A "One-Health" approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy

A cell-adapted SARS-CoV-2 mutant, showing a deletion in the spike protein spanning the furin cleavage site, has reduced virulence at the lung level in K18-hACE2 mice

Here we investigated the virulence properties of a unique cell-adapted SARS-CoV-2 mutant showing a ten-amino acid deletion encompassing the furin cleavage site of the spike protein (Δ680SPRAARSVAS689; Δ680-689-B.1) in comparison to its parental strain (wt-B.1) and two Delta variants (AY.122 and AY.21) of concern. After intranasal inoculation, transgenic K18-hACE2 mice were monitored for 14 days for weight change, lethality, and clinical score; oral swabs were daily collected and tested for the presence of N protein subgenomic RNA. At 3 and 7 dpi mice were also sacrificed and organs collected for molecular, histopathological, and immune response profile investigations. The Δ680-689-B.1-infected mice exhibited reduced shedding, lower virulence at the lung level, and milder pulmonary lesions. In the lung, infection with Δ680-689-B.1 was associated with a significant lower expression of some cytokines at 3 dpi (IL-4, IL-27, and IL-28) and 7 dpi (IL-4, IL-27, IL-28, IFN-γ and IL-1α).

Evaluation of next generation sequencing approaches for SARS-CoV-2

Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.

One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy

The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In particular, the IZS of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system - SILAB - was implemented with a One Health module for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. Moreover, the "National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis" - GENPAT - formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.

A Deletion Encompassing the Furin Cleavage Site in the Spike Encoding Gene Does Not Alter SARS-CoV-2 Replication in Lung Tissues of Mink and Neutralization by Convalescent Human Serum Samples

SARS-CoV-2 has been shown to lose the furin polybasic cleavage site (FCS) following adaptation on cell culture. Deletion occurring in this region, which may include also the FCS flanking regions, seem not to affect virus replication in vitro; however, a chimeric SARS-CoV-2 virus without the sole FCS motif has been associated with lower virulence in mice and lower neutralization values. Moreover, SARS-CoV-2 virus lacking the FCS was shed to lower titers from experimentally infected ferrets and was not transmitted to cohoused sentinel animals, unlike wild-type virus. In this study, we investigated the replication kinetics and cellular tropism of a SARS-CoV-2 isolate carrying a 10-amino acid deletion in the spike protein spanning the FCS in lung ex vivo organ cultures of mink. Furthermore, we tested the neutralization capabilities of human convalescent SARS-CoV-2 positive serum samples against this virus. We showed that this deletion did not significantly hamper neither ex vivo replication nor neutralization activity by convalescent serum samples. This study highlights the importance of the preliminary phenotypic characterization of emerging viruses in ex vivo models and demonstrates that mink lung tissues are permissive to the replication of a mutant form of SARS-CoV-2 showing a deletion spanning the FCS. Notably, we also highlight the need for sequencing viral stocks before any infection study as large deletions may occur leading to the misinterpretation of results.

First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa

Influenza D virus (IDV) was first isolated in 2011 in the USA and has since been shown to circulate in cattle, pigs, sheep, wild boar, and camels. In Africa, there is limited data on the epidemiology of IDV and, so, we investigated the presence of IDV among domestic ruminants and wild animals in Namibia by screening nasal swabs using an IDV-specific molecular assay. IDV RNA was detected in bovines (n=2), giraffes (n=2) and wildebeest (n=1). The hemagglutinin-esterase-fusion (HEF) gene from one of the bovine and the wildebeest samples was successfully sequenced as well as the full genome for the second bovine sample. Phylogenetic analysis of the HEF gene positioned the African virus variants within the D/OK lineage but with a long branch. The African variant had an amino acid diversity of 2.41% and most likely represents a distinct genotype within the lineage. Notably, the polymerase acidic protein gene (PA) was more closely related to a different lineage (D/660), indicative of potential reassortment. This is the first genetic characterization of IDV in Africa and it adds important data to our understanding of the global IDV distribution.

Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia

Human orthopneumovirus (HRSV) is a virus belonging to the Pneumovirus genus that causes lower respiratory tract infections (LRTI) in infants worldwide. In Tunisia, thousands of infants hospitalized for LRTI are found to be positive for HRSV but no whole genome sequences of HRSV strains circulating in this country are available thus far. In this study, five nasal swab samples collected at different time points from a three-month-old female baby with severe immunodeficiency that was hospitalized for acute bronchiolitis were investigated by next generation sequencing. The Tunisian sequences from this study originated from samples collected in 2021, belong to the ON1 genotype of HRSV-A, and are clustered with European sequences from 2019 and not from 2020 or 2021. This is most likely related to local region-specific transmission of different HRSV-A variants due to the COVID-19 related travel restrictions. Overall, this is the first report describing the whole genome sequence of HRSV from Tunisia. However, more sequence data is needed to better understand the genetic diversity and transmission dynamic of HRSV.

Influenza A, Influenza B, and SARS-CoV-2 Similarities and Differences – A Focus on Diagnosis

In late December 2019, the first cases of viral pneumonia caused by an unidentified pathogen were reported in China. Two years later, SARS-CoV-2 was responsible for almost 450 million cases, claiming more than 6 million lives. The COVID-19 pandemic strained the limits of healthcare systems all across the world. Identifying viral RNA through real-time reverse transcription-polymerase chain reaction remains the gold standard in diagnosing SARS-CoV-2 infection. However, equipment cost, availability, and the need for trained personnel limited testing capacity. Through an unprecedented research effort, new diagnostic techniques such as rapid diagnostic testing, isothermal amplification techniques, and next-generation sequencing were developed, enabling accurate and accessible diagnosis. Influenza viruses are responsible for seasonal outbreaks infecting up to a quarter of the human population worldwide. Influenza and SARS-CoV-2 present with flu-like symptoms, making the differential diagnosis challenging solely on clinical presentation. Healthcare systems are likely to be faced with overlapping SARS-CoV-2 and Influenza outbreaks. This review aims to present the similarities and differences of both infections while focusing on the diagnosis. We discuss the clinical presentation of Influenza and SARS-CoV-2 and techniques available for diagnosis. Furthermore, we summarize available data regarding the multiplex diagnostic assay of both viral infections.

Knowledge, risk perception, and prevention preparedness towards COVID-19 among a cross-section of animal health professionals in Nigeria

Introduction

the on-going COVID-19 pandemic caused by the SARS-CoV-2 virus has imposed serious public health and economic threats on the entire world population. The SARS-CoV-2 has been identified from both domestic and wild animals constituting a threat to humans since most apparently healthy animals may potentially infect and cause the disease in humans, especially Animal Health Professionals (AHPs) who come directly in contact with animals. These professionals such as veterinarians play important roles among the One Health team in controlling the pandemic. This survey was conducted to assess the knowledge, risk perception, and prevention behaviors of AHPs in Nigeria who are important personnel in the control of emerging and re-emerging zoonotic and infectious diseases.

Methods

an online-based epidemiological cross-sectional pre-tested questionnaire survey was carried out from April to May 2020. A total of 427 AHPs joined this survey. Descriptive statistics, chi-square test, and binary logistic regression model were used to analyze the data collected.

Results

the respondents have a mean knowledge score of 7.34 ± 2.05 (from a total possible score of 11) with the majority (66.7%, n = 285) having satisfactory knowledge scores on COVID-19. A high proportion (240/353) of respondents reported bats to be the major wildlife incriminated in the transmission of the COVID-19 virus though other animals reported were tiger, monkey, lion, and pangolin. At least, a quarter 131 (30.7%) of respondents perceived that visiting live animal markets is of high zoonotic risk to the spread of coronavirus. Most respondents reported hands washing and sanitizing after handling animals, and using personal protective equipment when handling suspected animals. At p<0.05; respondents' age, marital status, professional status, and geopolitical zone were significantly linked with satisfactory knowledge. Veterinarians (OR=0.40; 95%CI: 0.22–0.75) were thrice less likely to possess unsatisfactory knowledge of COVID-19 than laboratory technologists.

Conclusion

participants in this survey have a satisfactory level of COVID-19 knowledge and good mitigation measures instituted while working at their stations. However, AHPs need more enlightenment about the various zoonotic risk pathway contributing to the transmission of COVID-19.

Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR

Several lineages of SARS-CoV-2 are currently circulating worldwide. During SARS-CoV-2 diagnostic activities performed in Abruzzo region (central Italy) several strains belonging to the B.1.177.75 lineage tested negative for the N gene but positive for the ORF1ab and S genes (+/+/- pattern) by the TaqPath COVID-19 CE-IVD RT-PCR Kit manufactured by Thermofisher. By sequencing, a unique mutation, synonymous 28948C > T, was found in the N-negative B.1.177.75 strains. Although we do not have any knowledge upon the nucleotide sequences of the primers and probe adopted by this kit, it is likely that N gene dropout only occurs when 28948C > T is coupled with 28932C > T, this latter present, in turn, in all B.1.177.75 sequences available on public databases. Furthermore, epidemiological analysis was also performed. The majority of the N-negative B.1.177.75 cases belonged to two clusters apparently unrelated to each other and both clusters involved young people. However, the phylogeny for sequences containing the +/+/- pattern strongly supports a genetic connection and one common source for both clusters. Though, genetic comparison suggests a connection rather than indicating the independent emergence of the same mutation in two apparently unrelated clusters. This study highlights once more the importance of sharing genomic data to link apparently unrelated epidemiological clusters and to, remarkably, update molecular tests.

Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes

Since the beginning of 2020, the betacoronavirus SARS-CoV-2 is causing a global pandemic of an acute respiratory disease termed COVID-19. The diagnostics of the novel disease is primarily based on direct virus detection by RT-PCR; however, the availability of test kits may become a major bottleneck, when millions of tests are performed per week. To increase the flexibility of SARS-CoV-2 diagnostics, three real-time RT-PCR assays listed on the homepage of the World Health Organization were selected and investigated regarding their compatibility with three different RT-PCR kits. Furthermore, the reaction volume of the PCR chemistry was reduced up to half of the original protocol to make the individual reactions more cost- and resource-effective. When testing dilution series of culture-grown virus, nearly identical quantification cycle values (Cq) were obtained for all RT-PCR assay/chemistry combinations. Regarding the SARS-CoV-2 detection in clinical samples, agreeing results were obtained for all combinations for virus negative specimens and swabs containing high to medium viral genome loads. In cases of very low SARS-CoV-2 genome loads (Cq > 36), inconsistent results were observed, with some test runs scoring negative and some positive. However, no preference of a specific target within the viral genome (E, RdRp, or N) or of a certain chemistry was seen. In summary, a reduction of the reaction volume and the type of PCR chemistry did not influence the PCR sensitivity.

SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels

BACKGROUND

Faced with the ongoing global pandemic of coronavirus disease, the 'National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis' (GENPAT) formally established at the 'Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise' (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model.

RESULTS

GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. 'UK variant') are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model.

CONCLUSIONS

The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.

Brief Research Report: Veterinary Student Perspective on COVID-19 and Veterinary Medicine

COVID-19 has had significant effects on the field of veterinary medicine. Adaptation to pandemic-related and post-pandemic challenges requires engagement from all levels of the professional pipeline, including veterinary college students. Insights gained from this group may inform curriculum design, help the veterinary profession innovate, maximize opportunities for positive change, and avoid negative outcomes. The current study aimed to understand the potential impacts of the COVID-19 pandemic on veterinary medicine, as foreseen by second-year veterinary students in an online discussion during a public health course in the spring of 2020. Twenty-one percent of the 113 students agreed to participate in this qualitative research study. We used an inductive coding process and distilled the student responses into descriptive themes to capture diverse perspectives and understand possible post-pandemic pathways for the veterinary profession. Four themes emerged from the student discussion posts, describing how veterinarians might be affected by the COVID-19 pandemic: (1) economic and social impacts, (2) adapting to challenges, (3) collaborations to improve public health, and (4) disparities and diversity. These themes are a starting point for discussion and innovation as veterinarians plan for the post-pandemic world; further investigation will provide additional guidance for veterinary leaders.

A Review of Research on Tourism Industry, Economic Crisis and Mitigation Process of the Loss: Analysis on Pre, During and Post Pandemic Situation

Throughout time, the global tourism industry and economy have been significantly affected by disasters and crises. At present, COVID-19 represents one of these disasters as it has been causing a serious economic downturn with huge implications in tourism. In this review paper, we have analysed more than 100 papers regarding the effect and consequences of a pandemic on tourism and related industries, the economic situation in countries and areas, and mitigation of the loss incurred due to pandemic situations. The article (1) is based on past research on tourism and economy, (2) examines the effects of a pandemic on listed sectors and mitigation processes, and (3) suggests future research and approaches to help progress the field. We have gathered and categorised the literature reviews into several parts. In addition, we have listed the name of authors, journal names, books, websites, and relevant data.

SARS-CoV-2 natural infection in animals: a systematic review of studies and case reports and series

COVID-19 pandemic is essentially a zoonotic disease. In this context, early in 2020, transmission from humans to certain animals began reporting; the number of studies has grown since. To estimate the pooled prevalence of SARS-CoV-2 natural infection in animals and to determine differences in prevalence between countries, years, animal types and diagnostic methods (RT-PCR or serological tests). A systematic literature review with meta-analysis using eight databases. Observational studies were included but analyzed separately. We performed a random-effects model meta-analysis to calculate the pooled prevalence and 95% confidence interval (95% CI) for prevalence studies and case series. After the screening, 65 reports were selected for full-text assessment and included for qualitative and quantitative analyses. A total of 24 reports assessed SARS-CoV-2 infection by RT-PCR, combining a total of 321,785 animals, yielding a pooled prevalence of 12.3% (95% CI 11.6%–13.0%). Also, a total of 17 studies additionally assessed serological response against SARS-CoV-2, including nine by ELISA, four by PRTN, one by MIA, one by immunochromatography (rest, two studies, the method was not specified), combining a total of 5319 animals, yielding a pooled prevalence of 29.4% (95% CI 22.9%–35.9%). A considerable proportion of animals resulted infected by SARS-CoV-2, ranking minks among the highest value, followed by dogs and cats. Further studies in other animals are required to define the extent and importance of natural infection due to SARS-CoV-2. These findings have multiple implications for public human and animal health. One Health approach in this context is critical for prevention and control.

Whole-Genome Sequences of SARS-CoV-2 Lineage B.1.525 Strains (Variant η) Detected from Patients in the Abruzzo Region (Central Italy) during Spring 2021

Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are emerging worldwide. Here, we report the complete genome sequences of 13 severe acute SARS-CoV-2 strains belonging to lineage B.1.525 (variant η).

Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.

Machine Learning and Geo-Based Multi-Criteria Decision Support Systems in Analysis of Complex Problems

Many complex problems require a multi-criteria decision, such as the COVID-19 pandemic that affected nearly all activities in the world. In this regard, this study aims to develop a multi-criteria decision support system considering the sustainability, feasibility, and success rate of possible approaches. Therefore, two models have been developed: Geo-AHP (applying geo-based data) and BN-Geo-AHP using probabilistic techniques (Bayesian network). The ranking method of Geo-APH is generalized, and the equations are provided in a way that adding new elements and variables would be possible by experts. Then, to improve the ranking, the application of the probabilistic technique of a Bayesian network and the role of machine learning for database and weight of each parameter are explained, and the model of BN-Geo-APH has been developed. In the next step, to show the application of the developed Geo-AHP and BN-Geo-AHP models, we selected the new pandemic of COVID-19 that affected nearly all activities, and we used both models for analysis. For this purpose, we first analyzed the available data about COVID-19 and previous studies about similar virus infections, and then we ranked the main approaches and alternatives in confronting the pandemic of COVID-19. The analysis of approaches with the selected alternatives shows the first ranked approach is massive vaccination and the second ranked is massive swabs or other tests. The third is the use of medical masks and gloves, and the last ranked is the lockdown, mostly due to its major negative impact on the economy and individuals.

2D materials as a diagnostic platform for the detection and sensing of the SARS-CoV-2 virus: a bird's-eye view

Worldwide infections and fatalities caused by the SARS-CoV-2 virus and its variants responsible for COVID-19 have significantly impeded the economic growth of many nations. People in many nations have lost their livelihoods, it has severely impacted international relations and, most importantly, health infrastructures across the world have been tormented. This pandemic has already left footprints on human psychology, traits, and priorities and is certainly going to lead towards a new world order in the future. As always, science and technology have come to the rescue of the human race. The prevention of infection by instant and repeated cleaning of surfaces that are most likely to be touched in daily life and sanitization drives using medically prescribed sanitizers and UV irradiation of textiles are the first steps to breaking the chain of transmission. However, the real challenge is to develop and uplift medical infrastructure, such as diagnostic tools capable of prompt diagnosis and instant and economic medical treatment that is available to the masses. Two-dimensional (2D) materials, such as graphene, are atomic sheets that have been in the news for quite some time due to their unprecedented electronic mobilities, high thermal conductivity, appreciable thermal stability, excellent anchoring capabilities, optical transparency, mechanical flexibility, and a unique capability to integrate with arbitrary surfaces. These attributes of 2D materials make them lucrative for use as an active material platform for authentic and prompt (within minutes) disease diagnosis via electrical or optical diagnostic tools or via electrochemical diagnosis. We present the opportunities provided by 2D materials as a platform for SARS-CoV-2 diagnosis.

Epidemiological Significance of SARS-CoV-2 RNA Dynamic in Naso-Pharyngeal Swabs

From 16 March to 15 December 2020, 132,357 naso-pharyngeal/oropharyngeal swabs were collected in the province of Teramo, Abruzzo Region, Italy, and tested for the presence of SARS-CoV-2 genomic RNA by a commercially available molecular assay. A total of 12,880 swabs resulted positive. For 8212 positive patients (4.150 women and 4.062 men) the median age was statistically different between women (median: 49.55 ± 23.9 of SD) and men (median: 48.35 ± 23.5 of SD) while no differences were found in the comparison between the cycle threshold for the N protein-encoding gene (C_T N) median values and gender. Differences were observed in the C_T N gene median values of swabs collected from March to September as well as in the pairwise comparison between September and October and between November and December. The C_T N gene median values observed in specific periods characterizing the SARS-CoV-2 epidemic in 2020 were also compared with the incidence of COVID-19 cases; a strong inverse correlation was highlighted (Pearson correlation coefficient = -0.978). Our findings confirm the usefulness of the C_T N values as an indirect detection parameter to monitor viral loads in the population.

Animal Reservoirs and Hosts for Emerging Alphacoronaviruses and Betacoronaviruses

The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.

Genome Sequences of Three SARS-CoV-2 P.1 Strains Identified from Patients Returning from Brazil to Italy

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. We report the complete sequences of three SARS-CoV-2 P.1 strains obtained from nasopharyngeal swab specimens from three patients returning from Brazil to Italy.

Pooling of Nasopharyngeal Swab Samples To Overcome a Global Shortage of Real-Time Reverse Transcription-PCR COVID-19 Test Kits

The global outbreak and rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have created an urgent need for large-scale testing of populations. There is a demand for high-throughput testing protocols that can be used for efficient and rapid testing of clinical specimens. We evaluated a pooled PCR protocol for testing nasopharyngeal (NP) swabs using known positive/negative and untested clinical samples that were assigned to pools of 5 or 10. In total, 630 samples were used in this study. Individual positive samples with cycle threshold (C_T ) values as high as 33 could be consistently detected when pooled with 4 negative samples (pool of 5), and individual positive samples with C_T values up to 31 could be consistently detected when pooled with 9 negative samples (pool of 10). Pooling of up to 5 samples can be employed in laboratories for the diagnosis of COVID-19 for efficient utilization of resources, rapid screening of a greater number of people, and faster reporting of test results.

Erasing the Invisible Line to Empower the Pandemic Response

A challenging debate has arisen on the role of veterinary expertise in facing the SARS-CoV-2 pandemic. It seems totally unreasonable that in most countries, veterinary diagnostic and tracing forces were not deployed at the start to perform strategic tasks, which could have mitigated the outcome of this dramatic health emergency. Erasing the invisible line between human and veterinary virology will empower the response to future pandemics.

Early Diffusion of SARS-CoV-2 Infection in the Inner Area of the Italian Sardinia Island

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the coronavirus disease 2019 (COVID-19) pandemic, which started as a severe pneumonia outbreak in Wuhan, China, in December 2019. Italy has been the first European country affected by the pandemic, registering a total of 300,363 cases and 35,741 deaths until September 24, 2020. The geographical distribution of SARS-CoV-2 in Italy during early 2020 has not been homogeneous, including regions severely affected as well as administrative areas being only slightly interested by the infection. Among the latter, Sardinia represents one of the lowest incidence areas likely due to its insular nature.

Methods

Next-generation sequencing of a small number of complete viral genomes from clinical samples and their virologic and phylogenetic characterization was performed.

Results

We provide a first overview of the SARS-CoV-2 genomic diversity in Sardinia in the early phase of the March-May 2020 pandemic based on viral genomes isolated in the most inner regional hospital of the island. Our analysis revealed a remarkable genetic diversity in local SARS-CoV-2 viral genomes, showing the presence of at least four different clusters that can be distinguished by specific amino acid substitutions. Based on epidemiological information, these sequences can be linked to at least eight different clusters of infection, four of which likely originates from imported cases. In addition, the presence of amino acid substitutions that were not previously reported in Italian patients has been observed, asking for further investigations in a wider population to assess their prevalence and dynamics of emergence during the pandemic.

Conclusion

The present study provides a snapshot of the initial phases of the SARS-CoV-2 infection in inner area of the Sardinia Island, showing an unexpected genomic diversity.

Understanding the implications of SARS-CoV-2 re-infections on immune response milieu, laboratory tests and control measures against COVID-19

Several months after the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), cases of re-infection after recovery were reported. The extent and duration of protective immunity after SARS-CoV-2 infection is not fully understood. As such, the possibility of re-infection with SARS-CoV-2. Furthermore, cases of re-infection were mainly due to different variants or mutant SARS-CoV-2. Following the fast and pandemic-scale spread of COVID-19, mutations in SARS-CoV-2 have raised new diagnostic challenges which include the redesign of the oligonucleotide sequences used in RT-PCR assays to avoid potential primer-sample mismatches, and decrease sensitivities. Since the initial wave of the pandemic, some regions had experienced fresh outbreaks, predisposing people to be susceptible to SARS-CoV-2 re-infection. Hence, this article sought to offer detailed biology of SARS-CoV-2 re-infections and their implications on immune response milieu, diagnostic laboratory tests and control measures against COVID-19.

Prevention and control of COVID-19 in pastoral community through One Health Approach

The vast majority of its population being a pastoralist community, the Somali region in Ethiopia shares the longest border with its neighboring east African countries. These communities face a high risk for transmission of imported COVID-19 cases and remain vulnerable due to lack of access to health delivery and low utilisation of services. Valuable lessons from other countries, has placed the One Health Approach as an appropriate, feasible and applicable preventive and control measure for COVID-19. This paper discusses the epidemiological and social susceptibility of pastoral communities in the transmission of COVID-19 and the introduction of One Health Approach as an effective inter-disciplinary response and management.

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with >1000 cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely sampled from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide "lockdown" (8 March-3 June). These were combined with 460 published SARS-CoV-2 sequences sampled across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy.

One Health in the context of coronavirus outbreaks: A systematic literature review

The ongoing coronavirus disease 2019 (COVID-19) pandemic threatens global health thereby causing unprecedented social, economic, and political disruptions. One way to prevent such a pandemic is through interventions at the human-animal-environment interface by using an integrated One Health (OH) approach. This systematic literature review documented the three coronavirus outbreaks, i.e. SARS, MERS, COVID-19, to evaluate the evolution of the OH approach, including the identification of key OH actions taken for prevention, response, and control. The OH understandings identified were categorized into three distinct patterns: institutional coordination and collaboration, OH in action/implementation, and extended OH (i.e. a clear involvement of the environmental domain). Across all studies, OH was most often framed as OH in action/implementation and least often in its extended meaning. Utilizing OH as institutional coordination and collaboration and the extended OH both increased over time. OH actions were classified into twelve sub-groups and further categorized as classical OH actions (i.e. at the human-animal interface), classical OH actions with outcomes to the environment, and extended OH actions. The majority of studies focused on human-animal interaction, giving less attention to the natural and built environment. Different understandings of the OH approach in practice and several practical limitations might hinder current efforts to achieve the operationalization of OH by combining institutional coordination and collaboration with specific OH actions. The actions identified here are a valuable starting point for evaluating the stage of OH development in different settings. This study showed that by moving beyond the classical OH approach and its actions towards a more extended understanding, OH can unfold its entire capacity thereby improving preparedness and mitigating the impacts of the next outbreak.

SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species

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Replication and tropism of SARS-CoV-2 in cattle, sheep, and pigs using EVOCs, were investigated.

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Respiratory tissues of cattle and sheep, but not those of pigs, are able to sustain viral replication.

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A SARS-CoV-2 isolate harbouring mutation D614 G in the S protein has greater replication capabilities.

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SARS-CoV-2 binds to ACE2-expressing cells of the respiratory tract of cattle and sheep.

There is strong evidence that severe acute respiratory syndrome 2 virus (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, originated from an animal reservoir. However, the exact mechanisms of emergence, the host species involved, and the risk to domestic and agricultural animals are largely unknown. Some domestic animal species, including cats, ferrets, and minks, have been demonstrated to be susceptible to SARS-CoV-2 infection, while others, such as pigs and chickens, are not. Importantly, the susceptibility of ruminants to SARS-CoV-2 is unknown, even though they often live in close proximity to humans. We investigated the replication and tissue tropism of two different SARS-CoV-2 isolates in the respiratory tract of three farm animal species - cattle, sheep, and pigs - using respiratory ex vivo organ cultures (EVOCs). We demonstrate that the respiratory tissues of cattle and sheep, but not of pigs, sustain viral replication in vitro of both isolates and that SARS-CoV-2 is associated to ACE2-expressing cells of the respiratory tract of both ruminant species. Intriguingly, a SARS-CoV-2 isolate containing an amino acid substitution at site 614 of the spike protein (mutation D614G) replicated at higher magnitude in ex vivo tissues of both ruminant species, supporting previous results obtained using human cells. These results suggest that additional in vivo experiments involving several ruminant species are warranted to determine their potential role in the epidemiology of this virus.

A COVID-19 Hotspot Area: Activities and Epidemiological Findings

By late March 2020, Villa Caldari, a small village of the municipality of Ortona (Abruzzo region), was registering an incidence rate of COVID-19 cases ten times greater than the overall municipality and was declared a hotspot area. Twenty-two days later, epidemiological investigation and sampling were performed, to evaluate SARS-CoV-2 circulation and the presence of SARS-CoV-2 antibodies. Overall, 681 nasopharyngeal swabs and 667 blood samples were collected. Only one resident of the village resulted in being positive for RNA viral shedding, while 73 were positive for SARS-CoV-2 antibodies. The overall seroprevalence was 10.9%. The difference between the seroprevalence of infection in asymptomatic and symptomatic individuals was significant (χ² = 14.50 p-value = 0.0001). Amongst the residents positive for antibodies, fatigue and/or muscle pain, fever and anosmia were the most experienced symptoms, whose most frequent onset was observed during the first two weeks of March. Familial and habit-related clusters were highlighted. Nevertheless, the investigations showed a low SARS-CoV-2 circulation in the village at the time of the sampling, demonstrating virus transmission could be limited when strict emergency measures are followed. Given the favorable results, the emergency measures were then lifted.

Whole Genome Sequencing Characterization of HEV3-e and HEV3-f Subtypes among the Wild Boar Population in the Abruzzo Region, Italy: First Report

Hepatitis E virus (HEV) is an emergent zoonotic pathogen, causing worldwide acute and chronic hepatitis in humans. HEV comprises eight genotypes and several subtypes. HEV genotypes 3 and 4 (HEV3 and HEV4) are zoonotic. In Italy, the most part of HEV infections (80%) is due to autochthonous HEV3 circulation of the virus, and the key role played by wild animals is generally accepted. Abruzzo is an Italian region officially considered an HEV "hot spot", with subtype HEV3-c being up to now the only one reported among wild boars. During the year 2018-2019, a group of wild boars in Abruzzo were screened for HEV; positive RNA liver samples were subjected to HEV characterization by using the whole genome sequencing (WGS) approach methodology. This represents the first report about the detection of HEV-3 subtypes e and f in the wild boar population in this area. Since in Italy human infections from HEV 3-e and f have been associated with pork meat consumption, our findings deserve more in-depth analysis with the aim of evaluating any potential correlation between wild animals, the pork chain production and HEV human infections.

Emergence of European and North American mutant variants of SARS-CoV-2 in South-East Asia

The SARS-CoV-2 coronavirus is responsible for the current COVID-19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this virus is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID-19 is increasing at an alarming pace within subtropical South-East Asian nations with high temperatures and humidity. To understand this spread, we analysed 444 genome sequences of SARS-CoV-2 available on the GISAID platform from six South-East Asian countries. Multiple sequence alignments and maximum-likelihood phylogenetic analyses were performed to analyse and characterize the non-synonymous (NS) mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in other countries indicates possible transmission routes. Unique spike protein and non-structural protein mutations were observed circulating within confined area of a given country. We divided the circulating viral strains into four major groups and three subgroups on the basis of the most frequent NS mutations. Strains with a unique set of four co-evolving mutations were found to be circulating at a high frequency within India, specifically. Group 2 strains characterized by two co-evolving NS mutants which alter in RdRp (P323L) and spike (S) protein (D614G) were found to be common in Europe and North America. These European and North American variants have rapidly emerged as dominant strains within South-East Asia, increasing from a 0% prevalence in January to an 81% by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present a large threat to South-East Asia for the coming winter.

SARS-CoV-2 RNA Persistence in Naso-Pharyngeal Swabs

Since February 2020, Italy has been seriously affected by the SARS-CoV-2 pandemic. To support the National Health Care system, naso-pharyngeal/oropharyngeal swabs collected from suspected cases of Teramo province, Abruzzo region, are tested at Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, for the presence of SARS-CoV-2 RNA. Out of 12,446 tested individuals, 605 returned positive results at least once, with prevalence significantly higher in men. A reduction of the level of viral RNA in the first swab per each positive patient collected over time was also observed. Moreover, 81 patients had at least one positive sample and two final negative tests: positivity in swabs lasted from 14 to 63 days, with a median value of 30 days. This shows the potential for the virus to coexist with patients for a long time, although we highlighted intermittent positivity in several cases. The evolution of the SARS-CoV-2 epidemiological situation and knowledge on viral shedding should be closely monitored, to interpret the findings correctly and adjust accordingly the surveillance activities.

Evidence for mutations in SARS-CoV-2 Italian isolates potentially affecting virus transmission

Italy is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) transmission and disease impact after coronavirus disease‐2019 pandemia started in China. Even though the presence of mutations on spike glycoprotein and nucleocapsid in Italian isolates has been reported, the potential impact of these mutations on viral transmission has not been evaluated. We have compared SARS‐CoV‐2 genome sequences from Italian patients with virus sequences from Chinese patients. We focussed upon three nonsynonymous mutations of genes coding for S(one) and N (two) viral proteins present in Italian isolates and absent in Chinese ones, using various bioinformatics tools. Amino acid analysis and changes in three‐dimensional protein structure suggests the mutations reduce protein stability and, particularly for S1 mutation, the enhanced torsional ability of the molecule could favor virus binding to cell receptor(s). This theoretical interpretation awaits experimental and clinical confirmation.

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two highly prevalent mutation have been developed by SARS‐CoV‐2, one on the Spike glycoprotein and one on the Nucleocapsid protein

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The enhanced torsional ability of Spike protein could favor virus binding to human cell receptors

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mutations on the Nucleocapsid region could influence the modulation of a number of virus properties, including cell signaling

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the study of SARS‐CoV‐2 mutations could be important for vaccines developmen

A Guide to COVID-19: a global pandemic caused by the novel coronavirus SARS-CoV-2

The emergence of the SARS-CoV-2 strain of the human coronavirus has thrown the world into the midst of a new pandemic. In the human body, the virus causes COVID-19, a disease characterized by shortness of breath, fever, and pneumonia, which can be fatal in vulnerable individuals. SARS-CoV-2 has characteristics of past human coronaviruses, with close genomic similarities to SARS-CoV, the virus that causes the disease SARS. Like these related coronaviruses, SARS-CoV-2 is transmitted through the inhalation of droplets and interaction with contaminated surfaces. Across the world, laboratories are developing candidate vaccines for the virus - with vaccine trials underway in the United States and the United Kingdom - and considering various drugs for possible treatments and prophylaxis. Here, we provide an overview of SARS-CoV-2 by analyzing its virology, epidemiology, and modes of transmission while examining the current progress of testing procedures and possible treatments through drugs and vaccines.

Severe acute respiratory syndrome coronavirus 2: virus mutations in specific European populations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is being intensively studied, particularly its evolution, in the increasingly available sequences between countries/continents with classical phylogenetic tree representation. More recently, certain protein mutations have been correlated with specific functional impacts. Our clinical data from patients suggest that clinical symptoms differ between European countries. Among other factors, SARS-CoV-2 mutations could explain these disparities. Our analyses point to an association of diverse mutations, including co-evolving ones, in a few SARS-CoV-2 proteins within specific countries. We therefore suggest combining clinical information from patients and the determination of the associated SARS-CoV-2 genome to better understand the specific symptoms.

Association of procalcitonin levels with the progression and prognosis of hospitalized patients with COVID-19

Rationale: Coronavirus disease 2019 (COVID-19) was first announced in Wuhan, and has rapidly evolved into a pandemic. However, the risk factors associated with the severity and mortality of COVID-19 are yet to be described in detail. Methods: We retrospectively reviewed the information of 1525 cases from the Leishenshan Hospital in Wuhan. Univariate and multivariate Cox regression analyses were generated to explore the relationship between procalcitonin (PCT) level and the progression and prognosis of COVID-19. Univariate and multivariate logistic regression analyses were performed to explore the relationship between disease severity in hospitalized patients and their PCT levels. Survival curves and the cumulative hazard function for COVID-19 progression were conducted in the two groups. To further detect the relationship between the computed tomography score and survival days, curve-fitting analyses were performed. Results: Patients in the elevated PCT group had a higher incidence of severe and critical severity conditions (P < 0.001), death, and higher computed tomography (CT) scores. There was an association between elevated PCT levels and mortality in the univariate ((hazard ratio [1], 3.377; 95% confidence interval [2], 1.012-10.344; P = 0.033) and multivariate Cox regression analysis (HR, 4.933; 95% CI, 1.170-20.788; P = 0.030). Similarly, patients with elevated PCT were more likely to have critically severe disease conditions in the univariate (odds ratio [2], 7.247; 95% CI, 3.559-14.757; P < 0.001) and multivariate logistic regression analysis (OR, 10.679; 95% CI, 4.562-25.000; P < 0.001). Kaplan-Meier curves showed poorer prognosis for patients with elevated PCT (P = 0.024). The CT score 1 for patients with elevated PCT peaked at day 40 following the onset of symptoms then decreased gradually, while their total CT score was relatively stable. Conclusion: PCT level was shown as an independent risk factor of in-hospital mortality among COVID-19 patients. Compared with inpatients with normal PCT levels, inpatients with elevated PCT levels had a higher risk for overall mortality and critically severe disease. These findings may provide guidance for improving the prognosis of patients with critically severe COVID-19.