Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2

To reconstruct the evolutionary dynamics of the 2019 novel-coronavirus recently causing an outbreak in Wuhan, China, 52 SARS-CoV-2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 7 10 124 subs/site/year (range, 1.1 7 10 124-15 7 10 124) and a mean tMRCA of the tree root of 73 days. The estimated R value was 2.6 (range, 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing

Contribution of transgender sex workers to the complexity of the HIV-1 epidemic in the metropolitan area of Milan

Objectives: Transgender people are disproportionately affected by the HIV-1 epidemic. We evaluated the origin of HIV-1 variants carried by South American transgenders living in Milan by combining accurate phylogenetic methods and epidemiological data. Methods: We collected 156 HIV-1 pol sequences obtained from transgender patients engaged in sex work (TSWs) followed between 1999 and 2015 at L. Sacco Hospital, Milan, Italy. Phylogenetic analyses were conducted by HIV-TRACE, MrBayes, MacClade and Beast programs. Reference sequences were retrieved from Los Alamos and local databases. Last negative testing or proxy data from clinical records of infected individuals were used to investigate the country of infection. Results: Among South American TSWs, the most represented HIV-1 subtypes were B (70.5%), F1 (12.8%) and C (4.4%). Gene flow migrations of B subtype indicated significant fluxes from TSWs to Italians (21.3%) belonging to all risk groups (26.4% to heterosexuals (HEs), 18.9% to men who have sex with men (MSM), 15.1% to injecting drug users). The largest proportion of bidirectional fluxes were observed between Italians and TSWs (24.6%). For F1 subtype, bidirectional viral fluxes involved TSWs and Italians (7.1% and 14.3%), and a similar proportion of fluxes linked TSWs and Italian HEs or MSM (both 15.8%). Significant fluxes were detected from Italians to TSWs for subtype C involving both MSM (30%) and HEs (40%). Country of HIV-1 acquisition was identified for 72 subjects; overall, the largest proportion of patients with B subtype (73.5%) acquired HIV-1 infection in South America. Conclusions: Our results indicated that South American transgenders largely contribute to the heterogeneity of HIV-1 variants in our country. The high number of clusters based on all subtypes indicated numerous transmission chains in which TSWs were constantly intermixed with HEs and MSM. Our results strongly advocate interventions to facilitate prevention, diagnosis and HIV-1 care continuum among transgender people

Clinical characterization and whole genome sequence-based typing of two cases of endophthalmitis due to Listeria monocytogenes

Endophthalmitis due to Listeria monocytogenes is a rare form of listeriosis. Here, we report two cases that occurred in patients with different medical history, a 46-years-old woman with no comorbidities and an elderly man with several comorbidities. There was no history of trauma or surgery in either patient suggesting an endogenous origin. Despite antibiotic treatment, both patients showed poor visual acuity outcomes. Subtyping clinical isolates using whole genome sequencing could allow to characterise Listeria monocytogenes strains involved in rare clinical manifestation, such as in unusual anatomical sites, even in immunocompetent patients

Human‐to‐cat sars‐cov‐2 transmission: Case report and full‐genome sequencing from an infected pet and its owner in Northern Italy

There have been previous reports of the human‐to‐cat transmission of SARS‐CoV‐2, but there are only a few molecular studies that have compared the whole genome of the virus in cats and their owners. We here describe a case of domestic SARS‐CoV‐2 transmission from a healthcare worker to his cat for which nasopharyngeal swabs of both the cat and its owner were used for full-genome analysis. The results indicate that quarantine measures should be extended to pets living in SARS‐CoV‐2‐infected households

Phylogenetic analysis of human immunodeficiency virus type 2 group B

Context: Human immunodeficiency virus type 2 (HIV-2) infections are mainly restricted to West Africa; however, in the recent years, the prevalence of HIV-2 is a growing concern in some European countries and the Southwestern region of India. Despite the presence of different HIV-2 groups, only A and B Groups have established human-to-human transmission chains. Aims: This work aimed to evaluate the phylogeographic inference of HIV-2 Group B worldwide to estimate their data of origin and the population dynamics. Materials and Methods: The evolutionary rates, the demographic history for HIV-2 Group B dataset, and the phylogeographic analysis were estimated using a Bayesian approach. The viral gene flow analysis was used to count viral gene out/in flow among different locations. Results: The root of the Bayesian maximum clade credibility tree of HIV-2 Group B dated back to 1957. The demographic history of HIV-2 Group B showed that the epidemic remained constant up to 1970 when started an exponential growth. From 1985 to early 2000s, the epidemic reached a plateau, and then it was characterized by two bottlenecks and a new plateau at the end of 2000s. Phylogeographic reconstruction showed that the most probable location for the root of the tree was Ghana. Regarding the viral gene flow of HIV-2 Group B, the only observed viral gene flow was from Africa to France, Belgium, and Luxembourg. Conclusions: The study gives insights into the origin, history, and phylogeography of HIV-2 Group B epidemic. The growing number of infections of HIV-2 worldwide indicates the need for strengthening surveillance

Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves

Ebola virus Zaire (EBOV) has reemerged in Africa, emphasizing the global importance of this pathogen. Amidst the response to the current epidemic, several gaps in our knowledge of EBOV evolution are evident. Specifically, uncertainty has been raised regarding the potential emergence of more virulent viral variants through amino acid substitutions. Glycoprotein (GP), an essential component of the EBOV genome, is highly variable and a potential site for the occurrence of advantageous mutations. For this study, we reconstructed the evolutionary history of EBOV by analyzing 65 GP sequences from humans and great apes over diverse locations across epidemic waves between 1976 and 2014. We show that, although patterns of spatial dispersion throughout Africa varied, the evolution of the virus has largely been characterized by neutral genetic drift. Therefore, the radical emergence of more transmissible variants is unlikely, a positive finding, which is increasingly important on the verge of vaccine deployment

Genetic diversity of hepatitis B virus (HBV) in Madagascar

Hepatitis B virus (HBV) is a DNA virus belonging to Hepadnaviridae family. Chronic infection with HBV is one major risk factor of hepatic disease. In Madagascar, former studies classified the country as part of high endemic area, as HBV prevalence can reach 23% in general population. However, this prevalence differs largely between urban and rural areas and is estimated to be respectively 5% and 26%. The aims of the present study were to describe the genetic diversity of HBV strains from different regions of Madagascar, and to describe the viral gene flow throughout the country by using phylogenetic analysis. This is the first large-scale molecular and phylogenetic study analyzing HBV sequences from 28 different Malagasy areas, never sampled in the past. In this study, the most prevalent genotype/sub-genotypes was E. Migration analysis showed a gene flow from zone 3 (rural) to zone 2 (suburban) and a greater gene flow from the middle part of Madagascar to the north than to the south. It is important to study the HBV infections in Madagascar and to monitor the potential spread of this viral strain inside this country

Bayesian phylogeography of Crimean-Congo hemorrhagic fever virus in Europe

Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In order to reconstruct the origin and pathway of the worldwide dispersion of the virus at global and regional (eastern European) level, we investigated the phylogeography of the infection by analysing 121 publicly available CCHFV S gene sequences including two recently characterised Albanian isolates. The spatial and temporal phylogeny was reconstructed using a Bayesian Markov chain Monte Carlo approach, which estimated a mean evolutionary rate of 2.96 7 10-4 (95%HPD=1.6 and 4.7 7 10-4) substitutions/site/year for the analysed fragment. All of the isolates segregated into seven highly significant clades that correspond to the known geographical clades: in particular the two new isolates from northern Albania clustered significantly within the Europe 1 clade. Our phylogeographical reconstruction suggests that the global CCHFV clades originated about one thousand years ago from a common ancestor probably located in Africa. The virus then spread to Asia in the XV century and entered Europe on at least two occasions: the first in the early 1800s, when a still circulating but less or non-pathogenic virus emerged in Greece and Turkey, and the second in the early 1900s, when a pathogenic CCHFV strain began to spread in eastern Europe. The most probable location for the origin of this European clade 1 was Russia, but Turkey played a central role in spreading the virus throughout Europe. Given the close proximity of the infected areas, our data suggest that the movement of wild and domestic ungulates from endemic areas was probably the main cause of the dissemination of the virus in eastern Europe

Genetic characterisation of Measles virus variants identified during a large epidemic in Milan, Italy, March–December 2017

In 2017, Italy experienced a large measles epidemic with 5408 cases and four deaths. As Subnational Reference Laboratory of the Measles and Rubella surveillance NETwork (MoRoNET), the EpiSoMI (Epidemiology and Molecular Surveillance of Infections) Laboratory (University of Milan) set up rapid and active surveillance for the complete characterisation of the Measles virus (Mv) responsible for the large measles outbreak in Milan and surrounding areas (Lombardy, Northern Italy). The aims of this study were to describe the genetic profile of circulating viruses and to track the pathway of measles transmission. Molecular analysis was performed by sequencing the highly variable 450 nucleotides region of the N gene (N-450) of Mv genome. Two-hundred and ninety-nine strains of Mv were analysed. The phylogenetic analysis showed five different variants, two not previously described in the studied area, belonging to D8 and B3 genotypes. Three events of continuous transmission of autochthonous variants (D8-Osaka, D8-London and B3-Milan variants) and two events of continuous transmission of imported variants (B3-Dublin and D8-Hulu Langat) tracked five different transmission pathways. These pathways outlined two epidemic peaks: the first in April and the second in July 2017. The correlation between Mv variant and the epidemiological data may enable us to identify the sources of virus importation and recognise long-lasting virus transmission pathways

Genomica in Sanità Pubblica. Evidenze scientifiche e prospettive di integrazione nella pratica della prevenzione

I miglioramenti registrati negli ultimi anni nella qualità del sequenziamento di nuova generazione, nella riduzione dei costi associati e in una complessiva evoluzione delle scienze omiche, hanno favorito lo sviluppo della medicina personalizzata o di precisione. Ad oggi, anche a livello di popolazione si possono ottenere dei benefici rilevanti attraverso tale approccio. La Sanità Pubblica di precisione consiste nel fornire il giusto intervento, alla popolazione che ne ha necessità, nel momento e con le modalità opportune. Significa, quindi, promuovere metodologie accurate per identificare e misurare le patologie ma anche le esposizioni, i comportamenti e la suscettibilità. La Sanità Pubblica di precisione è in evoluzione e non è legata semplicemente a geni, trattamenti e malattia ma alla precisa identificazione e risposta ai bisogni di salute. È necessario, quindi, discutere dell’inclusione delle scienze omiche in Sanità Pubblica. La medicina si è evoluta da un modello di diagnosi e trattamento basato essenzialmente sui sintomi ad uno sempre più dipendente dalla definizione bioinformatica di profili di rischio e/o patologici. Tali profili sono delineati mediante la produzione di informazioni attingendo a solide banche dati biologiche con il supporto dell’intelligenza artificiale. D’altra parte l’evoluzione nella pratica sanitaria è un processo complesso che include, tra l’altro, la sostenibilità dei costi sanitari, la valutazione dell’efficienza nella pratica clinica, l'integrazione dei nuovi progressi tecnologici e la rimodulazione dell'organizzazione dei servizi. Nel Gruppo di Lavoro Genomica in Sanità Pubblica della SItI, attivo dal 2012, sono coinvolti prevalentemente docenti universitari ma anche operatori del Ministero della Salute e dei Dipartimenti di Prevenzione. In questo special issue illustriamo alcuni argomenti di ricerca trattati. Non stupirà l’eterogeneità dei temi proposti vista la trasversalità delle scienze omiche in molteplici aspetti della salute umana. In particolare sono illustrati esempi che vanno dalla prevenzione di tumori ad alta incidenza, alla prevenzione di patologie infettive, sia per gli aspetti acuti che cronici, tenendo conto di caratteristiche genetiche ed epigenetiche della popolazione. Inoltre, illustriamo le prospettive di integrazione offerte allo studio del microbiota umano nella prevenzione. Procediamo con la discussione delle modalità di valutazione dei test genetici e genomici per la loro integrazione nell’offerta del Servizio Sanitario Nazionale. Infine, è illustrato il coinvolgimento della popolazione nell’impiego delle tecnologie omiche al fine di promuovere un cambiamento culturale nei confronti delle tecnologie disponibili e nella tutela della salute individuale e collettiva