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

Molecular analysis of hepatitis C virus infection in Bulgarian injecting drug users

Intravenous drug users constitute a group at risk for hepatitis C virus (HCV) infection. Today, no data are available on the molecular epidemiology of HCV in Bulgaria despite the fact that in recent years the incidence of acute hepatitis C infection among Bulgarian intravenous drug users increased sixfold and about 2/3 of them developed a chronic infection. The aim of this study was to determine the circulation of hepatitis C genotypes among drug users and to study the evolution and transmission history of the virus by molecular clock and Bayesian methods, respectively. Sequencing of NS5B gene showed that the genotype 3a was the most prevalent type among intravenous drug users. In the Bayesian tree, the 3a subtypes grouped in one main clade with one small cluster well statistically supported. The root of the tree was dated back to the year 1836, and the main clade from Bulgaria was dated 1960. The effective number of infections remained constant until about years 1950s, growing exponentially from the 1960s to the 1990s, reaching a plateau in the years 2000. The not significant intermixing with isolates from other countries may suggest a segregated circulation of the epidemic between 1940s and 1980s. The plateau reached by the epidemic in the early 2000s may indicate the partial success of the new preventive policies adopted in Bulgaria. J. Med. Virol. 83:1565-1570, 2011. © 2011 Wiley-Liss, Inc

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

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

Human papillomavirus detection in paraffin-embedded colorectal cancer tissues

Human papillomavirus (HPV) has a well-recognized aetiological role in the development of cervical cancer and other anogenital tumours. Recently, an association between colorectal cancer and HPV infection has been suggested, although this is still controversial. This study aimed at detecting and characterizing HPV infection in 57 paired biopsies from colorectal cancers and adjacent intact tissues using a degenerate PCR approach. All amplified fragments were genotyped by means of sequencing. Overall, HPV prevalence was 12.3 %. In particular, 15.8% of tumour tissues and 8.8% of non-cancerous tissue samples were HPV DNA-positive. Of these samples, 85.7% were genotyped successfully, with 41.7% of sequences identifying four genotypes of the HR (high oncogenic risk) clade Group 1; the remaining 58.3% of HPVgenotyped specimens had an unclassified \u3b2-HPV. Examining additional cases and analysing whole genomes will help to outline the significance of these findings

Genetic analysis of human and swine influenza A viruses isolated in Northern Italy during 2010–2015

Summary Influenza A virus (IAV) infection in swine plays an important role in the ecology of influenza viruses. The emergence of new IAVs comes through different mechanisms, with the genetic reassortment of genes between influenza viruses, also originating from different species, being common. We performed a genetic analysis on 179 IAV isolates from humans (n. 75) and pigs (n. 104) collected in Northern Italy between 2010 and 2015, to monitor the genetic exchange between human and swine IAVs. No cases of human infection with swine strains were noticed, but direct infections of swine with H1N1pdm09 strains were detected. Moreover, we pointed out a continuous circulation of H1N1pdm09 strains in swine populations evidenced by the introduction of internal genes of this subtype. These events contribute to generating new viral variants—possibly endowed with pandemic potential—and emphasize the importance of continuous surveillance at both animal and human level

Potential of the three-Terminal heterojunction bipolar transistor solar cell for space applications

Multi-Terminal multi-junction solar cells (MJSC) offer higher efficiency potential than series connected (two-Terminal) ones. In addition, for terrestrial applications, the efficiency of multi-Terminal solar cells is less sensitive to solar spectral variations than the two-Terminal series-connected one. In space, generally, cells are always illuminated with AM0 spectrum and no impact is expected from spectral variations. Still, in space, the multi-Terminal approach offers some advantages in comparison with the series-connected architecture approach derived from a higher end of life (EOL) efficiency. In this work we review the potential of multi-Terminal solar cells for achieving extended EOL efficiencies with emphasis in the potential of the three-Terminal heterojunction bipolar transistor solar cell, a novel multi-Terminal MJSC architecture with a simplified structure not requiring, for example, tunnel junctions

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

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