Publications by authors named "Marco Salemi"

163 Publications

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020.

PLoS One 2021 13;16(1):e0245352. Epub 2021 Jan 13.

Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.

In February and March, 2020, environmental surface swab samples were collected from the handle of the main entry door of a major university building in Florida, as part of a pilot surveillance project screening for influenza. Samples were taken at the end of regular classroom hours, between the dates of February 1-5 and February 19-March 4, 2020. Influenza A(H1N1)pdm09 virus was isolated from the door handle on four of the 19 days sampled. Both SARS-CoV-2 and A(H1N1)pdm09 virus were detected in a sample collected on February 21, 2020. Based on sequence analysis, the Florida SARS-CoV-2 strain (designated UF-11) was identical to strains being identified in Washington state during the same time period, while the earliest similar sequences were sampled in China/Hubei between Dec 30th 2019 and Jan 5th 2020. The first human case of COVID-19 was not officially reported in Florida until March 1st. In an analysis of sequences from COVID-19 patients in this region of Florida, there was only limited evidence of subsequent dissemination of the UF-11 strain. Identical or highly similar strains, possibly related through a common transmission chain, were detected with increasing frequency in Washington state between end of February and beginning of March. Our data provide further documentation of the rapid early spread of SARS-CoV-2 and underscore the likelihood that closely related strains were cryptically circulating in multiple U.S. communities before the first "official" cases were recognized.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245352PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7806172PMC
January 2021

Collection of SARS-CoV-2 Virus from the Air of a Clinic Within a University Student Health Care Center and Analyses of the Viral Genomic Sequence.

Aerosol Air Qual Res 2020 Jun 25;20(6):1167-1171. Epub 2020 May 25.

Department of Environmental Engineering Sciences, University of Florida.

The progression of COVID-19 worldwide can be tracked by identifying mutations within the genomic sequence of SARS-CoV-2 that occur as a function of time. Such efforts currently rely on sequencing the genome of SARS-CoV-2 in patient specimens (direct sequencing) or of virus isolated from patient specimens in cell cultures. A pilot SARS-CoV-2 air sampling study conducted at a clinic within a university student health care center detected the virus vRNA, with an estimated concentration of 0.87 virus genomes L air. To determine whether the virus detected was viable ('live'), attempts were made to isolate the virus in cell cultures. Virus-induced cytopathic effects (CPE) were observed within two days post-inoculation of Vero E6 cells with collection media from air samples; however, rtRT-PCR tests for SARS-CoV-2 vRNA from cell culture were negative. Instead, three other fast-growing human respiratory viruses were isolated and subsequently identified, illustrating the challenge in isolating SARS-CoV-2 when multiple viruses are present in a test sample. The complete SAR-CoV-2 genomic sequence was nevertheless determined by Sanger sequencing and most closely resembles SARS-CoV-2 genomes previously described in Georgia, USA. Results of this study illustrate the feasibility of tracking progression of the COVID-19 pandemic using environmental aerosol samples instead of human specimens. Collection of a positive sample from a distance more than 2 m away from the nearest patient traffic implies the virus was in an aerosol.
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http://dx.doi.org/10.4209/aaqr.2020.02.0202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7792982PMC
June 2020

Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets.

J Neurovirol 2021 Jan 6. Epub 2021 Jan 6.

Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.

Despite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals' quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified. We investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n = 11), with or without CD8+ lymphocyte depletion, based on detectable (n = 6) or non-detectable (n = 5) presence of the virus in frontal cortex tissues. Significant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion. In addition, transcripts of four poly (ADP-ribose) polymerases (PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction. Our results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology.
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http://dx.doi.org/10.1007/s13365-020-00927-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786889PMC
January 2021

Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements.

Int J Mol Sci 2020 Dec 23;22(1). Epub 2020 Dec 23.

Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA.

Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has mainly been driven by purifying selection, suggesting the presence of conserved structural features. Our dynamic simulations identified two main long-range covariant dynamic movements of the novel glycoprotein, and showed that, as a result of the evolutionary duality, they are preserved. The first movement involves the receptor binding domain with the -terminal domain and the -terminal domain 2 and is maintained across human, bat and pangolin coronaviruses. The second is a complex network of long-range dynamics specific to SARS-CoV-2 involving the novel PRRA and the conserved KR*SF cleavage sites, as well as conserved segments in -terminal domain 3. These movements, essential for host cell binding, are maintained by hinges conserved across human, bat, and pangolin coronaviruses glycoproteins. The hinges, located around Threonine 333 and Proline 527 within the -terminal domain and -terminal domain 2, represent candidate targets for the future development of novel pan-coronavirus inhibitors. In summary, we show that while recombination created a new configuration that increased the covariant dynamic movements of the SARS-CoV-2 glycoprotein, negative selection preserved its inter-domain structure throughout evolution in different hosts and inter-species transmissions.
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http://dx.doi.org/10.3390/ijms22010080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794730PMC
December 2020

Authors' Reply to: Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on "A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis".

JMIR Public Health Surveill 2020 11 11;6(4):e24661. Epub 2020 Nov 11.

Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.

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http://dx.doi.org/10.2196/24661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688377PMC
November 2020

Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics.

bioRxiv 2020 Nov 6. Epub 2020 Nov 6.

Although the global response to COVID-19 has not been entirely unified, the opportunity arises to assess the impact of regional public health interventions and to classify strategies according to their outcome. Analysis of genetic sequence data gathered over the course of the pandemic allows us to link the dynamics associated with networks of connected individuals with specific interventions. In this study, clusters of transmission were inferred from a phylogenetic tree representing the relationships of patient sequences sampled from December 30, 2019 to April 17, 2020. Metadata comprising sampling time and location were used to define the global behavior of transmission over this earlier sampling period, but also the involvement of individual regions in transmission cluster dynamics. Results demonstrate a positive impact of international travel restrictions and nationwide lockdowns on global cluster dynamics. However, residual, localized clusters displayed a wide range of estimated initial secondary infection rates, for which uniform public health interventions are unlikely to have sustainable effects. Our findings highlight the presence of so-called "super-spreaders", with the propensity to infect a larger-than-average number of people, in countries, such as the USA, for which additional mitigation efforts targeting events surrounding this type of spread are urgently needed to curb further dissemination of SARS-CoV-2.
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http://dx.doi.org/10.1101/2020.11.06.370999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7654859PMC
November 2020

Genetic Markers of Adaptation of Plasmodium falciparum to Transmission by American Vectors Identified in the Genomes of Parasites from Haiti and South America.

mSphere 2020 10 21;5(5). Epub 2020 Oct 21.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

The malaria parasite, , was introduced into Hispaniola and other regions of the Americas through the slave trade spanning the 16th through the 19th centuries. During this period, more than 12 million Africans were brought across the Atlantic to the Caribbean and other regions of the Americas. Since malaria is holoendemic in West Africa, a substantial percentage of these individuals carried the parasite. St. Domingue on Hispaniola, now modern-day Haiti, was a major port of disembarkation, and malaria is still actively transmitted there. We undertook a detailed study of the phylogenetics of the Haitian parasites and those from Colombia and Peru utilizing whole-genome sequencing. Principal-component and phylogenetic analyses, based upon single nucleotide polymorphisms (SNPs) in protein coding regions, indicate that, despite the potential for millions of introductions from Africa, the Haitian parasites share an ancestral relationship within a well-supported monophyletic clade with parasites from South America, while belonging to a distinct lineage. This result, in stark contrast to the historical record of parasite introductions, is best explained by a severe population bottleneck experienced by the parasites introduced into the Americas. Here, evidence is presented for targeted selection of rare African alleles in genes which are expressed in the mosquito stages of the parasite's life cycle. These genetic markers support the hypothesis that the severe population bottleneck was caused by the required adaptation of the parasite to transmission by new definitive hosts among the () spp. found in the Caribbean and South America. Historical data suggest that millions of parasite lineages were introduced into the Americas during the trans-Atlantic slave trade, which would suggest a paraphyletic origin of the extant isolates in the Western Hemisphere. Our analyses of whole-genome variants show that the American parasites belong to a well-supported monophyletic clade. We hypothesize that the required adaptation to American vectors created a severe bottleneck, reducing the effective introduction to a few lineages. In support of this hypothesis, we discovered genes expressed in the mosquito stages of the life cycle that have alleles with multiple, high-frequency or fixed, nonsynonymous mutations in the American populations which are rarely found in African isolates. These alleles appear to be in gene products critical for transmission through the anopheline vector. Thus, these results may inform efforts to develop novel transmission-blocking vaccines by identifying parasite proteins functionally interacting with the vector that are important for successful transmission. Further, to the best of our knowledge, these are the first whole-genome data available from Haitian isolates. Defining the genome of these parasites provides genetic markers useful for mapping parasite populations and monitoring parasite movements/introductions.
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http://dx.doi.org/10.1128/mSphere.00937-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7580960PMC
October 2020

Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study.

Viruses 2020 08 22;12(9). Epub 2020 Aug 22.

Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, FL 32610, USA.

Molecular HIV surveillance is a promising public health strategy for curbing the HIV epidemic. Clustering technologies used by health departments to date are limited in their ability to infer/forecast cluster growth trajectories. Resolution of the spatiotemporal dynamics of clusters, through phylodynamic and phylogeographic modelling, is one potential strategy to develop a forecasting tool; however, the projected utility of this approach needs assessment. Prior to incorporating novel phylodynamic-based molecular surveillance tools, we sought to identify possible issues related to their feasibility, acceptability, interpretation, and utility. Qualitative data were collected via focus groups among field experts ( = 17, 52.9% female) using semi-structured, open-ended questions. Data were coded using an iterative process, first through the development of provisional themes and subthemes, followed by independent line-by-line coding by two coders. Most participants routinely used molecular methods for HIV surveillance. All agreed that linking molecular sequences to epidemiological data is important for improving HIV surveillance. We found that, in addition to methodological challenges, a variety of implementation barriers are expected in relation to the uptake of phylodynamic methods for HIV surveillance. The participants identified several opportunities to enhance current methods, as well as increase the usability and utility of promising works-in-progress.
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http://dx.doi.org/10.3390/v12090921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551766PMC
August 2020

New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations.

J Chem Inf Model 2020 Oct 17;60(10):5011-5025. Epub 2020 Aug 17.

Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy.

Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious questions. Thirteen VP1 structures with mutations mapping to the RNA entry site were analyzed using molecular dynamics simulations, and the results were combined with the experimental findings reported previously. The results revealed structural fluctuations in the protein-protein recognition sites and in the bottleneck of the RNA entry site that may affect the interaction of different proteins and delay the initiation of the viral replication, respectively. Altogether, the structural analysis of VP1 in the region crucial for the initiation of the viral replication, mainly the bottleneck site, may boost efforts to develop antivirals, as they might complement the available vaccines.
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http://dx.doi.org/10.1021/acs.jcim.0c00475DOI Listing
October 2020

Correction: A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.

JMIR Public Health Surveill 2020 08 10;6(3):e22853. Epub 2020 Aug 10.

Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.

[This corrects the article DOI: 10.2196/19170.].
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http://dx.doi.org/10.2196/22853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445602PMC
August 2020

Sociodemographic, ecological, and spatiotemporal factors associated with HIV drug resistance in Florida: a retrospective analysis.

J Infect Dis 2020 Jul 9. Epub 2020 Jul 9.

Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA.

Background: Persons living with HIV (PWH) with resistance to antiretroviral therapy (ART) are vulnerable to adverse HIV-related health outcomes and can contribute to transmission of HIV drug resistance (HIVDR) when non-virally suppressed. The degree to which HIVDR contributes to disease burden in Florida -the US state with the highest HIV incidence- is unknown.

Methods: We explored sociodemographic, ecological, and spatial-temporal associations of HIVDR. HIV-1 sequences (n=34,447) collected during 2012-2017 were obtained from the Florida Department of Health. HIVDR was categorized by ART class: nucleoside reverse transcriptase inhibitors (NRTI), non-NRTI (NNRTI), protease inhibitors (PI), and integrase inhibitors (INSTI). Multi-drug resistance (MDR) and transmitted-drug resistance (TDR) were also evaluated. Multivariable fixed-effects logistic regression models were fitted to associate individual and county-level sociodemographic and ecological health indicators with HIVDR.

Results: HIVDR prevalence was 19.2% (NRTI), 29.7% (NNRTI), 6.6% (PI), 23.5% (TDR), 13.2% (MDR), and 8.2% (INSTI) with significant variation by Florida county. Individuals who were older, Black, or acquired HIV through mother-to-child transmission had significantly higher odds of HIVDR. HIVDR was linked to counties with lower socioeconomic status, higher unemployment, and poor mental health.

Conclusions: Our findings indicate HIVDR prevalence is higher in Florida than aggregate North American estimates with significant geographic and socioecological heterogeneity.
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http://dx.doi.org/10.1093/infdis/jiaa413DOI Listing
July 2020

A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.

JMIR Public Health Surveill 2020 06 1;6(2):e19170. Epub 2020 Jun 1.

Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been growing exponentially, affecting over 4 million people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published both in scientific journals and through non-peer-reviewed channels to investigate the genetic heterogeneity and spatiotemporal dissemination of SARS-CoV-2. However, a systematic investigation of phylogenetic information and sampling bias in the available data is lacking. Although the number of available genome sequences of SARS-CoV-2 is growing daily and the sequences show increasing phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution.

Objective: The objective of this study was to determine the quality of the currently available SARS-CoV-2 full genome data in terms of sampling bias as well as phylogenetic and temporal signals to inform and guide the scientific community.

Methods: We used maximum likelihood-based methods to assess the presence of sufficient information for robust phylogenetic and phylogeographic studies in several SARS-CoV-2 sequence alignments assembled from GISAID (Global Initiative on Sharing All Influenza Data) data released between March and April 2020.

Results: Although the number of high-quality full genomes is growing daily, and sequence data released in April 2020 contain sufficient phylogenetic information to allow reliable inference of phylogenetic relationships, country-specific SARS-CoV-2 data sets still present severe limitations.

Conclusions: At the present time, studies assessing within-country spread or transmission clusters should be considered preliminary or hypothesis-generating at best. Hence, current reports should be interpreted with caution, and concerted efforts should continue to increase the number and quality of sequences required for robust tracing of the epidemic.
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http://dx.doi.org/10.2196/19170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265655PMC
June 2020

Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host.

Virus Evol 2020 Jan 27;6(1):veaa005. Epub 2020 Apr 27.

Department of Pathology, Immunology, and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32601, USA.

Human immunodeficiency virus (HIV) is a rapidly evolving virus, allowing its genetic sequence to act as a fingerprint for epidemiological processes among, as well as within, individual infected hosts. Though primarily infecting the CD4+ T-cell population, HIV can also be found in monocytes, an immune cell population that differs in several aspects from the canonical T-cell viral target. Using single genome viral sequencing and statistical phylogenetic inference, we investigated the viral RNA diversity and relative contribution of each of these immune cell types to the viral population within the peripheral blood. Results provide evidence of an increased prevalence of circulating monocytes harboring virus in individuals with high viral load in the absence of suppressive antiretroviral therapy. Bayesian phyloanatomic analysis of three of these individuals demonstrated a measurable role for these cells, but not the circulating T-cell population, as a source of cell-free virus in the plasma, supporting the hypothesis that these cells can act as an additional conduit of virus spread.
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http://dx.doi.org/10.1093/ve/veaa005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7185683PMC
January 2020

Under-the-Radar Dengue Virus Infections in Natural Populations of Aedes aegypti Mosquitoes.

mSphere 2020 04 29;5(2). Epub 2020 Apr 29.

Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA

The incidence of locally acquired dengue infections increased during the last decade in the United States, compelling a sustained research effort concerning the dengue mosquito vector, , and its microbiome, which has been shown to influence virus transmission success. We examined the "metavirome" of four populations of mosquitoes collected in 2016 to 2017 in Manatee County, FL. Unexpectedly, we discovered that dengue virus serotype 4 (DENV4) was circulating in these mosquito populations, representing the first documented case of such a phenomenon in the absence of a local DENV4 human case in this county over a 2-year period. We confirmed that all of the mosquito populations carried the same DENV4 strain, assembled its full genome, validated infection orthogonally by reverse transcriptase PCR, traced the virus origin, estimated the time period of its introduction to the Caribbean region, and explored the viral genetic signatures and mosquito-specific virome associations that potentially mediated DENV4 persistence in mosquitoes. We discuss the significance of prolonged maintenance of the DENV4 infections in that occurred in the absence of a DENV4 human index case in Manatee County with respect to the inability of current surveillance paradigms to detect mosquito vector infections prior to a potential local outbreak. Since 1999, dengue outbreaks in the continental United States involving local transmission have occurred only episodically and only in Florida and Texas. In Florida, these episodes appear to be coincident with increased introductions of dengue virus into the region through human travel and migration from countries where the disease is endemic. To date, the U.S. public health response to dengue outbreaks has been largely reactive, and implementation of comprehensive arbovirus surveillance in advance of predictable transmission seasons, which would enable proactive preventative efforts, remains unsupported. The significance of our finding is that it is the first documented report of DENV4 transmission to and maintenance within a local mosquito vector population in the continental United States in the absence of a human case during two consecutive years. Our data suggest that molecular surveillance of mosquito populations in high-risk, high-tourism areas of the United States may enable proactive, targeted vector control before potential arbovirus outbreaks.
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http://dx.doi.org/10.1128/mSphere.00316-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193045PMC
April 2020

Delayed Expression of PD-1 and TIGIT on HIV-Specific CD8 T Cells in Untreated HLA-B*57:01 Individuals Followed from Early Infection.

J Virol 2020 07 1;94(14). Epub 2020 Jul 1.

Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden

While the relationship of protective human leukocyte antigen (HLA) class I alleles and HIV progression is well defined, the interaction of HLA-mediated protection and CD8 T-cell exhaustion is less well characterized. To gain insight into the influence of HLA-B*57:01 on the deterioration of CD8 T-cell responses during HIV infection in the absence of antiretroviral treatment, we compared HLA-B*57:01-restricted HIV-specific CD8 T-cell responses to responses restricted by other HLA class I alleles longitudinally after control of peak viremia. Detailed characterization of polyfunctionality, differentiation phenotypes, transcription factor, and inhibitory receptor expression revealed progression of CD8 T-cell exhaustion over the course of the infection in both patient groups. However, early effects on the phenotype of the total CD8 T-cell population were apparent only in HLA-B*57-negative patients. The HLA-B*57:01-restricted, HIV epitope-specific CD8 T-cell responses showed beneficial functional patterns and significantly lower frequencies of inhibitory receptor expression, i.e., PD-1 and coexpression of PD-1 and TIGIT, within the first year of infection. Coexpression of PD-1 and TIGIT was correlated with clinical markers of disease progression and declining percentages of the T-bet Eomes CD8 T-cell population. In accordance with clinical and immunological deterioration in the HLA-B*57:01 group, the difference in PD-1 and TIGIT receptor expression did not persist to later stages of the disease. Given the synergistic nature of TIGIT and PD-1, the coexpression of those inhibitory receptors should be considered when evaluating T-cell pathogenesis, developing immunomodulatory therapies or vaccines for HIV, and when using immunotherapy or vaccination for other causes in HIV-infected patients. HIV-mediated T-cell exhaustion influences the patient´s disease progression, immune system and subsequently non-AIDS complications, and efficacy of vaccinations against other pathogens. Consequently, the possibilities of interfering with exhaustion are numerous. Expanding the use of immunomodulatory therapies to include HIV treatment depends on information about possible targets and their role in the deterioration of the immune system. Furthermore, the rise of immunotherapies against cancer and elevated cancer incidence in HIV-infected patients together increase the need for detailed knowledge of T-cell exhaustion and possible interactions. A broader approach to counteract immune exhaustion to alleviate complications and improve efficacy of other vaccines also promises to increase patients' health and quality of life.
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http://dx.doi.org/10.1128/JVI.02128-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343205PMC
July 2020

A minor population of macrophage-tropic HIV-1 variants is identified in recrudescing viremia following analytic treatment interruption.

Proc Natl Acad Sci U S A 2020 05 16;117(18):9981-9990. Epub 2020 Apr 16.

Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136;

HIV-1 persists in cellular reservoirs that can reignite viremia if antiretroviral therapy (ART) is interrupted. Therefore, insight into the nature of those reservoirs may be revealed from the composition of recrudescing viremia following treatment cessation. A minor population of macrophage-tropic (M-tropic) viruses was identified in a library of recombinant viruses constructed with individual envelope genes that were obtained from plasma of six individuals undergoing analytic treatment interruption (ATI). M-tropic viruses could also be enriched from post-ATI plasma using macrophage-specific (CD14) but not CD4+ T cell-specific (CD3) antibodies, suggesting that M-tropic viruses had a macrophage origin. Molecular clock analysis indicated that the establishment of M-tropic HIV-1 variants predated ATI. Collectively, these data suggest that macrophages are a viral reservoir in HIV-1-infected individuals on effective ART and that M-tropic variants can appear in rebounding viremia when treatment is interrupted. These findings have implications for the design of curative strategies for HIV-1.
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http://dx.doi.org/10.1073/pnas.1917034117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211992PMC
May 2020

Toxigenic evolution and establishment of reservoirs in aquatic ecosystems.

Proc Natl Acad Sci U S A 2020 04 30;117(14):7897-7904. Epub 2020 Mar 30.

Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610;

The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized that is also capable of growth and long-term survival in aquatic ecosystems. While prior studies have shown that aquatic reservoirs are important in the persistence of the disease on the Indian subcontinent, an epidemiological view postulating that locally evolving environmental contributes to outbreaks outside Asia remains debated. The single-source introduction of toxigenic O1 in Haiti, one of the largest outbreaks occurring this century, with 812,586 suspected cases and 9,606 deaths reported through July 2018, provided a unique opportunity to evaluate the role of aquatic reservoirs and assess bacterial transmission dynamics across environmental boundaries. To this end, we investigated the phylogeography of both clinical and aquatic toxigenic O1 isolates and show robust evidence of the establishment of aquatic reservoirs as well as ongoing evolution of isolates from aquatic sites. Novel environmental lineages emerged from sequential population bottlenecks, carrying mutations potentially involved in adaptation to the aquatic ecosystem. Based on such empirical data, we developed a mixed-transmission dynamic model of , where aquatic reservoirs actively contribute to genetic diversification and epidemic emergence, which underscores the complexity of transmission pathways in epidemics and endemic settings and the need for long-term investments in cholera control at both human and environmental levels.
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http://dx.doi.org/10.1073/pnas.1918763117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149412PMC
April 2020

Whole genome sequencing of carbapenem-resistant : evolutionary analysis for outbreak investigation.

Future Microbiol 2020 02 14;15:203-212. Epub 2020 Feb 14.

Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.

Carbapenemase-resistant represents a major concern in hospital setting. The evolutionary history of carbapenem-resistant strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. A great increase carbapenem-resistant causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.
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http://dx.doi.org/10.2217/fmb-2019-0074DOI Listing
February 2020

The global spread of 2019-nCoV: a molecular evolutionary analysis.

Pathog Glob Health 2020 03 12;114(2):64-67. Epub 2020 Feb 12.

Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.

The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019-2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the bat family. In agreement with epidemiological observations, the most likely geographic origin of the new outbreak was the city of Wuhan, China, where 2019-nCoV time of the most recent common ancestor emerged, according to molecular clock analysis, around November 25, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to . Moreover, our study describes the same population genetic dynamic underlying the SARS 2003 epidemic, and suggests the urgent need for the development of effective molecular surveillance strategies of among animals and of the bat family.
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http://dx.doi.org/10.1080/20477724.2020.1725339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099638PMC
March 2020

Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach.

Genes (Basel) 2019 12 24;11(1). Epub 2019 Dec 24.

Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Emerging Pathogens Institute, P.O. Box 100009, Gainesville, FL 32610-3633, USA.

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.
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http://dx.doi.org/10.3390/genes11010028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016848PMC
December 2019

Isolation of Mayaro Virus from a Venezuelan Patient with Febrile Illness, Arthralgias, and Rash: Further Evidence of Regional Strain Circulation and Possible Long-Term Endemicity.

Am J Trop Med Hyg 2019 12;101(6):1219-1225

Laboratory of Cellular Signaling and Parasite Biochemistry, Instituto de Estudios Avanzados (IDEA), Caracas, Venezuela.

Fifty-two febrile patients living in Barquisimeto, Venezuela, were screened for arbovirus infection by virus culture during an outbreak of what was thought to be Zika virus infection. We report identification of Mayaro virus (MAYV) on culture of plasma from one patient, an 18-year-old woman with acute febrile illness, arthralgias, and psoriasiform rash. The strain was sequenced and was found to be most closely related to a 1999 strain from French Guiana, which, in turn, was related to two 2014 strains from Haiti. By contrast, previously reported outbreak-related MAYV strains from a sylvatic area approximately 80 miles from where the case patient lived were most closely related to Peruvian isolates. The two strain groups show evidence of having diverged genetically approximately 100 years ago.
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http://dx.doi.org/10.4269/ajtmh.19-0357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896866PMC
December 2019

Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus.

ACM BCB 2019 Sep;2019:259-268

Department of Engineering Roma Tre University Rome, Italy.

Methicillin-resistant (MRSA) is currently the most commonly identified antibiotic-resistant pathogen in US hospitals. Resistance to methicillin is carried by SCCmec genetic elements. Multilocus sequence typing (MLST) covers internal fragments of seven housekeeping genes of In conjunction with mec typing, MLST has been used to create an international nomenclature for . MLST sequence types with a single nucleotide polymorphism (SNP) considered distinct. In this work, relationships among MLST SNPs and methicillin/oxacillin resistance or susceptibility were studied, using a public data base, by means of cross-tabulation tests, multivariable (phylogenetic) logistic regression (LR), decision trees, rule bases, and random forests (RF). Model performances were assessed through multiple cross-validation. Hierarchical clustering of SNPs was also employed to analyze mutational covariation. The number of instances with a known methicillin (oxacillin) antibiogram result was 1526 (649), where 63% (54%) was resistant to methicillin (oxacillin). In univariable analysis, several MLST SNPs were found strongly associated with antibiotic resistance/susceptibility. A RF model predicted correctly the resistance/susceptibility to methicillin and oxacillin in 75% and 63% of cases (cross-validated). Results were similar for LR. Hierarchical clustering of the aforementioned SNPs yielded a high level of covariation both within the same and different genes; this suggests strong genetic linkage between SNPs of housekeeping genes and antibiotic resistant associated genes. This finding provides a basis for rapid identification of antibiotic resistant lineages using a small number of genomic markers. The number of sites could subsequently be increased moderately to increase the sensitivity and specificity of genotypic tests for resistance that do not rely on the direct detection of the resistance marker itself.
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http://dx.doi.org/10.1145/3307339.3342138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779167PMC
September 2019

Influence of directional positive Darwinian selection-driven evolution on arboviruses Dengue and Zika virulence and pathogenesis.

Mol Phylogenet Evol 2019 11 29;140:106607. Epub 2019 Aug 29.

Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE 50740-465, Brazil; Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, United States.

Dengue (DENV) and Zika (ZIKV) viruses are antigenically and evolutionarily related; immunological cross-reactions between them have been associated to both cross-protection and infection-enhanced mechanisms. Here, DENV-1-4 and ZIKV were investigated through Bayesian coalescent-based approaches and selection-driven Darwinian evolution methods using robust datasets. Our findings show that both DENV and ZIKV, driven essentially by directional positive selection, have undergone evolution and diversification and that their entire polyproteins are subject to an intense directional evolution. Interestingly, positively selected codons mapped here are directly associated to DENV-1-2 virulence as well as the ZIKV burgeoning 2015-16 outbreak in the Americas, therefore, having impact on the pathogenesis of these viruses. Biochemical prediction analysis focusing on markers involved in virulence and viral transmission dynamics identified alterations in N-Glycosylation-, Phosphorylation- and Palmitoylation-sites in ZIKV sampled from different countries, hosts and isolation sources. Taking into account both DENV-ZIKV co-circulation either into and/or out of flavivirus-endemic regions, as well as recombination and quasispecies scenarios, these results indicate the action of a selection-driven evolution affecting the biology, virulence and pathogenesis of these pathogens in a non-randomized environment.
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http://dx.doi.org/10.1016/j.ympev.2019.106607DOI Listing
November 2019

Mayaro as a Caribbean traveler: Evidence for multiple introductions and transmission of the virus into Haiti.

Int J Infect Dis 2019 Oct 2;87:151-153. Epub 2019 Aug 2.

Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA. Electronic address:

Mayaro virus (MAYV) is a mosquito-transmitted alphavirus that is being recognized with increasing frequency in South America. As part of on-going surveillance of a school cohort in Haiti, we identified MAYV infections in 5 children across a 7-month time span, at two different school campuses. All had a history of fever, and three had headaches; none complained of arthralgias. On analysis of whole genome sequence data, three strains were genotype D, and two were genotype L; phylogenetic and molecular clock analysis was consistent with at least 3 independent introductions of the virus into Haiti, with ongoing transmission of a common genotype D strain in a single school. Our data highlight the clear potential for spread of the virus in the northern Caribbean and North America.
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http://dx.doi.org/10.1016/j.ijid.2019.07.031DOI Listing
October 2019

Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.

Sci Rep 2019 07 16;9(1):10291. Epub 2019 Jul 16.

Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Alfred Nobels allé 10, 141 52, Huddinge, Stockholm, Sweden.

Clonal lineages of ESBL (Extended-Spectrum β-Lactamase)-producing E. coli belonging to sequence type 131 (ST131) have disseminated globally during the last 30 years, leading to an increased prevalence of resistance to fluoroquinolones and extended-spectrum cephalosporins in clinical isolates of E. coli. We aimed to study if Swedish ESBL-producing ST131 isolates originated from single or multiple introductions to the population by assessing the amount of genetic variation, on chromosomal and plasmid level, between Swedish and international E. coli ST131. Bayesian inference of Swedish E. coli ST131 isolates (n = 29), sequenced using PacBio RSII, together with an international ST131 dataset showed that the Swedish isolates were part of the international ST131 A, C1 and C2 clades. Highly conserved plasmids were identified in three clusters although they were separated by several years, which indicates a strong co-evolution between some ST131 lineages and specific plasmids. In conclusion, the tight clonal relationship observed within the ST131 clades, together with highly conserved plasmids, challenges investigation of strain transmission events. A combination of few SNPs on a genome-wide scale and an epidemiological temporospatial link, are needed to track the spread of the ST131 subclones.
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http://dx.doi.org/10.1038/s41598-019-46580-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635401PMC
July 2019

The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis.

Sci Rep 2019 02 25;9(1):2640. Epub 2019 Feb 25.

Emerging Pathogens Institute, University of Florida, Gainesville, Florida, 32608, United States of America.

The epidemic in South Africa is characterized by high genetic diversity driven by multiple independent introductions. The bulk of these introductions occurred between 1985-2000 during which time HIV prevalence increased exponentially. Epidemic growth has stabilized in recent years with the implementation of several interventions. Here we identified distinct HIV clades from a large sequence dataset of southern African HIV sequences (n = 15,332). Each clade was characterized using phylodynamic and phylogeographic methods to infer their growth through time and space. The estimated date of origin for the 18 clades that were found, fell between 1979-1992 with strong growth during the 1990's. Phylogeographic reconstruction revealed wide dispersal of clades throughout the country with the city of Johannesburg as the focal point of viral dispersal. We found clear signs of decreasing growth rate in four of the clades since the advent of interventions, while other clades have continued to growth and expand. Our results demonstrate that interventions do not affect the HIV epidemic universally with major difference between different clades over time and space. Here we demonstrate the utility and flexibility of molecular epidemiological methods and demonstrate how they can potentially be a powerful tool in HIV epidemic monitoring in South Africa.
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http://dx.doi.org/10.1038/s41598-018-37749-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389914PMC
February 2019

Emergence of Madariaga virus as a cause of acute febrile illness in children, Haiti, 2015-2016.

PLoS Negl Trop Dis 2019 01 10;13(1):e0006972. Epub 2019 Jan 10.

Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America.

Madariaga virus (MADV), also known as South American eastern equine encephalitis virus, has been identified in animals and humans in South and Central America, but not previously in Hispaniola or the northern Caribbean. MADV was isolated from virus cultures of plasma from an 8-year-old child in a school cohort in the Gressier/Leogane region of Haiti, who was seen in April, 2015, with acute febrile illness (AFI). The virus was subsequently cultured from an additional seven AFI case patients from this same cohort in February, April, and May 2016. Symptoms most closely resembled those seen with confirmed dengue virus infection. Sequence data were available for four isolates: all were within the same clade, with phylogenetic and molecular clock data suggesting recent introduction of the virus into Haiti from Panama sometime in the period from October 2012-January 2015. Our data document the movement of MADV into Haiti, and raise questions about the potential for further spread in the Caribbean or North America.
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http://dx.doi.org/10.1371/journal.pntd.0006972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328082PMC
January 2019

Viral Enrichment Methods Affect the Detection but Not Sequence Variation of West Nile Virus in Equine Brain Tissue.

Front Vet Sci 2018 18;5:318. Epub 2018 Dec 18.

Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.

West Nile virus (WNV), a small, positive sense, single stranded RNA virus continues to encroach into new locales with emergence of new viral variants. Neurological disease in the equine can be moderate to severe in the face of low to undetectable virus loads. Physical methods of virus enrichment may increase sensitivity of virus detection and enhance analysis of viral diversity, especially for deep sequencing studies. However, the use of these techniques is limited mainly to non-neural tissues. We investigated the hypothesis that elimination of equine brain RNA enhances viral detection without limiting viral variation. Eight different WNV viral RNA enrichment and host RNA separation methods were evaluated to determine if elimination of host RNA enhanced detection of WNV and increase the repertoire of virus variants for sequencing. Archived brain tissue from 21 different horses was inoculated with WNV, homogenized, before enrichment and separation. The protocols utilized combinations of low-speed centrifugation, syringe filtration, and nuclease treatment. Viral and host RNA were analyzed using real-time PCR targeting the WNV Envelope (E) protein and equine G3PDH to determine relative sensitivity for WNV and host depletion, respectively. To determine the effect of these methods on viral variation, deep sequencing of the E protein was performed. Our results demonstrate that additional separation and enrichment methods resulted in loss of virus in the face of host RNA depletion. DNA sequencing showed no significant difference in total sequence variation between the RNA enrichment protocols. For equine brain infected with WNV, direct RNA extraction followed by host RNA depletion was most suitable. This study highlights the importance of evaluating viral enrichment and separation methods according to tissue type before embarking on studies where quantification of virus and viral variants is essential to the outcome of the study.
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http://dx.doi.org/10.3389/fvets.2018.00318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305279PMC
December 2018

Islands as Hotspots for Emerging Mosquito-Borne Viruses: A One-Health Perspective.

Viruses 2018 12 25;11(1). Epub 2018 Dec 25.

Emerging Pathogens Institute University of Florida, Gainesville, FL 32611, USA.

During the past ten years, an increasing number of arbovirus outbreaks have affected tropical islands worldwide. We examined the available literature in peer-reviewed journals, from the second half of the 20th century until 2018, with the aim of gathering an overall picture of the emergence of arboviruses in these islands. In addition, we included information on environmental and social drivers specific to island setting that can facilitate the emergence of outbreaks. Within the context of the One Health approach, our review highlights how the emergence of arboviruses in tropical islands is linked to the complex interplay between their unique ecological settings and to the recent changes in local and global sociodemographic patterns. We also advocate for greater coordination between stakeholders in developing novel prevention and mitigation approaches for an intractable problem.
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http://dx.doi.org/10.3390/v11010011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356932PMC
December 2018