The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5–11 December, to 17.5% (25/143 samples) in the week 12–18, to 65.9% (89/135 samples) in the week 19–25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased fromone in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons

The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5-11 December, to 17.5% (25/143 samples) in the week 12-18, to 65.9% (89/135 samples) in the week 19-25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased from one in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons. In conclusion, we designed an RT-qPCR assay capable to detect the Omicron variant, which can be successfully used for the purpose of wastewater-based epidemiology. We also described the history of the introduction and diffusion of the Omicron variant in the Italian population and territory, confirming the effectiveness of sewage monitoring as a powerful surveillance tool

Mammal responses to global changes in human activity vary by trophic group and landscape

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human–wildlife interactions along gradients of human influence.Peer reviewe

Autoantibodies against chemokines post-SARS-CoV-2 infection correlate with disease course

Infection with severe acute respiratory syndrome coronavirus 2 associates with diverse symptoms, which can persist for months. While antiviral antibodies are protective, those targeting interferons and other immune factors are associated with adverse coronavirus disease 2019 (COVID-19) outcomes. Here we discovered that antibodies against specific chemokines were omnipresent post-COVID-19, were associated with favorable disease outcome and negatively correlated with the development of long COVID at 1 yr post-infection. Chemokine antibodies were also present in HIV-1 infection and autoimmune disorders, but they targeted different chemokines compared with COVID-19. Monoclonal antibodies derived from COVID-19 convalescents that bound to the chemokine N-loop impaired cell migration. Given the role of chemokines in orchestrating immune cell trafficking, naturally arising chemokine antibodies may modulate the inflammatory response and thus bear therapeutic potential

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

SARS-CoV-2 transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant1 now reported in 94 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b22. We measured neutralising antibody responses following first and second immunisations using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the RBM (5 out of 31), but not in RBD neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect a newly emergent Variant of Concern (VOC 202102/02) led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b

A Molecular View of Autophagy in Lepidoptera

Metamorphosis represents a critical phase in the development of holometabolous insects, during which the larval body is completely reorganized: in fact, most of the larval organs undergo remodeling or completely degenerate before the final structure of the adult insect is rebuilt. In the past, increasing evidence emerged concerning the intervention of autophagy and apoptosis in the cell death processes that occur in larval organs of Lepidoptera during metamorphosis, but a molecular characterization of these pathways was undertaken only in recent years. In addition to developmentally programmed autophagy, there is growing interest in starvation-induced autophagy. Therefore we are now entering a new era of research on autophagy that foreshadows clarification of the role and regulatory mechanisms underlying this self-digesting process in Lepidoptera. Given that some of the most important lepidopteran species of high economic importance, such as the silkworm, Bombyx mori, belong to this insect order, we expect that this information on autophagy will be fully exploited not only in basic research but also for practical applications

Distribuzione e consistenza della popolazione di Scoiattolo grigio <em>Sciurus carolinensis</em> Gmelin, 1788 nel levante genovese

<strong>Abstract</strong> <strong>Distribution and population size of the Grey squirrel <em>Sciurus carolinensis</em> Gmelin, 1788 in Province of Genova (NW Italy)</strong> In Liguria, the Grey squirrel population originated from an introduction of five pairs in an urban park (Genoa Nervi) in 1966. A first study, carried out in the 1996 by interviews, located a second group 3 km far, in Bogliasco locality. In this study, conducted in 2001-04, the population size of Genoa Nervi and the presence of the species in surrounding areas were investigated. In 2002 the population size was estimated in 115/286 individuals by distance sampling method, while, by direct observation, it varied from 80 individuals (2004) to 114 individuals (2003). The sampling by hair tubes in surrounding areas confirmed the presence of a group of grey squirrels in Bogliasco and excluded a further dispersal of the species. <strong>Riassunto</strong> In Liguria, la popolazione di Scoiattolo grigio <em>Sciurus carolinensis</em> ha avuto origine dall'introduzione di 5 coppie nei parchi urbani di Genova Nervi nel 1966. Un primo studio condotto nel 1996 ha localizzato, tramite interviste, un secondo nucleo a 3 km di distanza, in località Bogliasco. Il presente studio, condotto nel 2001-2004, è stato finalizzato alla valutazione della consistenza della popolazione nei parchi di Nervi, mediante il metodo <em>distance sampling</em> e osservazioni dirette, e all'accertamento della presenza della specie nelle aree circostanti mediante l'utilizzo di <em>hair tube</em>. La stima della popolazione con il metodo <em>distance sampling</em> è risultata di 115/286 individui nel 2002, mentre quella ottenuta mediante osservazioni dirette è variata da 80 individui nel 2004 a 114 individui nel 2003. Gli accertamenti compiuti nelle aree circostanti i parchi di Nervi hanno consentito di confermare la presenza di un nucleo di scoiattoli a Bogliasco e di escludere un'ulteriore espansione della specie

Ricerca del virus dell\u2019epatite E (HEV) nei cinghiali nella Tenuta Presidenziale di Castelporziano

Nell\u2019uomo, il virus dell\u2019epatite E (HEV) \ue8 la causa pi\uf9 comune di epatite virale acuta, responsabile su scala globale di circa 20 milioni di casi ogni anno, di cui 70.000 letali. HEV, in particolare i due genotipi esclusivamente umani HEV-1 e HEV-2, \ue8 endemico in molti Paesi in via di sviluppo. Nei Paesi industrializzati, negli ultimi 10 anni, si \ue8 osservato un aumento del numero di casi di epatite E in pazienti senza anamnesi di viaggi in aree endemiche, sostenuti dai genotipi zoonotici HEV-3 e HEV-4. Queste infezioni sono in genere asintomatiche ma, in un numero ridotto di soggetti, possono evolvere in forme di epatite acuta. Ceppi di HEV-3 e HEV-4 sono stati identificati nei suini domestici, nei cinghiali, nei cervi e nei conigli. In queste specie l\u2019infezione \ue8 asintomatica e si trasmette all\u2019uomo principalmente per via alimentare mediante prodotti a base di carne, consumati crudi o poco cotti (salsicce contenenti fegato di suino o carne di cinghiale, sashimi di cervo). La presenza del genotipo zoonotico HEV-3 \ue8 stata segnalata in numerose popolazioni di cinghiale in tutta Europa. In Italia, numerosi studi ne hanno segnalato la presenza in popolazioni di cinghiale di quasi tutte le Regioni con prevalenze variabili tra 1,8% e 52%. Ad oggi, non \ue8 chiaro se l\u2019infezione abbia avuto un\u2019origine comune nelle popolazioni di suini domestici e selvatici o se l\u2019infezione abbia iniziato a circolare nel selvatico a seguito di contatti con suini domestici (allevamento brado, immissioni a scopo venatorio di capi selvatici allevati in modo promiscuo). Il presente lavoro ha avuto lo scopo di indagare la presenza di HEV nella popolazione di cinghiali della Tenuta Presidenziale di Castelporziano. Questa popolazione ha la peculiare caratteristica di essere composta esclusivamente da cinghiali autoctoni e di non avere avuto contatti con altre popolazioni animali esterne alla Tenuta negli ultimi quarant\u2019anni. Durante i mesi di novembre-gennaio del 2017-2020 sono stati prelevati 115 fegati da altrettanti cinghiali abbattuti nell\u2019ambito dei piani di controllo condotti nella Tenuta e finalizzati alla conservazione della biodiversit\ue0 protetta nell\u2019area e al suo mantenimento in equilibrio. Porzioni di fegato, organo all\u2019interno del quale avviene la replicazione del virus, sono state utilizzate per la ricerca dell\u2019RNA di HEV mediante il metodo molecolare della Real-Time RT-PCR. Le analisi hanno rilevato la presenza del materiale genetico del virus in 2 dei 115 campioni analizzati. La prevalenza rilevata \ue8 estremamente bassa (1,7%) e nettamente inferiore a quella presente in altre popolazioni di cinghiale. Ci\uf2 potrebbe suggerire una possibile recente introduzione del virus all\u2019interno della Tenuta con un rischio estremamente ridotto di contaminazione delle carcasse. In conclusione questo risultato porta a ritenere che l\u2019isolamento degli animali o la loro densit\ue0 possa essere importante nel determinare la diffusione del virus nelle popolazioni di cinghiale.Monitoring of hepatitis E virus (HEV in wild boar population within the Tenuta Presidenziale of Castelporziano. In humans, hepatitis E virus (HEV) is a common cause of acute viral hepatitis. The HEV is endemic in many developing countries. In Europe, in the last 10 years there has been an increase in cases of autochthonous hepatitis E, linked to zoonotic genotypes 3 and 4 (HEV-3 and HEV-4), which may cause asymptomatic infections that may evolve into acute hepatitis. The HEV-3 and HEV-4 have been identified in domestic pigs, wild boars, deer and rabbits. In these species, the infection is asymptomatic and is transmitted to humans mainly by consumption of raw or undercooked food (sausages containing pork liver or wild boar meat, deer sashimi). Wild boar is susceptible to the infection and animals positive for the HEV-3 zoonotic genotype have also been identified throughout Italy, in almost all Regions with prevalence varying between 1.8% and 52%. It is unclear whether the infection had a common origin in domestic and feral pig populations. The present work aims to investigate the presence of the virus in the wild boar population present within the Tenuta Presidenziale of Castelporziano, which has remained isolated over the last forty years. During November-January 2017-2020, 115 livers were taken from wild boars killed as part of the control plans for protection of biodiversity. Liver samples, the organ of viral replication, were used for the detection of Hepatitis E virus RNA by using the molecular method of Real-Time RT-PCR. Results revealed the presence of the genetic material of the virus in 2 of the 115 animals analyzed. The prevalence found is extremely low (1.7%) and significantly lower than that found in other wild boar populations. This could suggest a possible recent introduction of the virus inside the Tenuta. In conclusion, this result leads us to believe that the isolation of animals may be important to prevent the spread of the virus in wild boar populations

Molecular survey of HEV infection in wild boar population in Italy

Hepatitis E virus (HEV) is an RNA virus causing an acute generally self-limited disease in humans. An increasing number of autochthonous cases linked to zoonotic transmission of HEV genotype 3 have been reported over the last 10\ua0years in Europe. Pigs and wild boars are considered the main reservoirs. The principal route of transmission in Europe is food-borne, linked by direct or indirect evidence to the consumption of raw or undercooked pork products and wild boar meat. In this study, we sampled 92 wild boar (Sus scrofa) livers during active surveillance in five municipalities in Central Italy throughout the hunting season 2016\u20132017. HEV RNA was detected in 52.2% of liver sampled with prevalence ranging from 0.0% to 65.7%. HEV-positive wild boars were detected in all but one area of hunting. Phylogenetic analysis showed that strains clustered within the two subtypes HEV-3c and HEV-3f and displayed a wide range of phylogenetic diversity. Several strains were circulating in the areas investigated; animals possibly belonging to the same family group hunted by the same team were infected with a unique strain (100% nucleotide identity). As wild animals are a proven source of HEV transmission to humans and pigs, the high prevalence observed (mean 52.2%) poses a question on the risk of consuming raw or undercooked wild boar meat, and thus, this subject deserves further investigations