Molecular Footprint of Parasite Co-introduction with Nile Tilapia in the Congo Basin

Nile tilapia, one of the most popular aquaculture species worldwide, has been introduced into the Congo Basin several times. In previous morphological studies, we showed that some of the monogenean gill parasites were co-introduced with Nile tilapia and some spilled over to native Congolese cichlids. In this study, we investigated the co-introduced monogeneans of Nile tilapia genetically from three major parts of the Congo Basin; Upper, Middle and Lower Congo. We generated sequences of Congolese native and introduced monogeneans from native and introduced tilapias and evaluate their position in a phylogeny. Additionally, we generated sequences of the same species of monogeneans co-introduced with Nile tilapia in Madagascar and of a native population of Nile tilapia from Burundi. Our results confirm the co-introductions in the Congo. We found that co-introduced parasites are less genetically diverse than native ones, and that there was no geographical pattern between introduced populations. Furthermore, our COI haplotype networks suggest multiple introduction events of Nile tilapia into the Congo Basin. Additionally, we tested the barcoding gap and the performance of mitochondrial COI and nuclear ribosomal ITS-1, 28S and 18S markers. We found a significant intra/interspecific barcoding gap of 15% for COI, but none for the other markers. Our molecular results reveal that Cichlidogyrus halli, C. papernastrema, C. tiberianus, C. cirratus and C. zambezensis are in need of taxonomic revision.

Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

COVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating SARS-CoV-2 strains in India will enable the scientific community to understand the emergence of new variants and their impact on human health. The first case of COVID-19 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of cases within next three months. More than 5000 COVID-19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh were analyzed during the nation -wide lockdown and unlock period. A total of 136 cases were found positive over a span of three months that included virus introduction to the region and its further spread. Whole genome sequences employing Oxford nanopore technology were generated for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh state of India. This period witnessed index cases with multiple travel histories responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were identified. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades including A2a, A4 and B. The cluster-wise segregation was observed, suggesting multiple introduction links and subsequent evolution of virus in the region. This is the first comprehensive whole genome sequence analysis from central India, which revealed the emergence and evolution of SARS-CoV-2 during thenation-wide lockdown and unlock.

Genetic diversity in Colocasia esculenta and Xanthosoma mafaffa in Togo, West Africa

Taro and new cocoyam are root and leaf crops commonly grown in tropical to warm temperate regions. In Togo, they are neglected and underutilised. Here we report the genetic diversity of 26 accessions of taro and 101 accessions of new cocoyam. Analysis of simple sequence repeats revealed low polymorphic information content of 0.43 and 0.25 in taro and new cocoyam, respectively. PCA scatterplots and Neighbour Joining dendrograms based on the SSR data clustered accessions into groups that more-or-less correspond to morphological diversity in both species. AMOVA within and between morphological groups revealed greater variances within groups than between. This indicates weak genetic differentiation between morphological groups, particularly for taro. Genetic diversity was greater among taro cultivars. Taro has a longer history of introduction and dispersal in Africa, and has had more opportunity for multiple introduction and local cultivar development. Different strategies are suggested for future development of these crops in Togo and Africa. For taro, further studies of existing diversity and recent experimental introduction, has spread widely in Africa with little genetic diversity. For this crop, international collaboration is needed to clarify taxonomy, and to introduced further cultivars for evaluation under local conditions in Africa.

Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak

Romania officially declared its first Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) case on February 26, 2020. The first and largest coronavirus disease 2019 (COVID-19) outbreak in Romania was recorded in Suceava, North-East region of the country, and originated at the Suceava regional county hospital. Following sheltering-in-place measures, infection rates decreased, only to rise again after relaxation of measures. This study describes the spread of SARS-CoV-2 in Suceava and other parts of Romania and analyses the mutations and their association with clinical manifestation of the disease during the period of COVID-19 outbreak. Sixty-two samples were sequenced via high-throughput platform and screened for variants. For selected mutations, putative biological significance was assessed, and their effects on disease severity. Phylogenetic analysis was conducted on Romanian genomes (n = 112) and on sequences originating from Europe, United Kingdom, Africa, Asia, South, and North America (n = 876). The results indicated multiple introduction events for SARS-CoV-2 in Suceava, mainly from Italy, Spain, United Kingdom, and Russia although some sequences were also related to those from the Czechia, Belgium, and France. Most Suceava genomes contained mutations common to European lineages, such as A20268G, however, approximately 10% of samples were missing such mutations, indicating a possible different arrival route. While overall genome regions ORF1ab, S, and ORF7 were subject to most mutations, several recurring mutations such as A105V were identified, and these were mainly present in severe forms of the disease. Non-synonymous mutations, such as T987N (Thr987Asn in NSP3a domain), associated with changes in a protein responsible for decreasing viral tethering in human host were also present. Patients with diabetes and hypertension exhibited higher risk ratios (RR) of acquiring severe forms of the disease and these were mainly related to A105V mutation. This study identified the arrival routes of SARS-CoV-2 in Romania and revealed potential associations between the SARS-CoV-2 genomic organization circulating in the country and the clinical manifestation of COVID-19 disease.

Population structure of Pyrenophora teres f. teres barley pathogens from different continents

Net-form net blotch disease caused by Pyrenophora teres f. teres (Ptt) results in significant yield losses to barley industries. Up-to-date knowledge of the genetic diversity and structure of pathogen populations is critical for better understanding the disease epidemiology and unravelling pathogen survival and dispersal mechanisms. Thus, this study investigated long distance dispersal and adaptation by analysing the genetic structure of 250 Ptt isolates collected from Australia, Canada, Hungary and Republic of South Africa (RSA), and historical isolates from Canada, Denmark, Japan and Sweden. The population genetic structure detected by discriminant analysis of principal component, using 5890 Diversity Arrays Technology (DArT) markers, revealed the presence of four clusters. Two of these contained isolates from all regions, and all isolates from RSA were grouped in these two. Australia and Hungary showed three clusters each. One of the Australian clusters contained only Australian isolates. One of the Hungarian clusters contained only Hungarian isolates and one Danish isolate. STRUCTURE analysis indicated that some isolates from Australia and Hungary shared recent ancestry with RSA, Canada and historical isolates and were thus admixed. Subdivisions of the Neighbor-joining network indicated that isolates from distinct countries were closely related, suggesting multiple introduction events conferred genetic heterogeneity in these countries. Through a Neighbor-joining analysis and amplification with form-specific DNA markers two hybrid isolates, CBS 281.31 from Japan and H-919 from Hungary collected in 1931 and 2018, respectively, were detected. These results provide a foundation for exploring improved management of disease incursions and pathogen control through strategic deployment of resistances.

Spread beyond the border: Small Scale genetic structure of the introduced Banggai cardinalfish (Pterapogon kauderni) population in the Bali Strait

The living marine aquarium trade has been known to mediate various aquatic invaders to spread and established a new population outside of their natural home range. In most cases, the introduce species cause a cascaded effect which harm the native species and their ecosystem. The successful of the invasion event often related to the genetic properties of the introduced species. Therefore, using a molecular approach based on a mitochondrial DNA marker, the present work aimed to evaluate the population genetic structure of the introduced P. kauderni population in Bali Strait. Samples were collected from four sites in Gilimanuk Bay, Bali Strait. Our results showed a high haplotype diversity and low nucleotide diversity that might be a signal of a bottleneck. Overall, we found five haplotypes comprising two unique haplotypes and three shared haplotypes. Genetic structure was detected in some localities, which indicates Pterapogon kauderni might originated from various genetically distinct populations. However, we could not conclusively determine the observed patterns of the genetic structure within each site. These patterns are likely related to the multiple introduction event of P. kauderni in Bali Strait. Additional samples from both side (introduced and native habitat) combined with more rapidly evolving markers may describe the structure more clearly.

Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from coronavirus disease 2019 (COVID-19) positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe, Asia, Africa, Australia and North America. The phylogenetic analysis revealed that the sequence of the sample of the first local patient collected on 10 March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19 March also clustered in the same group with the samples collected in March and April from Belgium, France, India and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16 March clustered with England and the sample collected on 30 March showed the highest genetic divergence to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and their application in tracing possible exposure in disease transmission during the pandemic.

Emerging SARS-CoV-2 diversity revealed by rapid whole genome sequence typing

BackgroundDiscrete classification of SARS-CoV-2 viral genotypes can identify emerging strains and detect geographic spread, viral diversity, and transmission events.MethodsWe developed a tool (GNUVID) that integrates whole genome multilocus sequence typing and a supervised machine learning random forest-based classifier. We used GNUVID to assign sequence type (ST) profiles to each of 69,686 SARS-CoV-2 complete, high-quality genomes available from GISAID as of October 20th 2020. STs were then clustered into clonal complexes (CCs), and then used to train a machine learning classifier. We used this tool to detect potential introduction and exportation events, and to estimate effective viral diversity across locations and over time in 16 US states.ResultsGNUVID is a scalable tool for viral genotype classification (available at https://github.com/ahmedmagds/GNUVID) that can be used to quickly process tens of thousands of genomes. Our genotyping ST/CC analysis uncovered dynamic local changes in ST/CC prevalence and diversity with multiple replacement events in different states. We detected an average of 20.6 putative introductions and 7.5 exportations for each state. Effective viral diversity dropped in all states as shelter-in-place travel-restrictions went into effect and increased as restrictions were lifted. Interestingly, our analysis showed correlation between effective diversity and the date that state-wide mask mandates were imposed.ConclusionsOur classification tool uncovered multiple introduction and exportation events, as well as waves of expansion and replacement of SARS-CoV-2 genotypes in different states. Combined with future genomic sampling the GNUVID system could be used to track circulating viral diversity and identify emerging clones and hotspots.