Sars virus italy

N protein, responsible for the formation of helical nucleocapsid, can elicit humoral and cell mediated immune response and has potential value in vaccine development. However, none of the observed mutations has been so far associated with changes in viral pathogenicity or transmissibility.

The phylogenetic reconstruction we report suggests possible multiple introduction of SARS-CoV-2 virus in Italy, supporting previously reported analysis conducted on a more limited number of sequences 3 — 5. The analysis consistently places the strains described in this study in 2 distinct clusters in B1 clade. No other sequence from Italy clusters in B2 or GISAID V clade, indicating the positive effect of containment measures established by health authorities in both Italy and China to limit viral transmission directly from China.

The same measures were unable to contain a wave of subsequent multiple introductions in Italy of strains that were widely circulating in Europe, all clustering with clade B1. The inclusion of the viral sequences from infections occurring in the Lazio region helps to demonstrate the dynamics of virus circulation in Italy. In particular, a small number of mutations have been detected in these strains, but the real impact and role that these mutations may have on the pathogenicity and transmissibility of SARS-CoV-2 remains to be determined.

A limitation of our research is that only a portion of viral sequences, including the sequences from Italy, have been published as of April 10, ; phylogenetic analysis could substantially change when more sequences are made available. Furthermore, increased sequencing capacity is necessary for contact tracing and enhanced surveillance activity.

We thank the contributors of genome sequences of the newly emerging coronavirus the originating and submitting laboratories for sharing their sequences and other metadata through the GISAID Initiative, on which this research is based. All the authors read and approved the manuscript. Table of Contents — Volume 26, Number 8—August Please use the form below to submit correspondence to the authors or contact them at the following address:. Highlight and copy the desired format.

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The score is derived from an automated algorithm, and represents a weighted count of the amount of attention Altmetric picked up for a research output. Section Navigation. Facebook Twitter LinkedIn Syndicate. Table 1 Table 2. Article Metrics. Related Articles. Abstract We report phylogenetic and mutational analysis of severe acute respiratory syndrome coronavirus 2 virus strains from the Lazio region of Italy and provide information about the dynamics of virus spread.

The Study. Figure Figure. This colleague tested negative, however, so the first introduction of the virus into Italy remains unclear. Identifying the first introduction of the virus is of epidemiological interest, for the tracking and mapping of COVID spread in a country.

In Italy, and elsewhere, there have been speculations to the effect that COVID had been silently circulating before the first case was identified. Indeed, other countries have been trying to ascertain whether earlier infections had occurred. In France, where the COVID epidemic was believed to have started in late January , a retrospective analysis of a stored respiratory sample from a patient hospitalised in December , demonstrated that the patient was positive for SARS-CoV-2, suggesting that, in France, the epidemic started much earlier than previously thought Deslandes et al.

These patients have been shown to shed the virus in their stools even if asymptomatic or pre-symptomatic Jiang et al. Sewage samples can thus be used to monitor the levels of virus circulating in the population, an approach called wastewater-based epidemiology WBE. Several studies performed in the Netherlands Medema et al. Another Italian study confirmed the occurrence of the virus in sewage samples collected in April Rimoldi et al. Similarly, in the current study we retrospectively searched for genomic traces of SARS-CoV-2 in a collection of sewage samples gathered from WWTPs in northern Italy between October and February , in the framework of different projects on enteric viruses.

The samples were analysed to ascertain whether SARS-CoV-2 was circulating in the weeks and months before the virus was believed to have arrived in Italy. Forty sewage samples were analysed for the study. The location and number of inhabitants expressed as population equivalents served by these WWTPs are summarised in Fig.

Location and number of inhibitants served by the WTPs included in the study. Numbers in correspondence of the WTP code represent the inhibitants served by each plant.

Precautions taken during sample treatment were reported elsewhere La Rosa et al. Sample concentration was performed using the two-phase PEG-dextran separation method recommended by the WHO Guidelines for environmental surveillance of poliovirus circulation WHO, , with modifications.

The clarified wastewater was neutralized pH 7. However, this resulted in PCR inhibition median Therefore, after performing comparative extraction experiments with and without chloroform, using samples spiked with the human Alphacoronavirus HCoV E and field samples see Supplementary Material , the chloroform purification step was reintroduced to improve the purification of samples before RNA extraction, and obtain a higher detection sensitivity.

The recovery efficiency of the concentration and extraction procedure was assessed through separate spiking experiments performed in quadruplicate using the Alphacoronavirus HCoV E ATCC VR and the protocol detailed in Supplementary Materials.

This was not done on field samples in order to avoid interferences with future virome analyses. The subsequent washing phases were performed as per manufacturer's instructions. PCR reaction was performed using 2. To avoid false-positive results, standard precautions were taken and results were confirmed in two independent experiments.

For standard curve construction, the two targeted regions were synthetized and quantified by Eurofins Genomics Germany.

For standard curve construction, the targeted region was synthetized and purified by BioFab Research Italy , and was quantified by fluorometric measure Qubit, Thermo Scientific. In vitro synthetized RNA containing the target region was used as an external amplification control to check for PCR inhibition. Reactions for quantitative analysis were performed in duplicate.

Molecular biology grade water served as the no-template control; two negative controls were included in each run to check for reagent contamination and for environmental contamination, respectively. All amplification plots were visually checked for exponential amplification, the threshold was manually set at the midpoint of the exponential phase, and a Cq cut-off value of 40 was applied to all results.

To evaluate their performance in wastewater samples, the same RNA dilutions were used to spike nucleic acids extracted from sewage concentrates that had tested negative for SARS-CoV The recovery efficiency of the concentration and extraction procedure, evaluated with seeded experiments performed in quadruplicate, using the Alphacoronavirus HCoVE ATCC VR showed an average recovery of 2.

Only these samples, that tested positive by both nested and real-time PCR, were considered as confirmed positive samples. Samples below 5. Of the 15 positive samples, 8 were taken earlier than February 21, i. In all three cities, the virus was also detected in the samples collected in January and February, with only one exception - the February sample from Bologna.

Here, however, the negative real-time RT- q PCR result may have been affected by the slightly higher-than-usual inhibition in this amplification Virus concentration in the samples Table 2 and Fig. The highest concentration was recorded in a sample collected in Turin, in February plant C, 5. Italy is one of the first and most severely affected countries in Europe, with a high number of documented cases and deaths.

The first documented cases were two Chinese tourists who fell ill in Italy in late January 30th January after flying in from Wuhan, where the epidemic began. The first autochthonous case of infection was recorded in Italy on 21st February A sustained local transmission has been documented, so that by 11th August , The vast majority of cases were reported in Northern Italy. Phylogenetic analyses on SARS-CoV-2 sequences conducted at the beginning of the epidemic, clustered Italian sequences far from the first two Chinese tourists' strains, and suggested that there may have been multiple introductions of the virus into Italy Bartolini et al.

To test this hypothesis, we analysed sewage samples collected between October and February in Northern Italy in the framework of projects on enteric viruses, and stored in the archive of the Department of Environment and Health at the Italian National Institute of Health. Across Europe and Italy, the most widespread is strain G, while the L strain from Wuhan is gradually disappearing. These mutations, however, do not impinge on the process of developing effective vaccines.

Despite its mutations, the virus shows little variability, and this is good news for the researchers working on a viable vaccine. Researchers at the University of Bologna drew from the analysis of 48, coronavirus genomes, which were isolated by researchers in labs all over the world. This study was published in the journal Frontiers in Microbiology.

It was then possible for researchers to map the spread and the mutations of the virus during its journey to all continents. The first results are encouraging.

The coronavirus presents little variability, approximately seven mutations per sample. Common influenza has a variability rate that is more than double. Currently, there are six strains of coronavirus. The original one is the L strain, that appeared in Wuhan in December