevalence of phenotypic trimethoprim/sulfamethoxazole resistance in 20 534 clinical Staphylococcus aureus isolates (19 096 MSSA and 1438 MRSA) of non-redundant patients at Heidelberg University Hospital over 8 years and performed WGS on trimethoprim/sulfamethoxazole-resistant MRSA. From 2012 to 2019, trimethoprim/sulfamethoxazole resistance in MSSA (674/19 096; 3.5%) ranged between 1.5% and 7.2% and in MRSA (135/1438; 9.4%) between 0.5% and 20.2%, reaching a peak in 2016 and 2018, respectively (Ptrend < 0.001). Trimethoprim/sulfamethoxazole resistance was more likely in outpatients than inpatients (P = 0.005), younger patients (P < 0.001), skin and soft tissue infections (SSTIs) (MRSA only, P = 0.05), submissions from pulmonology (MRSA only, P = 0.001), the upper respiratory tract (MSSA only, P < 0.001) and general surgery (MSSA only, P = 0.001). WGS of 76 trimethoprim/sulfamethoxazole-resistant MRSA revealed that 59% belonged to major pandemic CA-MRSA clones (ST22, ST8, ST398, ST772, ST30), 47% harboured Panton-Valentine leucocidin (PVL), 97% SCCmec IV/V, 71% dfrG and 28% dfrA. SNP-based phylogeny of trimethoprim/sulfamethoxazole-resistant MRSA core genomes favoured independent introduction over clonal expansion as the source, most prominently of dfrA+ trimethoprim/sulfamethoxazole-resistant ST22 MRSA from the Gaza Strip. The presented results support that trimethoprim/sulfamethoxazole-resistant S. aureus, formerly associated with SSTI from outpatients and S. aureus in the (sub)tropics, is on the rise in the temperate zone, potentially due to migration. Closer monitoring of trimethoprim/sulfamethoxazole resistance in S. aureus is recommended to safeguard the effectiveness of antifolate compounds.

Shaming and Blaming

Shaming and Blaming Brian Manternach (bio) THE INDEPENDENT TEACHER INTRODUCTION Years ago, I attended a lecture given by a prominent voice pedagogue. During his presentation, he asked those of us in attendance to stand up and point to the lowest area in our bodies that we believe the diaphragm reaches during inhalation. I stood and pointed to my lower belly. Then he encouraged us to look around the room and check our answers. I noticed some people with answers similar to mine, others who were pointing to a higher area in their bodies, and a few who decided not to venture a guess. After some time passed, the presenter shook his head and chuckled. He asked us to sit down and proceeded to explain, in a tone that I heard as rife with condescension, the "physical impossibility" that the diaphragm could descend to the lower abdomen. It felt to me like those of us who were wrong were being scolded. I quickly wished I had been one of the people who had decided not to stake a claim on the issue. Nevertheless, the tone for the presentation was set and I kept my guesses to myself for the remainder of the talk. That day, I learned something new about the respiratory system that I have never forgotten. I also learned how it feels when you offer what you believe to be an educated assumption and are ridiculed for doing so. SHAMING I have thought about my experience in that presentation many times in the 15 years since it happened. Primarily, I wondered why I reacted so strongly and had such a visceral objection to that method of teaching. Am I just too sensitive? Does my reaction say more about my own insecurities than it does about the way this particular pedagogue delivers information? I understand the importance of acting on the best knowledge we have at any given time. I also understand that, since no one can know everything, we have to be OK with being wrong once in a while. This presentation certainly highlighted at least one anatomic fact that I did not know. Why was I not just grateful to have the new information? I started to gain some perspective on this experience as I began to explore the work of author and "shame researcher" Brené Brown. Brown, PhD, LMSW, is a research professor at the University of Houston Graduate College of Social Work, but is likely best known for her frequently viewed TED talks and for authoring multiple books that have reached number one on the New York Times bestseller list. Her popular work clearly has struck a chord in mainstream culture. [End Page 103] Brown defines shame as "the intensely painful feeling or experience of believing we are flawed and therefore unworthy of acceptance and belonging."1 When we experience shame, she says, we are steeped in the fear of being ridiculed or diminished. We are afraid that we have exposed or revealed a part of us that jeopardizes our connection to others.2 Looking back at that presentation, I wonder if the pedagogue intended to shame those in attendance. I wonder why he did not simply say, "It's a common misconception that the diaphragm descends into the lower abdomen when we inhale," which would have presented the information without publicly calling out those of us who did not yet know that. Is there justification for the tactic he chose? Brown addresses this question, describing that much of her own formal education emphasized the notion that "You CANNOT shame or belittle people into changing their behaviors."3 Through her research, however, she has come to amend that belief. Now she proposes that shame and humiliation can indeed be used to change behavior. But the problem she discovered is that those behavioral changes do not last. In addition, shame inflicts pain that has the potential to scar both the person using shame and the person being shamed.4 Brown acknowledges that some researchers believe that two types of shame exist: "healthy shame," which can serve as a motivator, and the more negative "toxic shame." Brown, however, disagrees with this concept, noting that her own research...

Collection, genotyping and virus elimination of cassava landraces from Tanzania and documentation of farmer knowledge.

Cassava (Manihot esculenta Crantz.) has been a vital staple and food security crop in Tanzania for several centuries, and it is likely that its resilience will play a key role in mitigating livelihood insecurities arising from climate change. The sector is dominated by smallholder farmers growing traditional landrace varieties. A recent surge in virus diseases and awareness in the commercial potential of cassava has prompted a drive to disseminate improved varieties in the country. These factors however also threaten the existence of landraces and associated farmer knowledge. It is important that the landraces are conserved and utilized as the adaptive gene complexes they harbor can drive breeding for improved varieties that meet agro-ecological adaptation as well as farmer and consumer needs, thereby improving adoption rates. Here we report on cassava germplasm collection missions and documentation of farmer knowledge in seven zones of Tanzania. A total of 277 unique landraces are identified through high-density genotyping. The large number of landraces is attributable to a mixed clonal/sexual reproductive system in which the soil seed bank and incorporation of seedlings plays an important role. A striking divergence in genetic relationships between the coastal regions and western regions is evident and explained by (i) independent introductions of cassava into the country, (ii) adaptation to prevailing agro-ecological conditions and (iii) farmer selections according to the intended use or market demands. The main uses of cassava with different product profiles are evident, including fresh consumption, flour production, dual purpose incorporating both these uses and longer-term food security. Each of these products have different trait requirements. Individual landraces were not widely distributed across the country with limited farmer-to-farmer diffusion with implications for seed systems.

Structure of African Populations of Pyricularia oryzae from Rice.

Rice blast, caused by the filamentous ascomycete Pyricularia oryzae, is one of the most devastating diseases of rice. Four genetic clusters were previously identified, and three have a large geographic distribution. Asia is the center of diversity and the origin of most migrations to other continents, and sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all P. oryzae populations on rice. Despite the importance of rice blast disease, little is known about the diversity and the population structure of the pathogen in Africa (including Madagascar). The present study was intended to describe the structure of African populations of P. oryzae and identify the relationship between African and worldwide genetic clusters. A set of 2,057 strains (937 African and 1,120 Madagascan strains) were genotyped with 12 simple sequence repeat markers to assess the diversity and the population structure of P. oryzae. Four genetic clusters were identified in Africa and Madagascar. All four clusters previously identified are present in Africa. Populations from West Africa, East Africa, and Madagascar are highly differentiated. The geographic structure is consistent with limited dispersion and with some migration events between neighboring countries. The two mating types are present in Africa with a dominance of Mat1.2, but no female-fertile strain was detected, supporting the absence of sexual reproduction on this continent. This study showed an unsuspected high level of genetic diversity of P. oryzae in Africa and suggested several independent introductions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

African swine fever: Why the situation in Germany is not comparable to that in the Czech Republic or Belgium.

After the first occurrence of African swine fever (ASF) in Germany in September 2020, control measures were implemented that resembled those taken in the Czech Republic and Belgium, the only two countries that succeeded in eliminating ASF from their territory so far in the current epidemic. In the present study, the epidemiological course of ASF in the first 6 months since introduction in these three countries is compared. Within 6 months, Germany experienced more cases than the Czech Republic and Belgium. The affected area in Germany, measured using minimal convex polygons, is much larger than the respective areas in the Czech Republic and in Belgium. All cases in the Czech Republic and in Belgium clustered in one single defined area, suggesting point-source introductions, whereas in Germany four distinct spatial clusters were observed, which indicates that multiple incursions had occurred along the border with Poland. While the overall course of the disease was comparable, when individual clusters were considered, the summarized data showed clear differences between the situation in Germany compared to that in the Czech Republic and Belgium. Germany experienced several independent introductions, caused by continuous infection pressure along the border to Poland, while the infection was only introduced on a single occasion each into the Czech Republic and Belgium. These differences may require appropriate adaptation of control measures, in particular concerning fencing along the border.

Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru.

Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To investigate early transmission events and the genomic diversity of SARS‐CoV‐2 isolates circulating in Peru in the early COVID‐19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community‐driven transmission of SARS‐CoV‐2 as suggested by clusters of related viruses found in patients living in different regions of Peru.

Genomic data support multiple introductions and explosive demographic expansions in a highly invasive aquatic insect.

The study of the genetic makeup and demographic fate of alien species is essential to understand their capacity to recover from founder effects, adapt to new environmental conditions and, ultimately, become invasive and potentially damaging. Here, we employ genomic data to gain insights into key demographic processes that might help to explain the extraordinarily successful invasion of the Western Mediterranean region by the North American boatman Trichocorixa verticalis (Hemiptera: Corixidae). Our analyses revealed the genetic distinctiveness of populations from the main areas comprising the invasive range and coalescent-based simulations supported that they originated from independent introductions events probably involving different source populations. Testing of alternative demographic models indicated that all populations experienced a strong bottleneck followed by a recent and instantaneous demographic expansion that restored a large portion (>30%) of their ancestral effective population sizes shortly after introductions took place (<60years ago). Considerable genetic admixture of some populations suggest that hypothetical barriers to dispersal (i.e., land and sea water) are permeable to gene flow and/or that they originated from introductions involving multiple lineages. This study demonstrates the repeated arrival of propagules with different origins and short time lags between arrival and establishment, emphasizing the extraordinary capacity of the species to recover from founder effects and genetically admix in invaded areas. This can explain the demonstrated capacity of this aquatic insect to spread and outcompete native species once it colonizes new suitable regions. Future genomic analyses of native range populations could help to infer the genetic makeup of introduced populations and track invasion routes.