Fabio Scarpa

Università degli Studi di Sassari | UNISS · Dipartimento di Medicina Veterinaria

Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental l...

Supported by the GISAID data, we discuss on the more or less probable increase in the number of COVID-19 cases in the very next future. Currently, all the sequenced case in Europe, USA and Asia refer to Omicron-related variants and recombinations. Accordingly, the increasing in the attention to the Covid situation is currently not justified by look...

Biological invasions are a major threat to the conservation of biodiversity, as invasive species affect native biota through competition, predation, pathogen introduction, habitat alteration, and hybridisation. The present study focuses on a southern pike population, Esox cisalpinus (Teleostei: Esocidae), that has been introduced outside the specie...

Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental l...

The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 has some additional spike mutations in some key antigenic sites, which confer further immune escape ability over other circulating lineages. In such a context, here, we perform a genome-based surve...

The genus Salariopsis (Blenniidae) comprises freshwater blenny fish that inhabits Mediterranean Sea, Black Sea, and north-east Atlantic areas. Three species were formally described to date: Salariopsis fluviatilis. S. economidisi, and S. atlantica. In this study, 103 individuals were collected from different Italian regions (Sardinia, Liguria, Pied...

Tracking SARS-CoV-2 variants along with vaccinations are fundamental for severe COVID-19 disease prevention. A study was performed that focused on 43 patients with the SARS-CoV-2 infection who were admitted to the Emergency Department. RT-PCR–positive nasopharyngeal samples were sequenced using the MiSeq II system for variant detection. The main re...

The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare specimens have been observed somehow resistant to the parasite, stretching th...

The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 carries out some additional spike mutations in some key antigenic site which confer it further immune escape ability over other circulating lineage. In such a context, here we performed a genome-ba...

Monkeypox is caused by a sylvatic, double-stranded DNA zoonotic virus. Since 1 January 2022, monkeypox cases have been reported to WHO from 106 Member States across six WHO regions, and as of 2 October 2022, a total of 68,900 confirmed cases, including 25 deaths, occurred. Here, by using a whole genome approach, we perform a genetic and phylodynami...

Simple Summary: Knowledge of genetic diversity is crucial to improve conservation plans for endangered species and ensure their long-term persistence. However, it may be difficult to accurately estimate genetic diversity when it is unfeasible to obtain sufficiently large sample sizes, which is often the case for marine endangered species. Here, we...

Due to the continuing evolution of SARS‐CoV‐2, the formation of new variants is not a novelty or a sporadic case, but it is a certainty that periodically recurs [1]. One of the most recent variant is represented by the subvariant BA.2.75, also known as Centaurus. In comparison to the BA.2 variant, BA.2.75 carries nine additional mutations in the se...

Malignant Catarrhal Fever is a globally distributed disease that is fatal to susceptible species such as cattle. Sheep represent the reservoir species, and the Mediterranean island of Sardinia, which hosts a large number of these animals, is one geographic area where virus can easily spread. The aim of our study was to investigate a case of Maligna...

Orf virus (ORFV) is distributed worldwide and is the causative agent of contagious ecthyma that mainly occurs in sheep and goats. This disease was reported for the first time at the end of 18th century in Europe but very little is currently known about the temporal and geographic origins of this virus. In the present study, the use of new Italian w...

Taenia saginata is a globally distributed tapeworm responsible for human taeniasis due to the ingestion of raw or undercooked beef. T. saginata is present in several Asian countries, including China, Thailand, Lao PDR, Cambodia, and Vietnam, but little is known about its genetic variation. Studying the tapeworm's phylogeographic patterns is crucial...

The ongoing discussion about the real origin of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) feeds acrimonious debates. Where did SARS-CoV-2 come from? Was SARS-CoV-2 transmitted in the wild from an animal to a person before exploding in Wuhan or was it an engineered virus escaped from a research or laboratory in Wuhan? Right no...

Genetic variation, evolution, and conservation are three strictly interconnected words, but none of them exist without the others, unless wanting to waive a complete and operational sense [...]

African swine fever virus (ASFV) is one of the pathogens of highest concern worldwide. Despite different virus lineages co-circulating in several areas, dual infections in the same animal have been rarely observed, suggesting that ASF superinfections are infrequent events. Here we present the first genome-wide detection and analysis of two intragen...

Recent research hypothesised that the Siculo-Tunisian Strait might fit, at least for some species, the picture of a genetic transitional zone instead of a sharp genetic break between the Western and Eastern Mediterranean basins. The present study aimed at using the common Octopus, Octopus vulgaris as an empirical test-case to evaluate this hypothes...

African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions of Africa, Europe and Asia, causing massive economi...

Leptospirosis is a zoonotic disease of global importance caused by a pathogenic group of bacteria belonging to the genus Leptospira. Here, we report four draft genome sequences of Leptospira interrogans serovar Pomona isolated in Sardinia (Italy) from four different species of mammals (i.e., dolphin, wild boar, bovine, and fox).

Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks re...

Citation: Sanna, D.; Azzena, I.; Scarpa, F.; Cossu, P.; Pira, A.; Gagliardi, F.; Casu, M. First Record of the Alien Species Procambarus virginalis Lyko, 2017 in Fresh Waters of Sardinia and Insight into Its Genetic Variability. Life 2021, 11, 606. Abstract: In the fresh waters of Sardinia (Italy), the non-indigenous crayfish species Procambarus cla...

During an epidemiological survey that aimed to discover the causes for the mass mortality of Pinna nobilis, a strain of Rhodococcus was found in a moribund individual. Here, we report its 7,037,134-bp draft genome sequence, which, after the annotation and genome survey, was identified as belonging to Rhodococcus qingshengii PN_19. T he fan mussel,...

Orf virus (ORFV) represents the causative agent of contagious ecthyma, clinically characterized by mild papular and pustular to severe proliferative lesions, mainly occurring in sheep and goats. In order to provide hints on the evolutionary history of this virus, we carried out a study aimed to assess the genetic variation of ORFV in Sardinia that...

Pinna nobilis is the largest bivalve of the Mediterranean Sea, where it represents a flagship species. As a possible consequence of several human disturbing activities, at the beginning of the ‘80s, populations of fan mussel started a severe demographic decline. To reverse this trend, P. nobilis was included in a regime of full protection which led...

Exploitation of fisheries and aquaculture practices are exposing marine fish populations to increasing genetic risks. Therefore, the integration of genetic information into fisheries and aquaculture management is becoming crucial to ensure species’ long-term persistence. The raising commercial value of grey mullet ( Mugil cephalus ) and its roe rep...

Leishmaniasis is a widespread, vector-borne parasitosis causing clinical manifestations in animals and in humans. In dogs, Canine Leishmaniasis has been reported in as much as 50 countries and the Mediterranean basin is known to be one of the most affected zones. Within these areas, the Island of Sardinia (Italy) has long been considered endemic fo...

I.A.); picossu@uniss.it (P.C.); gsesposito@uniss.it (G.E.); eantuofermo@uniss.it (E.A.); marcasu@uniss.it (M.C.) Abstract: The fan mussel, Pinna nobilis, represents the largest bivalve endemic to the Mediterranean Sea. Since 2016, dramatic mass mortality of this species has been observed in several areas. The first surveys suggested that Haplospori...

African swine fever virus (ASFV), the cause of a devastating disease affecting domestic and wild pigs, has been present in Sardinia since 1978. In the framework of the regional ASF eradication plan, 4484 illegal pigs were culled between December 2017 and February 2020. The highest disease prevalence was observed in the municipality with the highest...

This study provides updated information on the distribution of the phlebotomine sand fly species and their genetic characterization in Sardinia, a Mediterranean island where leishmaniasis is endemic. From April to November 2017, sand flies were trapped in five different capture sites using sticky traps and light traps as collection methods, operate...

The cryptic diversity in the polychaete Syllis gracilis Grube, 1840, in the Mediterranean Sea was examined with an integrative morpho‐molecular approach. Individuals of S. gracilis were collected at eleven Mediterranean localities to provide an insight into the role of brackish environments in inducing cryptic speciation. The examination of morphol...

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo–West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus...

Aquaculture finfish production based on floating cage technology has raised increasing concerns on the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapees likely represent an important issue in the gilthead sea bream,...

The genus Alpioniscus Racovitza, 1908 (Trichoniscidae) from Sardinia is revised. Three new cave-dwelling species are described: A.onnisi Taiti & Argano, sp. n. , A.stochi Taiti & Argano, sp. n. , and A.sideralis Taiti & Argano, sp. n. . The genus Utopioniscus Schmalfuss, 2005 is considered to be a junior synonym of Alpioniscus , after morphological...

Five new species of Monocelididae (Platyhelminthes, Proseriata) are described from Eastern Atlantic. Three new Archilina species came from the Canary Islands. Two of them have the cirrus provided with a stylet, cylindrical in Archilina regina sp. nov. and spike-like in Archilina imperatrix sp. nov. Both species lack a vaginal pore: ventrally to the...

Ruditapes decussatus (Linnaeus, 1758) (Veneridae) is an Atlanto-Mediterranean bivalve whose populations have experienced reductions and, in some instances, hybridisation with allochthonous R. philippinarum. Acquisition of additional genetic knowledge concerning the present R. decussatus populations is essential to address adequate conservation plan...

Two new species of Otoplana (Proseriata: Otoplanidae) from the Canary Islands are here described: Otoplana norenburgi sp. nov. and Otoplana didomenicoi sp. nov. These new species are distinguished from their congeners by unique features of the sclerotized structures of the copulatory organ, in particular of the aculeus, swollen proximally in O. nor...

Since the opening of the Suez Canal in 1869 the Mediterranean Sea has been affected by a gradually increasing influx of species of Erythraean origin, which significantly modified species composition and ecological interactions of entire communities. Most studies have focused on macrofaunal species. Nevertheless, given the sandy nature of its shores...

Representatives of the Meidiamidae and Otomesostomidae (Platyhelminthes: Proseriata) are seldom encountered, and the monophyly and phylogenetic relationships of these families have never been assessed on molecular basis. Here, we present the first exhaustive molecular study of Proseriata at the family level, including species belonging to the gener...

The survival of endangered and rare species with slow growth and low dispersal capabilities critically depends on the persistence of populations within marine protected areas (MPAs). The effectiveness of MPAs at maintaining the species evolutionary potential will depend on the occurrence of self-sustaining and viable populations, harboring sufficie...

Esox cisalpinus (Teleostea: Esocidae) (syn. Esox flaviae) is an Italian freshwater autochthonous fish, whose originary range is limited to the Northern and Central Italy. However, this species has historically been introduced in several areas of Southern Italy, mainly for recreational purposes. In this paper we report the first record of E. cisalpi...

The order Proseriata (Platyhelminthes) represents one of the most abundant soft-bodied meiofaunal groups. These minute interstitial organisms are characterized by a very simple morphology, which often hides the occurrence of cryptic species. Accordingly, molecular analyses are often needed to provide reliable taxonomic assessment and/or species ide...

In 2009 an influenza A epidemic caused by a swine origin H1N1strain, unusual in human hosts, has been described. The present research is aimed to perform the first phylogenetic investigation on the influenza virus A (H1N1) strains circulating in Montenegro, from 1(st) December 2009, when the first case of death due to H1N1 was confirmed, and the ep...

Given the pending biodiversity crisis, species delimitation is a critically important task in conservation biology, but its efficacy based on single lines of evidence has been questioned as it may not accurately reflect species limits and relationships. Hence, the use of multiple lines of evidence has been portrayed as a means to overcome identific...

The Mediterranean Lessepsian migrations excite the interest of biologists who are devoted to inferring the effects of selection on the genetic structure of immigrants. The bluespotted cornetfish Fistularia commersonii is an Indo-Pacific species that was first recorded in the Levantine cost of Mediterranean, and within a few years, it rapidly expand...

Patterns of genetic variation in marine species reflect the interplay of species-specific traits, oceanographic features, historical processes and selection. In the Atlantic–Mediterranean regions, Patella ulyssiponensis (Mollusca: Gastropoda) was previously used as a model to investigate these patterns. Our study gained insight into the genetic pat...

Geminate species are a powerful tool for calibrating the molecular clock in marine organisms, and their adoption is mandatory for soft-bodied taxa, which lack fossil records. The first attempt to calibrate the molecular clock in taxa belonging to meiofaunal microturbellaria (Platyhelminthes: Proseriata) based on geminate species is presented here....

Four new species of Otoplanidae (Platyhelminthes: Rhabditophora: Proseriata) with ranges restricted to the central Mediterranean are described. These species are characterized by the presence of a tubular copulatory stylet and by a bursa lacking an open connection to the atrium. Both characters are novel for the family Otoplanidae. The four species...

Here we report the first insight into the mitochondrial (Cytochrome c Oxidase subunit I - COI and Cytochrome b - Cyt b) genetic variation of the only Mediterranean cephalocarid Lightiella magdalenina. COI sequences provide a scenario of low intraspecific variability, while significant genetic divergence occurs between L. magdalenina and L. incisa....

Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries various human activities led to the regression of its populations. As a consequence of stringent protection policies (P. nobilis is included in Annex IV of the Habitat Directive and Annex II of the Barcelona Convention), demographic expansion to many sites is c...

Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insig...

COI-16S dataset: network analysis. Median-joining network showing the haplotypes relationships among Pinna nobilis populations. Small red plots on the nodes, labelled as “mv”, show median vectors, representing hypothetic connecting sequences, calculated with a maximum parsimony method. Haplotypes diverge each other for a single mutation except wher...

COI, COI-16S, 16S datasets: genetic divergence estimates. Sample sizes and genetic diversity estimates obtained for the mitochondrial regions analysed in Pinna nobilis. N: sample sizes; S: number of polymorphic sites; H: number of haplotypes; h: haplotype diversity; π: nucleotide diversity; d: mean of pairwise nucleotide differences. Populations ar...

COI dataset: Bayesian COI haplogroup frequencies. N: absolute frequency; %: relative frequency within Mediterranean populations of Pinna nobilis. Populations are labelled as in Table 1. (DOC)

COI dataset: network analysis. Median-joining network showing the haplotypes relationships among Pinna nobilis populations. Small red plots on the nodes, labelled as “mv”, show median vectors, representing hypothetic connecting sequences, calculated with a maximum parsimony method. Haplotypes diverge each other for a single mutation except where Ar...

COI dataset: pairwise ΦST values among sampling localities. Pairwise ΦST values between Pinna nobilis populations with at least five individuals. Significance was assessed by permutation test. Significant values after correction for multiple testing are reported in bold. Populations are labelled as in Table 1. (DOC)

COI-16S dataset: haplotype frequencies. Frequency distribution of mitochondrial haplotypes in 244 individuals from 29 populations of Pinna nobilis. N: absolute frequency; %: relative frequency within Mediterranean populations. Populations are labelled as in Table 1. (DOC)

16S dataset: haplotype frequencies. Frequency distribution of haplotypes in 251 individuals from 29 populations of Pinna nobilis. N: absolute frequency; %: relative frequency within Mediterranean populations. Populations are labelled as in Table 1. (DOC)

COI-16S dataset: Bayesian COI-16S mitochondrial region haplogroup frequencies. N: absolute frequency; %: relative frequency within Mediterranean populations of Pinna nobilis. Populations are labelled as in Table 1. (DOC)

COI-16S dataset: pairwise ΦST values among samples localities. Pairwise ΦST values between Pinna nobilis populations with at least five individuals. Significance was assessed by permutation test. Significant values after correction for multiple testing are reported in bold. Populations are labelled as in Table 1. (DOC)

COI dataset: haplotype frequencies. Frequency distribution of COI haplotypes in 311 individuals from 34 populations of Pinna nobilis. N: absolute frequency; %: relative frequency within Mediterranean populations. Populations are labelled as in Table 1. (DOC)

The reproductive strategy of the simultaneous hermaphrodite Pseudomonocelis paupercula (Platyhelminthes: Proseriata) was investigated using multiple approaches including breeding experiments, anatomical reconstruc-tion, and parentage analysis of offspring. The 18 allozyme loci tested were monomorphic. Conversely, the ISSR markers showed differences...

This study aims at comparing patterns of genetic diversity in farmed and wild populations of the gilthead sea bream, Sparus aurata Linnaeus, 1758 (Sparidae) along the Sardinian shores. We aimed at assessing if farmed populations are genetically divergent and have lower genetic variability than wild populations. As a by-product we investigated genet...