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Gao R, Li W, Xu J, Guo J, Wang R, Zhang S, Zheng X, Wang J. Characteristics of Subtype and Molecular Transmission Networks among Newly Diagnosed HIV-1 Infections in Patients Residing in Taiyuan City, Shanxi Province, China, from 2021 to 2023. Viruses 2024; 16:1174. [PMID: 39066336 PMCID: PMC11281631 DOI: 10.3390/v16071174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
The HIV-1 pandemic, spanning four decades, presents a significant challenge to global public health. This study aimed to understand the molecular transmission characteristics of newly reported HIV infections in Taiyuan, Shanxi Province, China, to analyze the characteristics of subtypes and the risk factors of the transmission network, providing a scientific basis for precise prevention and intervention measures. A total of 720 samples were collected from newly diagnosed HIV-1 patients residing in Taiyuan between 2021 and 2023. Sequencing of partial genes of the HIV-1 pol gene resulted in multiple sequence acquisitions and was conducted to analyze their subtypes and molecular transmission networks. Out of the samples, 584 pol sequences were obtained, revealing 17 HIV-1 subtypes, with CRF07_BC (48.29%), CRF01_AE (31.34%), and CRF79_0107 (7.19%) being the dominant subtypes. Using a genetic distance threshold of 1.5%, 49 molecular transmission clusters were generated from the 313 pol gene sequences. Univariate analysis showed significant differences in the HIV transmission molecular network in terms of HIV subtype and household registration (p < 0.05). Multivariate logistic regression analysis showed that CRF79_0107 subtype and its migrants were associated with higher proportions of sequences in the HIV transmission network. These findings provide a scientific foundation for the development of localized HIV-specific intervention strategies.
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Affiliation(s)
- Ruihong Gao
- Academy of Medical Sciences, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, Shanxi, China;
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, Shanxi, China
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Wentong Li
- Academy of Medical Sciences, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, Shanxi, China;
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, Shanxi, China
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Jihong Xu
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Jiane Guo
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Rui Wang
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Shuting Zhang
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Xiaonan Zheng
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
| | - Jitao Wang
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, Shanxi, China
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030012, Shanxi, China; (J.X.); (J.G.); (R.W.); (S.Z.); (X.Z.)
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2
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Milstein MS, Shaffer CA, Suse P, Marawanaru E, Shoni R, Suse S, Issacs B, Larsen PA, Travis DA, Terio KA, Wolf TM. The establishment of a collaborative surveillance program with indigenous hunters to characterize primate health in Southern Guyana. Am J Primatol 2024; 86:e23622. [PMID: 38561573 DOI: 10.1002/ajp.23622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/05/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The consumption of primates is integral to the traditional subsistence strategies of many Indigenous communities throughout Amazonia. Understanding the overall health of primates harvested for food in the region is critical to Indigenous food security and thus, these communities are highly invested in long-term primate population health. Here, we describe the establishment of a surveillance comanagement program among the Waiwai, an Indigenous community in the Konashen Amerindian Protected Area (KAPA). To assess primate health in the KAPA, hunters performed field necropsies on primates harvested for food and tissues collected from these individuals were analyzed using histopathology. From 2015 to 2019, hunters conducted 127 necropsies across seven species of primates. Of this sample, 82 primates (between 2015 and 2017) were submitted for histopathological screening. Our histopathology data revealed that KAPA primates had little evidence of underlying disease. Of the tissue abnormalities observed, the majority were either due to diet (e.g., hepatocellular pigment), degenerative changes resulting from aging (e.g., interstitial nephritis, myocyte lipofusion), or nonspecific responses to antigenic stimulation (renal and splenic lymphoid hyperplasia). In our sample, 7.32% of individuals had abnormalities that were consistent with a viral etiology, including myocarditis and hepatitis. Internal parasites were observed in 53.66% of individuals and is consistent with what would be expected from a free-ranging primate population. This study represents the importance of baseline data for long-term monitoring of primate populations hunted for food. More broadly, this research begins to close a critical gap in zoonotic disease risk related to primate harvesting in Amazonia, while also demonstrating the benefits of partnering with Indigenous hunters and leveraging hunting practices in disease surveillance and primate population health assessment.
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Affiliation(s)
- Marissa S Milstein
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | | | - Phillip Suse
- Masakenari Village, Konashen Indigenous District, Region 9, Guyana
| | | | - Romel Shoni
- Masakenari Village, Konashen Indigenous District, Region 9, Guyana
| | - Steven Suse
- Masakenari Village, Konashen Indigenous District, Region 9, Guyana
| | - Bemner Issacs
- Masakenari Village, Konashen Indigenous District, Region 9, Guyana
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Dominic A Travis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
- The Marine Mammal Center, Sausalito, California, USA
| | - Karen A Terio
- University of Illinois Zoological Pathology Program, Brookfield, Illinois, USA
| | - Tiffany M Wolf
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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3
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Carvajal M, Saenz C, Fuentes N, Guevara R, Muñoz E, Prado-Vivar B, Diaz E, Alfonso-Cortes F, Coloma J, Grunauer M, Rojas-Silva P, Cardenas PA, Barragan V. SARS-CoV-2 infection in brown-headed spider monkeys ( Ateles fusciceps) at a wildlife rescue center on the coast of Ecuador-South America. Microbiol Spectr 2024; 12:e0274123. [PMID: 38364080 PMCID: PMC10986564 DOI: 10.1128/spectrum.02741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Human populations can be affected in unpredictable ways by the emergence and spread of zoonotic diseases. The COVID-19 (coronavirus disease of 2019) pandemic was a reminder of how devastating these events can be if left unchecked. However, once they have spread globally, the impact of these diseases when entering non-exposed wildlife populations is unknown. The current study reports the infection of brown-headed spider monkeys (Ateles fusciceps) at a wildlife rescue center in Ecuador. Four monkeys were hospitalized, and all tested positive for SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) by RT-qPCR (Quantitative Reverse Transcription PCR). Fecal samples (n = 12) from monkeys at the rescue center also tested positive; three zookeepers responsible for feeding and deworming the monkeys also tested positive, suggesting human-animal transmission. Whole genome sequencing identified most samples' omicron clade 22B BA.5 lineage. These findings highlight the threat posed by an emerging zoonotic disease in wildlife species and the importance of preventing spillover and spillback events during epidemic or pandemic events.IMPORTANCEAlthough COVID-19 (coronavirus disease of 2019) has been primarily contained in humans through widespread vaccination, the impact and incidence of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus) and its transmission and epidemiology in wildlife may need to be addressed. In some natural environments, the proximity of animals to humans is difficult to control, creating perfect scenarios where susceptible wildlife can acquire the virus from humans. In these places, it is essential to understand how transmission can occur and to develop protocols to prevent infection. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, a red-listed monkey species, at a wildlife recovery center in Ecuador. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, indicating the potential for transmission between humans and wildlife primates and the importance of preventing such events in the future.
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Affiliation(s)
- Mateo Carvajal
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Carolina Saenz
- Universidad San Francisco de Quito, Hospital de Fauna Silvestre TUERI-USFQ, Quito, Ecuador
| | | | - Rommel Guevara
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Erika Muñoz
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Belen Prado-Vivar
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Eduardo Diaz
- Universidad San Francisco de Quito, Escuela de Medicina Veterinaria, Quito, Ecuador
| | | | | | - Michelle Grunauer
- Universidad San Francisco de Quito, Escuela de Medicina, Quito, Ecuador
| | | | - Paul A. Cardenas
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Veronica Barragan
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
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4
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Costa RL, Gadelha L, D'arc M, Ribeiro-Alves M, Robertson DL, Schwartz JM, Soares MA, Porto F. HIHISIV: a database of gene expression in HIV and SIV host immune response. BMC Bioinformatics 2024; 25:125. [PMID: 38519883 PMCID: PMC10958971 DOI: 10.1186/s12859-024-05740-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disease progression. The simian immunodeficiency virus (SIV) infecting nonhuman primates (NHP) is widely used as a model for the study of the human immunodeficiency virus (HIV) both because they are evolutionarily linked and because they share physiological and anatomical similarities that are largely explored to understand the disease progression. The HIHISIV database was developed to support researchers to integrate and evaluate the large number of transcriptional data associated with the presence/absence of the pathogen (SIV or HIV) and the host response (NHP and human). The datasets are composed of microarray and RNA-Seq gene expression data that were selected, curated, analyzed, enriched, and stored in a relational database. Six query templates comprise the main data analysis functions and the resulting information can be downloaded. The HIHISIV database, available at https://hihisiv.github.io , provides accurate resources for browsing and visualizing results and for more robust analyses of pre-existing data in transcriptome repositories.
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Affiliation(s)
- Raquel L Costa
- DEXL Lab, National Laboratory for Scientific Computing, Petrópolis, Brazil.
| | - Luiz Gadelha
- German Human Genome-Phenome Archive (GHGA, W620), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Mirela D'arc
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Ribeiro-Alves
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Jean-Marc Schwartz
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Marcelo A Soares
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
- Programa de Oncovirologia, Divisão de Pesquisa Translacional, Instituto Nacional do Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Fábio Porto
- DEXL Lab, National Laboratory for Scientific Computing, Petrópolis, Brazil
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5
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Adhikari S, Phuyal S, Acharya KP. Addressing zoonotic disease transmission from temple monkeys to humans in Nepal. J Travel Med 2024; 31:taad157. [PMID: 38102759 DOI: 10.1093/jtm/taad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Evidence of infection with the zoonotic pathogens has been reported from temple monkeys in Nepal. In this paper, the possible spillover of zoonotic pathogens from monkeys to humans is discussed.
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Affiliation(s)
- Sonu Adhikari
- Department of Animal Breeding and Biotechnology, Agriculture and Forestry University (AFU), PO Box 13712, Rampur, Chitwan, Nepal
| | - Sarita Phuyal
- Central Referral Veterinary Hospital, Tripureshwar, Kathmandu 45104, Nepal
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Hegde CV, Mahur H, Singh DP, Darshan RS. Can ferritin be a surrogate marker for CD4 cells in human immunodeficiency virus patients? A cross-sectional study of association of serum ferritin levels with immunological staging of human immunodeficiency virus patients. Indian J Sex Transm Dis AIDS 2024; 45:31-33. [PMID: 38989078 PMCID: PMC11233032 DOI: 10.4103/ijstd.ijstd_32_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 07/12/2024] Open
Abstract
Introduction The human immunodeficiency virus (HIV)/AIDS in India came into public view in 1986 with the detection of the first case of HIV in Chennai, Tamil Nadu, and the first AIDS case in Mumbai, Maharashtra in 1987. In acute phase response, iron distribution occurs in the liver and mononuclear phagocytic system. A high prevalence of elevated serum ferritin levels is reported in HIV infection and serum ferritin levels increase with the clinical worsening of infection and with decreasing CD4 lymphocyte counts. This study is designed to find the role of acute phase reactant serum ferritin in the progression of the disease of HIV which is complicated by opportunistic infections, by finding the correlation of serum ferritin with immunological stages of HIV. Materials and Methods This cross-sectional study was conducted on 75 patients admitted to various wards of the Department of Medicine or attending medicine outdoor or ART Centre, Maharana Bhupal Government Hospital, RNT Medical College Udaipur. Serum ferritin, total iron binding capacity, and total serum iron were analyzed in Cobas® analyzer. CD4 cells are measured using the flow cytometry technique. The results were tabulated and subjected to statistical analysis. Results and Conclusion There was a negative correlation among serum ferritin and CD4 cells with r = -0.195 which was statistically significant (P < 0.05). As the CD4 cell count decreased incidence of serum ferritin increased. Elevation of serum ferritin levels is associated with a low count of the CD4+ in HIV-diagnosed patients. In a patient diagnosed with HIV, elevated serum ferritin indicates underlying inflammatory pathology. Serum ferritin can be used as a guide to further evaluation of underlying disease in HIV patients.
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Affiliation(s)
| | - Hemant Mahur
- Department of Internal Medicine, RNT Medical College, Udaipur, Rajasthan, India
| | - D P Singh
- Department of Internal Medicine, RNT Medical College, Udaipur, Rajasthan, India
| | - R S Darshan
- Department of Internal Medicine, RNT Medical College, Udaipur, Rajasthan, India
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7
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Wilde THC, Shukla RK, Madden C, Vodovotz Y, Sharma A, McGraw WS, Hale VL. Simian immunodeficiency virus and storage buffer: Field-friendly preservation methods for RNA viral detection in primate feces. mSphere 2023; 8:e0048423. [PMID: 38032220 PMCID: PMC10732032 DOI: 10.1128/msphere.00484-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Simian immunodeficiency virus (SIV), which originated in African monkeys, crossed the species barrier into humans and ultimately gave rise to HIV and the global HIV/AIDS epidemic. While SIV infects over 40 primate species in sub-Saharan Africa, testing for RNA viruses in wild primate populations can be challenging. Optimizing field-friendly methods for assessing viral presence/abundance in non-invasively collected biological samples facilitates the study of viruses, including potentially zoonotic viruses, in wild primate populations. This study compares SIV RNA preservation and recovery from non-human primate feces stored in four different buffers. Our results will inform future fieldwork and facilitate improved approaches to characterizing prevalence, shedding, and transmission of RNA viruses like SIV in natural hosts including wild-living non-human primates.
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Affiliation(s)
- Tessa H. C. Wilde
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | - Rajni Kant Shukla
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Christopher Madden
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Yael Vodovotz
- Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, USA
| | - Amit Sharma
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - W. Scott McGraw
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | - Vanessa L. Hale
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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Werner CS, Kasan K, Geyer JK, Elmasri M, Farrell MJ, Nunn CL. Using phylogeographic link-prediction in primates to prioritize human parasite screening. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:583-594. [PMID: 38384356 PMCID: PMC10878720 DOI: 10.1002/ajpa.24604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/20/2022] [Indexed: 02/23/2024]
Abstract
Objectives The ongoing risk of emerging infectious disease has renewed calls for understanding the origins of zoonoses and identifying future zoonotic disease threats. Given their close phylogenetic relatedness and geographic overlap with humans, non-human primates (NHPs) have been the source of many infectious diseases throughout human evolution. NHPs harbor diverse parasites, with some infecting only a single host species while others infect species from multiple families. Materials and Methods We applied a novel link-prediction method to predict undocumented instances of parasite sharing between humans and NHPs. Our model makes predictions based on phylogenetic distances and geographic overlap among NHPs and humans in six countries with high NHP diversity: Columbia, Brazil, Democratic Republic of Congo, Madagascar, China and Indonesia. Results Of the 899 human parasites documented in the Global Infectious Diseases and Epidemiology Network (GIDEON) database for these countries, 12% were shared with at least one other NHP species. The link prediction model identified an additional 54 parasites that are likely to infect humans but were not reported in GIDEON. These parasites were mostly host generalists, yet their phylogenetic host breadth varied substantially. Discussion As human activities and populations encroach on NHP habitats, opportunities for parasite sharing between human and non-human primates will continue to increase. Our study identifies specific infectious organisms to monitor in countries with high NHP diversity, while the comparative analysis of host generalism, parasite taxonomy, and transmission mode provides insights to types of parasites that represent high zoonotic risk.
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Affiliation(s)
- Courtney S. Werner
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Koray Kasan
- Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Julie K. Geyer
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mohamad Elmasri
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Maxwell J. Farrell
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Charles L. Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA
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9
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Volcic M, Wiesmüller L, Kirchhoff F. Small but Highly Versatile: The Viral Accessory Protein Vpu. Annu Rev Virol 2023; 10:243-259. [PMID: 37406340 DOI: 10.1146/annurev-virology-111821-100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Human and simian immunodeficiency viruses (HIVs and SIVs, respectively) encode several small proteins (Vif, Vpr, Nef, Vpu, and Vpx) that are called accessory because they are not generally required for viral replication in cell culture. However, they play complex and important roles for viral immune evasion and spread in vivo. Here, we discuss the diverse functions and the relevance of the viral protein U (Vpu) that is expressed from a bicistronic RNA during the late stage of the viral replication cycle and found only in HIV-1 and closely related SIVs. It is well established that Vpu counteracts the restriction factor tetherin, mediates degradation of the primary viral CD4 receptors, and inhibits activation of the transcription factor nuclear factor kappa B. Recent studies identified additional activities and provided new insights into the sophisticated mechanisms by which Vpu enhances and prolongs the release of fully infectious viral particles. In addition, it has been shown that Vpu prevents superinfection not only by degrading CD4 but also by modulating DNA repair mechanisms to promote degradation of nuclear viral complementary DNA in cells that are already productively infected.
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Affiliation(s)
- Meta Volcic
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany;
| | - Lisa Wiesmüller
- Division of Gynecological Oncology, Department of Obstetrics and Gynecology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany;
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10
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Bekker LG, Beyrer C, Mgodi N, Lewin SR, Delany-Moretlwe S, Taiwo B, Masters MC, Lazarus JV. HIV infection. Nat Rev Dis Primers 2023; 9:42. [PMID: 37591865 DOI: 10.1038/s41572-023-00452-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/19/2023]
Abstract
The AIDS epidemic has been a global public health issue for more than 40 years and has resulted in ~40 million deaths. AIDS is caused by the retrovirus, HIV-1, which is transmitted via body fluids and secretions. After infection, the virus invades host cells by attaching to CD4 receptors and thereafter one of two major chemokine coreceptors, CCR5 or CXCR4, destroying the host cell, most often a T lymphocyte, as it replicates. If unchecked this can lead to an immune-deficient state and demise over a period of ~2-10 years. The discovery and global roll-out of rapid diagnostics and effective antiretroviral therapy led to a large reduction in mortality and morbidity and to an expanding group of individuals requiring lifelong viral suppressive therapy. Viral suppression eliminates sexual transmission of the virus and greatly improves health outcomes. HIV infection, although still stigmatized, is now a chronic and manageable condition. Ultimate epidemic control will require prevention and treatment to be made available, affordable and accessible for all. Furthermore, the focus should be heavily oriented towards long-term well-being, care for multimorbidity and good quality of life. Intense research efforts continue for therapeutic and/or preventive vaccines, novel immunotherapies and a cure.
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Affiliation(s)
- Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, RSA, Cape Town, South Africa.
| | - Chris Beyrer
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Nyaradzo Mgodi
- University of Zimbabwe Clinical Trials Research Centre, Harare, Zimbabwe
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | | | - Babafemi Taiwo
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Mary Clare Masters
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Jeffrey V Lazarus
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic, University of Barcelona, Barcelona, Spain
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11
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Olabode AS, Mumby MJ, Wild TA, Muñoz-Baena L, Dikeakos JD, Poon AFY. Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses. Mol Biol Evol 2023; 40:msad164. [PMID: 37463439 PMCID: PMC10400143 DOI: 10.1093/molbev/msad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
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Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
| | - Mitchell J Mumby
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Tristan A Wild
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Laura Muñoz-Baena
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
- Department of Microbiology & Immunology, Western University, London, Canada
- Department of Computer Science, Western University, London, Canada
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12
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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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13
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Anand S, Hallsworth JE, Timmis J, Verstraete W, Casadevall A, Ramos JL, Sood U, Kumar R, Hira P, Dogra Rawat C, Kumar A, Lal S, Lal R, Timmis K. Weaponising microbes for peace. Microb Biotechnol 2023; 16:1091-1111. [PMID: 36880421 DOI: 10.1111/1751-7915.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.
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Affiliation(s)
- Shailly Anand
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - James Timmis
- Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, Maryland, USA
| | | | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Sukanya Lal
- PhiXgen Pvt. Ltd, Gurugram, Gurgaon, Haryana, India
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, India
| | - Kenneth Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
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14
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Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
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Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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15
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Jasinska AJ, Apetrei C, Pandrea I. Walk on the wild side: SIV infection in African non-human primate hosts-from the field to the laboratory. Front Immunol 2023; 13:1060985. [PMID: 36713371 PMCID: PMC9878298 DOI: 10.3389/fimmu.2022.1060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
HIV emerged following cross-species transmissions of simian immunodeficiency viruses (SIVs) that naturally infect non-human primates (NHPs) from Africa. While HIV replication and CD4+ T-cell depletion lead to increased gut permeability, microbial translocation, chronic immune activation, and systemic inflammation, the natural hosts of SIVs generally avoid these deleterious consequences when infected with their species-specific SIVs and do not progress to AIDS despite persistent lifelong high viremia due to long-term coevolution with their SIV pathogens. The benign course of natural SIV infection in the natural hosts is in stark contrast to the experimental SIV infection of Asian macaques, which progresses to simian AIDS. The mechanisms of non-pathogenic SIV infections are studied mainly in African green monkeys, sooty mangabeys, and mandrills, while progressing SIV infection is experimentally modeled in macaques: rhesus macaques, pigtailed macaques, and cynomolgus macaques. Here, we focus on the distinctive features of SIV infection in natural hosts, particularly (1): the superior healing properties of the intestinal mucosa, which enable them to maintain the integrity of the gut barrier and prevent microbial translocation, thus avoiding excessive/pathologic immune activation and inflammation usually perpetrated by the leaking of the microbial products into the circulation; (2) the gut microbiome, the disruption of which is an important factor in some inflammatory diseases, yet not completely understood in the course of lentiviral infection; (3) cell population shifts resulting in target cell restriction (downregulation of CD4 or CCR5 surface molecules that bind to SIV), control of viral replication in the lymph nodes (expansion of natural killer cells), and anti-inflammatory effects in the gut (NKG2a/c+ CD8+ T cells); and (4) the genes and biological pathways that can shape genetic adaptations to viral pathogens and are associated with the non-pathogenic outcome of the natural SIV infection. Deciphering the protective mechanisms against SIV disease progression to immunodeficiency, which have been established through long-term coevolution between the natural hosts and their species-specific SIVs, may prompt the development of novel therapeutic interventions, such as drugs that can control gut inflammation, enhance gut healing capacities, or modulate the gut microbiome. These developments can go beyond HIV infection and open up large avenues for correcting gut damage, which is common in many diseases.
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Affiliation(s)
- Anna J. Jasinska
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,*Correspondence: Ivona Pandrea,
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16
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Ellwanger JH, Fearnside PM, Ziliotto M, Valverde-Villegas JM, Veiga ABGDA, Vieira GF, Bach E, Cardoso JC, Müller NFD, Lopes G, Caesar L, Kulmann-Leal B, Kaminski VL, Silveira ES, Spilki FR, Weber MN, Almeida SEDEM, Hora VPDA, Chies JAB. Synthesizing the connections between environmental disturbances and zoonotic spillover. AN ACAD BRAS CIENC 2022; 94:e20211530. [PMID: 36169531 DOI: 10.1590/0001-3765202220211530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.
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Affiliation(s)
- Joel Henrique Ellwanger
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Philip Martin Fearnside
- Instituto Nacional de Pesquisas da Amazônia/INPA, Avenida André Araújo, 2936, Aleixo, 69067-375 Manaus, AM, Brazil
| | - Marina Ziliotto
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Jacqueline María Valverde-Villegas
- Institut de Génétique Moléculaire de Montpellier/IGMM, Centre National de la Recherche Scientifique/CNRS, Laboratoire coopératif IGMM/ABIVAX, 1919, route de Mende, 34090 Montpellier, Montpellier, France
| | - Ana Beatriz G DA Veiga
- Universidade Federal de Ciências da Saúde de Porto Alegre/UFCSPA, Departamento de Ciências Básicas de Saúde, Rua Sarmento Leite, 245, Centro Histórico, 90050-170 Porto Alegre, RS, Brazil
| | - Gustavo F Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunoinformática, Núcleo de Bioinformática do Laboratório de Imunogenética/NBLI, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Laboratório de Saúde Humana in silico, Avenida Victor Barreto, 2288, Centro, 92010-000 Canoas, RS, Brazil
| | - Evelise Bach
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Jáder C Cardoso
- Centro Estadual de Vigilância em Saúde/CEVS, Divisão de Vigilância Ambiental em Saúde, Secretaria da Saúde do Estado do Rio Grande do Sul, Avenida Ipiranga, 5400, Jardim Botânico, 90610-000 Porto Alegre, RS, Brazil
| | - Nícolas Felipe D Müller
- Centro Estadual de Vigilância em Saúde/CEVS, Divisão de Vigilância Ambiental em Saúde, Secretaria da Saúde do Estado do Rio Grande do Sul, Avenida Ipiranga, 5400, Jardim Botânico, 90610-000 Porto Alegre, RS, Brazil
| | - Gabriel Lopes
- Fundação Oswaldo Cruz/FIOCRUZ, Casa de Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Lílian Caesar
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Indiana University/IU, Department of Biology, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Bruna Kulmann-Leal
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Valéria L Kaminski
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal de São Paulo/UNIFESP, Instituto de Ciência e Tecnologia/ICT, Laboratório de Imunologia Aplicada, Rua Talim, 330, Vila Nair, 12231-280 São José dos Campos, SP, Brazil
| | - Etiele S Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunoinformática, Núcleo de Bioinformática do Laboratório de Imunogenética/NBLI, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Fernando R Spilki
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Matheus N Weber
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Sabrina E DE Matos Almeida
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Vanusa P DA Hora
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal do Rio Grande/FURG, Faculdade de Medicina, Rua Visconde de Paranaguá, 102, Centro, 96203-900, Rio Grande, RS, Brazil
| | - José Artur B Chies
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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17
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Russotto Y, Micali C, Pellicanò GF, Nunnari G, Venanzi Rullo E. HIV and Mediterranean Zoonoses: A Review of the Literature. Infect Dis Rep 2022; 14:694-709. [PMID: 36136825 PMCID: PMC9498920 DOI: 10.3390/idr14050075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
A zoonosis is an infectious disease that has jumped from a non-human animal to humans. Some zoonoses are very common in the Mediterranean area and endemic in specific regions, so they represent an important problem for public health. Human Immunodeficiency Virus (HIV) is a virus that has originated as a zoonosis and is now diffused globally, with the most significant numbers of infected people among the infectious diseases. Since the introduction of antiretroviral therapy (ART), the history for people living with HIV (PLWH) has changed drastically, and many diseases are now no different in epidemiology and prognosis as they are in not-HIV-infected people. Still, the underlying inflammatory state that is correlated with HIV and other alterations related to the infection itself can be a risk factor when infected with other bacteria, parasites or viruses. We reviewed the literature for infection by the most common Mediterranean zoonoses, such as Campylobacter, Salmonella, Brucella, Rickettsia, Borrelia, Listeria and Echinococcus, and a possible correlation with HIV. We included Monkeypox, since the outbreak of cases is becoming a concern lately. We found that HIV may be related with alterations of the microbiome, as for campylobacteriosis, and that there are some zoonoses with a significant prevalence in PLWH, as for salmonellosis.
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Affiliation(s)
- Ylenia Russotto
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Cristina Micali
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
- Correspondence: ; Tel.: +39-09-0221-2032
| | - Giovanni Francesco Pellicanò
- Department of Human Pathology of the Adult and the Developmental Age “G. Barresi”, University of Messina, 98124 Messina, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
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18
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Yee JL, Grant R, Haertel AJ, Allers C, Carpenter AB, Van Rompay KKA, Roberts JA. Multi-site proficiency testing for validation and standardization of assays to detect specific pathogen-free viruses, coronaviruses, and other agents in nonhuman primates. J Med Primatol 2022; 51:234-245. [PMID: 35426147 PMCID: PMC9851150 DOI: 10.1111/jmp.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023]
Abstract
In efforts to increase rigor and reproducibility, the USA National Primate Research Centers (NPRCs) have focused on qualification of reagents, cross-laboratory validations, and proficiency testing for methods to detect infectious agents and accompanying immune responses in nonhuman primates. The pathogen detection working group, comprised of laboratory scientists, colony managers, and leaders from the NPRCs, has championed the effort to produce testing that is reliable and consistent across laboratories. Through multi-year efforts with shared proficiency samples, testing percent agreement has increased from as low as 67.1% for SRV testing in 2010 to 92.1% in 2019. The 2019 average agreement for the four basic SPF agents improved to >96% (86.5% BV, 98.9 SIV, 92.1 SRV, and 97.0 STLV). As new pathogens such as SARS coronavirus type 2 emerge, these steps can now be quickly replicated to develop and implement new assays that ensure rigor, reproducibly, and quality for NHP pathogen detection.
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Affiliation(s)
- JoAnn L. Yee
- Primate Assay Laboratory, California National Primate Research Center, University of California, Davis, CA
| | - Richard Grant
- Primate Pathogen Detection Services Laboratory, Washington National Primate Research Center, University of Washington, Seattle, WA
| | - Andrew J. Haertel
- Oregon National Primate Research Center, Oregon Health Science University, Beaverton, OR
| | - Carolina Allers
- Pathogen Detection and Quantification Core, Tulane National Primate Research Center, Tulane University, Covington, LA
| | - Amanda B. Carpenter
- Primate Assay Laboratory, California National Primate Research Center, University of California, Davis, CA
| | - Koen K. A. Van Rompay
- Primate Assay Laboratory, California National Primate Research Center, University of California, Davis, CA,Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis , CA
| | - Jeffrey A. Roberts
- Primate Assay Laboratory, California National Primate Research Center, University of California, Davis, CA,Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, CA
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Productive Replication of HIV-1 but Not SIVmac in Small Ruminant Cells. Pathogens 2022; 11:pathogens11070799. [PMID: 35890043 PMCID: PMC9316499 DOI: 10.3390/pathogens11070799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 02/05/2023] Open
Abstract
Animal lentiviruses (LVs) have been proven to have the capacity to cross the species barrier, to adapt in the new hosts, and to increase their pathogenesis, therefore leading to the emergence of threatening diseases. However, their potential for widespread diffusion is limited by restrictive cellular factors that block viral replication in the cells of many species. In previous studies, we demonstrated that the restriction of CAEV infection of sheep choroid plexus cells was due to aberrant post-translation cleavage of the CAEV Env gp170 precursor. Later, we showed that the lack of specific receptor(s) for caprine encephalitis arthritis virus (CAEV) on the surface of human cells was the only barrier to their infection. Here, we examined whether small ruminant (SR) cells can support the replication of primate LVs. Three sheep and goat cell lines were inoculated with cell-free HIV-1 and SIVmac viral stocks or transfected with infectious molecular clone DNAs of these viruses. The two recombinant lentiviral clones contained the green fluorescent protein (GFP) reporter sequence. Infection was detected by GFP expression in target cells, and the infectious virus produced and released in the culture medium of treated cells was detected using the indicator TZM-bl cell line. Pseudotyped HIV-GFP and SIV-GFP with vesicular stomatitis virus G glycoprotein (VSV-G) allowed the cell receptors to be overcome for virus entry to further evaluate the viral replication/restriction in SR cells. As expected, neither HIV nor SIV viruses infected any of the SR cells. In contrast, the transfection of plasmid DNAs of the infectious molecular clones of both viruses in SR cells produced high titers of infectious viruses for human indicators, but not SR cell lines. Surprisingly, SR cells inoculated with HIV-GFP/VSV-G, but not SIV-GFP/VSV-G, expressed the GFP and produced a virus that efficiently infected the human indictor, but not the SR cells. Collectively, these data provide a demonstration of the lack of replication of the SIVmac genome in SR cells, while, in contrast, there was no restriction on the replication of the IV-1 genome in these cells. However, because of the lack of functional receptors to SIVmac and HIV-1 at the surface of SR cells, there is specific lentiviral entry.
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Zhou C, Liang S, Li Y, Zhang Y, Li L, Ye L, Yuan D, Su L. Characterization of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China. BMC Infect Dis 2022; 22:602. [PMID: 35799101 PMCID: PMC9263063 DOI: 10.1186/s12879-022-07576-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
Background Sichuan province is one of the highest AIDS epidemic provinces in China, with a large number of floating population. The annual number of cases of HIV/AIDS reported in Sichuan has been the highest province in China for several successive years. There is a lack of widespread and representative data on the distribution of HIV genotypes in Sichuan. We aim to investigate the characteristics of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China. Method Archived plasma samples (n = 1524) from HIV-1 newly-diagnosed individuals in April 2019 were selected by cross-sectional investigation from all 21 cities in Sichuan province. Phylogenetic relationship, transmission cluster, and genotypic drug resistance analyses were performed using HIV-1 polymerase (pol) gene sequences. We also analysed the association of demographic and virological factors with transmitted drug-resistance (TDR) and transmission clusters. Results Partial pol gene sequences were obtained from 1297 cases. HIV-1 epidemic strains in Sichuan province: the majority of genotypes were circulating recombinant form (CRF) 07_BC (675, 52.04%), CRF01_AE (343, 26.45%), CRF08_BC (115, 8.87%), CRF85_BC (67, 5.17%), subtype B (33, 2.54%), the other genotypes only accounted for 4.93%, and unique recombinant forms (URFs) (23, 1.77%) were observed in the study, and the difference of age, ethnicity, education, occupation, region and transmission pathway of different genotypes were statistically significant. According to WHO HIVDR surveillance threshold, the level of TDR has reached a medium level, with 72 of 1297 (5.55%) cases carrying drug-resistance mutation sites, TDR mutation frequency to nonnucleoside reverse transcriptase inhibitors (NNRTIs, 3.85%) was much higher than nucleoside reverse transcriptase inhibitors (NRTIs, 0.31%) and protease inhibitors (PIs, 1.70%), and CRF08_BC was a risk factor for TDR (odds ratio, 8.32; 95% CI 4.38–15.80 for CRF07_BC, P < 0.05). The most common drug resistance HIV-1 mutation pattern for NNRTI was V106 (1.31%, 17/1297) and E138 (1.16%, 15/1297), and for PI was M46 (0.69%, 9/1297). A total of 205 (15.8%) pol sequences were involved in the genetic transmission network clusters, CRF01_AE (odds ratio, 2.369; 95% CI 1.659–3.382; P < 0.05), subtype B (odds ratio, 13.723; 95% CI 6.338–29.71; P < 0.05), drug resistance (odds ratio, 0.306; 95% CI 0.106–0.881; P < 0.05) and different levels of education (P < 0.05) were significantly associated to be in clusters. Conclusion The distribution of HIV-1 genotypes in Sichuan is more diverse and complex, and the Men who have sex with men (MSM) is underrated, arguing for behavior scaling up intervention in this specific population besides the elderly people with heterosexual transmission risk groups. The risk of TDR mutation frequency increased in newly diagnosed patients highlights the significance of genotypic drug resistance monitoring and molecular surveillance of pretreatment HIV-1 drug resistance. The regimen composed of TDF, 3TC and EFV was still currently the preferred solution used free first-line therapy.
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Affiliation(s)
- Chang Zhou
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yan Zhang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Ling Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, 610041, Sichuan, China.
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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22
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Linheiro R, Sabatino S, Lobo D, Archer J. CView: A network based tool for enhanced alignment visualization. PLoS One 2022; 17:e0259726. [PMID: 35696379 PMCID: PMC9191720 DOI: 10.1371/journal.pone.0259726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/31/2022] [Indexed: 11/19/2022] Open
Abstract
To date basic visualization of sequence alignments have largely focused on displaying per-site columns of nucleotide, or amino acid, residues along with associated frequency summarizations. The persistence of this tendency to the recent tools designed for viewing mapped read data indicates that such a perspective not only provides a reliable visualization of per-site alterations, but also offers implicit reassurance to the end-user in relation to data accessibility. However, the initial insight gained is limited, something that is especially true when viewing alignments consisting of many sequences representing differing factors such as location, date and subtype. A basic alignment viewer can have potential to increase initial insight through visual enhancement, whilst not delving into the realms of complex sequence analysis. We present CView, a visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. Within the network, nodes are based on the clustering of sequence fragments that span windows placed consecutively along the alignment. Edges are placed between nodes of neighbouring windows where they share sequence identification(s), i.e. different regions of the same sequence(s). Thus, if a node is selected on the network, then the relationship that sequences passing through that node have to other regions of diversity within the alignment can be observed through path tracing. In addition to augmenting visual insight, CView provides export features including variant summarization, per-site residue and kmer frequencies, consensus sequence, alignment dissection as well as clustering; each useful across a range of research areas. The software has been designed to be user friendly, intuitive and interactive. It is open source and an executable jar, source code, quick start, usage tutorial and test data are available (under the GNU General Public License) from https://sourceforge.net/projects/cview/.
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Affiliation(s)
- Raquel Linheiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
| | - Stephen Sabatino
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- * E-mail:
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23
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Milbank C, Vira B. Wildmeat consumption and zoonotic spillover: contextualising disease emergence and policy responses. Lancet Planet Health 2022; 6:e439-e448. [PMID: 35550083 PMCID: PMC9084621 DOI: 10.1016/s2542-5196(22)00064-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 05/13/2023]
Abstract
Zoonotic diseases are estimated to constitute 75% of all emerging infectious diseases, of which more than 70% come from wild species. The potential threat of zoonotic spillover from the consumption of wildmeat has been the subject of policy and media attention, especially in the context of the COVID-19 pandemic; however, little is known about the actual conditions that contribute to the risk of spillover and associated disease transmission. In this Review, we compile existing evidence from available literature on the conditions of spillover associated with wildmeat consumption, including the types of wild animal and disease, modes of transmission, and the conditions in which spillover is thought to have occurred. We suggest that stronger understanding of the context of spillover from wildmeat is needed to enable more targeted and effective policy responses that reduce the risk of future pandemics of zoonotic origin. Such interventions could also lead to the avoidance of unintended adverse consequences for human communities that rely on wild produce, including wildmeat, as sources of dietary protein, fat, and micronutrients.
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Affiliation(s)
| | - Bhaskar Vira
- Department of Geography, University of Cambridge, Cambridge, UK
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24
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Lee CA, Hirsch VM. Mutation in the Disordered Linker Region of Capsid Disrupts Viral Kinetics of a Neuropathogenic SIV in Rhesus Macaques. Microbiol Spectr 2022; 10:e0047822. [PMID: 35297654 PMCID: PMC9045278 DOI: 10.1128/spectrum.00478-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 12/03/2022] Open
Abstract
TRIM5α polymorphism in rhesus macaques (RM) limits the genetic pool of animals in which we can perform simian immunodeficiency virus (SIV) studies without first screening animals for permissive TRIM5α genotypes. We have previously shown that polymorphisms in the TRIM5α B30.2/SPRY domain impact the level of SIVsmm viremia in RM and that amino acid substitutions (P37S/R98S) in the capsid N-terminal domain (CA-NTD) enables the virus to overcome restriction in RMs with the restrictive homozygous TRIM5αTFP/TFP genotype. Since this genotype also negatively impacted the development of central nervous system (CNS) lesions in animals infected with the parental source of CL757, we sought to generate a TRIM5αTFP/TFP-resistant clone, SIV-804E-CL757-P37S/R98S (CL757-SS), using a similar strategy. Unexpectedly, viral replication of CL757-SS was impaired in RMs with either the permissive TRIM5αTFP/Q or the restrictive TRIM5αTFP/TFP genotype. Analysis of the virus which emerged in the latter animals led to the discovery of a preexisting mutation relative to other SIVs. This P146T substitution in a conserved disordered linker region in the C-terminal domain of capsid (CA-CTD) has been shown to inhibit proper formation of HIV-1 capsid particles. Restoration of this residue to proline in the context of the TRIM5α-SS escape mutations not only restored viral replication, but also enhanced the infectivity of our previously reported neurotropic clone, even in RMs with permissive TRIM5α genotypes. IMPORTANCE SIV infection of rhesus macaques has become a valuable model for the development of AIDS vaccines and antiretroviral therapies. Polymorphisms in the rhesus macaque TRIM5α gene can affect SIV replication, making it necessary to genetically screen macaques for TRIM5α alleles that are permissive for SIV replication. This limits the pool of animals that can be used in a study, thereby making the acquisition of animals needed to fulfill study parameters difficult. We have constructed a viral clone that induces neuroAIDS in rhesus macaques regardless of their TRIM5α genotype, while also highlighting the important role the disordered linker domain plays in viral infectivity.
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Affiliation(s)
- Cheri A. Lee
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Vanessa M. Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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25
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Abstract
Retroviruses are widely distributed in all vertebrates, as are their endogenous forms, endogenous retroviruses (ERV), which serve as "fossil" evidence to trace the ancient origins and history of virus-host interactions over millions of years. The retroviral envelope (Env) plays a significant role in host range determination, but major information on their genetic diversification and evolution in anamniotes is lacking. Here, by incorporating multiple-round in silico similarity search and phylogenomic analysis, more than 30,000 copies of ERV lineages with gamma-type Env (GTE), covalently associated Env, were discovered by searching against all fish and amphibian genomes and transcriptomic assemblies, but no beta-type Env (BTE), noncovalently associated Env, was found. Furthermore, a nine-type classification system of anamniote GTE was proposed by combining phylogenetic and domain/motif analyses. The elastic genomic organization and overall phylogenetic incongruence between anamniotic Env and its neighboring polymerase (Pol) implied that early retroviral diversification in anamniotic vertebrates was facilitated by frequent recombination. At last, host cellular opioid growth factor receptor (OGFr) gene capturing by anamniotic ERVs with GTE was reported for the first time. Overall, our findings overturn traditional Pol genotyping and reveal a complex evolutionary history of anamniotic retroviruses inferred by Env evolution. IMPORTANCE Although the retroviral envelope (Env) protein in amniotes has been well studied, its evolutionary history in anamniotic vertebrates is ambiguous. By analyzing more than 30,000 copies of ERV lineages with gamma-type Env (GTE) in anamniotes, several important evolutionary features were identified. First, GTE was found to be widely distributed among different amphibians and fish. Second, nine types of GTE were discovered and defined, revealing their great genetic diversity. Third, the incongruence between the Env and Pol phylogenies suggested that frequent recombination shaped the early evolution of anamniote retroviruses. Fourth, an ancient horizontal gene transfer event was discovered from anamniotes to ERVs with GTE. These findings reveal a complex evolution pattern for retroviral Env in anamniotes.
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26
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Nawtaisong P, Robinson MT, Khammavong K, Milavong P, Rachlin A, Dittrich S, Dubot-Pérès A, Vongsouvath M, Horwood PF, Dussart P, Theppangna W, Douangngeum B, Fine AE, Pruvot M, Newton PN. Zoonotic Pathogens in Wildlife Traded in Markets for Human Consumption, Laos. Emerg Infect Dis 2022; 28:860-864. [PMID: 35318932 PMCID: PMC8962878 DOI: 10.3201/eid2804.210249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We tested animals from wildlife trade sites in Laos for the presence of zoonotic pathogens. Leptospira spp. were the most frequently detected infectious agents, found in 20.1% of animals. Rickettsia typhi and R. felis were also detected. These findings suggest a substantial risk for exposure through handling and consumption of wild animal meat.
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27
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Bimela JS, Nanfack AJ, Yang P, Dai S, Kong XP, Torimiro JN, Duerr R. Antiretroviral Imprints and Genomic Plasticity of HIV-1 pol in Non-clade B: Implications for Treatment. Front Microbiol 2022; 12:812391. [PMID: 35222310 PMCID: PMC8864110 DOI: 10.3389/fmicb.2021.812391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Combinational antiretroviral therapy (cART) is the most effective tool to prevent and control HIV-1 infection without an effective vaccine. However, HIV-1 drug resistance mutations (DRMs) and naturally occurring polymorphisms (NOPs) can abrogate cART efficacy. Here, we aimed to characterize the HIV-1 pol mutation landscape in Cameroon, where highly diverse HIV clades circulate, and identify novel treatment-associated mutations that can potentially affect cART efficacy. More than 8,000 functional Cameroonian HIV-1 pol sequences from 1987 to 2020 were studied for DRMs and NOPs. Site-specific amino acid frequencies and quaternary structural features were determined and compared between periods before (≤2003) and after (2004-2020) regional implementation of cART. cART usage in Cameroon induced deep mutation imprints in reverse transcriptase (RT) and to a lower extent in protease (PR) and integrase (IN), according to their relative usage. In the predominant circulating recombinant form (CRF) 02_AG (CRF02_AG), 27 canonical DRMs and 29 NOPs significantly increased or decreased in RT during cART scale-up, whereas in IN, no DRM and only seven NOPs significantly changed. The profound genomic imprints and higher prevalence of DRMs in RT compared to PR and IN mirror the dominant use of reverse transcriptase inhibitors (RTIs) in sub-Saharan Africa and the predominantly integrase strand transfer inhibitor (InSTI)-naïve study population. Our results support the potential of InSTIs for antiretroviral treatment in Cameroon; however, close surveillance of IN mutations will be required to identify emerging resistance patterns, as observed in RT and PR. Population-wide genomic analyses help reveal the presence of selective pressures and viral adaptation processes to guide strategies to bypass resistance and reinstate effective treatment.
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Affiliation(s)
- Jude S Bimela
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon.,Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Aubin J Nanfack
- Medical Diagnostic Center, Yaoundé, Cameroon.,Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Pengpeng Yang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Shaoxing Dai
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Judith N Torimiro
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Biochemistry, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Department of Microbiology, New York University School of Medicine, New York, NY, United States
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28
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Friant S, Bonwitt J, Ayambem WA, Ifebueme NM, Alobi AO, Otukpa OM, Bennett AJ, Shea C, Rothman JM, Goldberg TL, Jacka JK. Zootherapy as a potential pathway for zoonotic spillover: a mixed-methods study of the use of animal products in medicinal and cultural practices in Nigeria. ONE HEALTH OUTLOOK 2022; 4:5. [PMID: 35216623 PMCID: PMC8881094 DOI: 10.1186/s42522-022-00060-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Understanding how and why people interact with animals is important for the prevention and control of zoonoses. To date, studies have primarily focused on the most visible forms of human-animal contact (e.g., hunting and consumption), thereby blinding One Health researchers and practitioners to the broader range of human-animal interactions that can serve as cryptic sources of zoonotic diseases. Zootherapy, the use of animal products for traditional medicine and cultural practices, is widespread and can generate opportunities for human exposure to zoonoses. Existing research examining zootherapies omits details necessary to adequately assess potential zoonotic risks. METHODS We used a mixed-methods approach, combining quantitative and qualitative data from questionnaires, key informant interviews, and field notes to examine the use of zootherapy in nine villages engaged in wildlife hunting, consumption, and trade in Cross River State, Nigeria. We analyzed medicinal and cultural practices involving animals from a zoonotic disease perspective, by including details of animal use that may generate pathways for zoonotic transmission. We also examined the sociodemographic, cultural, and environmental contexts of zootherapeutic practices that can further shape the nature and frequency of human-animal interactions. RESULTS Within our study population, people reported using 44 different animal species for zootherapeutic practices, including taxonomic groups considered to be "high risk" for zoonoses and threatened with extinction. Variation in use of animal parts, preparation norms, and administration practices generated a highly diverse set of zootherapeutic practices (n = 292) and potential zoonotic exposure risks. Use of zootherapy was patterned by demographic and environmental contexts, with zootherapy more commonly practiced by hunting households (OR = 2.47, p < 0.01), and prescriptions that were gender and age specific (e.g., maternal and pediatric care) or highly seasonal (e.g., associated with annual festivals and seasonal illnesses). Specific practices were informed by species availability and theories of healing (i.e., "like cures like" and sympathetic healing and magic) that further shaped the nature of human-animal interactions via zootherapy. CONCLUSIONS Epidemiological investigations of zoonoses and public health interventions that aim to reduce zoonotic exposures should explicitly consider zootherapy as a potential pathway for disease transmission and consider the sociocultural and environmental contexts of their use in health messaging and interventions.
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Affiliation(s)
- Sagan Friant
- Department of Anthropology, The Pennsylvania State University, University Park, PA USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA USA
| | - Jesse Bonwitt
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329 USA
- Department of Anthropology, Durham University, Durham, UK
| | - Wilfred A. Ayambem
- Department of Forestry and Wildlife Resources Management, University of Calabar, Calabar, Nigeria
| | - Nzube M. Ifebueme
- Department of Forestry and Wildlife Resources Management, University of Calabar, Calabar, Nigeria
| | - Alobi O. Alobi
- Department of Forestry and Wildlife Resources Management, University of Calabar, Calabar, Nigeria
| | - Oshama M. Otukpa
- Department of Forestry and Wildlife Resources Management, University of Calabar, Calabar, Nigeria
| | - Andrew J. Bennett
- Department of Pathobiological Sciences, University of Wisconsin – Madison, Madison, WI USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, Frederick, MD USA
| | - Corrigan Shea
- Department of Pathobiological Sciences, University of Wisconsin – Madison, Madison, WI USA
| | - Jessica M. Rothman
- Department of Anthropology, Hunter College of the City University of New York, New York, NY USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin – Madison, Madison, WI USA
| | - Jerry K. Jacka
- Department of Anthropology, University of Colorado Boulder, Boulder, CO 80309 USA
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Bernstein AS, Ando AW, Loch-Temzelides T, Vale MM, Li BV, Li H, Busch J, Chapman CA, Kinnaird M, Nowak K, Castro MC, Zambrana-Torrelio C, Ahumada JA, Xiao L, Roehrdanz P, Kaufman L, Hannah L, Daszak P, Pimm SL, Dobson AP. The costs and benefits of primary prevention of zoonotic pandemics. SCIENCE ADVANCES 2022; 8:eabl4183. [PMID: 35119921 PMCID: PMC8816336 DOI: 10.1126/sciadv.abl4183] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The lives lost and economic costs of viral zoonotic pandemics have steadily increased over the past century. Prominent policymakers have promoted plans that argue the best ways to address future pandemic catastrophes should entail, "detecting and containing emerging zoonotic threats." In other words, we should take actions only after humans get sick. We sharply disagree. Humans have extensive contact with wildlife known to harbor vast numbers of viruses, many of which have not yet spilled into humans. We compute the annualized damages from emerging viral zoonoses. We explore three practical actions to minimize the impact of future pandemics: better surveillance of pathogen spillover and development of global databases of virus genomics and serology, better management of wildlife trade, and substantial reduction of deforestation. We find that these primary pandemic prevention actions cost less than 1/20th the value of lives lost each year to emerging viral zoonoses and have substantial cobenefits.
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Affiliation(s)
- Aaron S. Bernstein
- Boston Children’s Hospital and the Center for Climate, Health and the Global Environment, Boston, MA 02115, USA
- Corresponding author. (A.S.B.); (S.L.P.); (A.P.D.)
| | - Amy W. Ando
- Department of Agricultural and Consumer Economics, University of Illinois Urbana-Champaign, Champaign, IL 61801, USA
- Resources for the Future, 1616 P Street NW, Washington, DC 20036, USA
| | - Ted Loch-Temzelides
- Department of Economics and Baker Institute for Public Policy, Rice University, Houston, TX 77005, USA
| | - Mariana M. Vale
- Ecology Department, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Science and Technology in Ecology, Evolution and Biodiversity Conservation, Goiania, Brazil
| | - Binbin V. Li
- Environment Research Center, Duke Kunshan University, Kunshan, Jiangsu Province 215317, China
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Hongying Li
- EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018, USA
| | - Jonah Busch
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Colin A. Chapman
- Wilson Center, 1300 Pennsylvania Avenue NW, Washington, DC 20004, USA
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC 20004, USA
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an, China
| | - Margaret Kinnaird
- Practice Leader, Wildlife, WWF International, The Mvuli, Mvuli Road, Westlands, Kenya
| | - Katarzyna Nowak
- The Safina Center, 80 North Country Road, Setauket, NY 11733, USA
| | - Marcia C. Castro
- Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | | | - Jorge A. Ahumada
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Lingyun Xiao
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China
| | - Patrick Roehrdanz
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Les Kaufman
- Department of Biology and Pardee Center for the Study of the Longer-Range Future, Boston University, Boston, MA 02215, USA
| | - Lee Hannah
- Moore Center for Science, Conservation International, Arlington, VA 22202, USA
| | - Peter Daszak
- EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018, USA
| | - Stuart L. Pimm
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
- Corresponding author. (A.S.B.); (S.L.P.); (A.P.D.)
| | - Andrew P. Dobson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Santa Fe Institute, Hyde Park Road, Santa Fe, NM 87501, USA
- Corresponding author. (A.S.B.); (S.L.P.); (A.P.D.)
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Friedman SR, Jordan AE, Perlman DC, Nikolopoulos GK, Mateu-Gelabert P. Emerging Zoonotic Infections, Social Processes and Their Measurement and Enhanced Surveillance to Improve Zoonotic Epidemic Responses: A "Big Events" Perspective. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19020995. [PMID: 35055817 PMCID: PMC8776232 DOI: 10.3390/ijerph19020995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/23/2021] [Accepted: 01/10/2022] [Indexed: 02/04/2023]
Abstract
Zoonotic epidemics and pandemics have become frequent. From HIV/AIDS through COVID-19, they demonstrate that pandemics are social processes as well as health occurrences. The roots of these pandemics lie in changes in the socioeconomic interface between humanity and non-human host species that facilitate interspecies transmission. The degree to which zoonoses spread has been increased by the greater speed and extent of modern transportation and trade. Pre-existing sociopolitical and economic structures and conflicts in societies also affect pathogen propagation. As an epidemic develops, it can itself become a social and political factor, and change and interact with pre-existing sociobehavioral norms and institutional structures. This paper uses a "Big Events" approach to frame these processes. Based on this framework, we discuss how social readiness surveys implemented both before and during an outbreak might help public health predict how overall systems might react to an epidemic and/or to disease control measures, and thus might inform interventions to mitigate potential adverse outcomes or possibly preventing outbreaks from developing into epidemics. We conclude by considering what "pathways measures", in addition to those we and others have already developed, might usefully be developed and validated to assist outbreak and epidemic disease responses.
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Affiliation(s)
- Samuel R. Friedman
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA
- Center for Drug Use and HIV/HCV Research, New York, NY 10003, USA; (A.E.J.); (D.C.P.); (P.M.-G.)
- Correspondence:
| | - Ashly E. Jordan
- Center for Drug Use and HIV/HCV Research, New York, NY 10003, USA; (A.E.J.); (D.C.P.); (P.M.-G.)
| | - David C. Perlman
- Center for Drug Use and HIV/HCV Research, New York, NY 10003, USA; (A.E.J.); (D.C.P.); (P.M.-G.)
- Department of Infectious Diseases, Icahn School of Medicine, Mount Sinai Beth Israel, New York, NY 10003, USA
| | | | - Pedro Mateu-Gelabert
- Center for Drug Use and HIV/HCV Research, New York, NY 10003, USA; (A.E.J.); (D.C.P.); (P.M.-G.)
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA
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31
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Adla K, Dejan K, Neira D, Dragana Š. Degradation of ecosystems and loss of ecosystem services. One Health 2022. [DOI: 10.1016/b978-0-12-822794-7.00008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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32
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Sk MF, Haridev S, Roy R, Kar P. Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:941-962. [PMID: 34787532 DOI: 10.1080/1062936x.2021.1999318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A detailed computational study was performed to investigate the conformational changes of flap region and the mechanism underlying the binding of the inhibitor TMC-126 to HIV-1 protease (PR1) and its mutant variants through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculation. Further, we have studied the effectiveness of the inhibitor against HIV-2 protease (PR2). The MM-PBSA calculation suggests that TMC-126 loses its potency against mutant variants and PR2 compared to wild-type PR1 mainly due to the loss in intermolecular electrostatic interactions. The potency of the inhibitor decreases in the order: wild type PR1 > M46L > MDR20 > I50V > PR2 > V32I > A28S. Our study reveals that the flap of PR1 adopts a semi-open conformation due to the mutation I50V or MDR20. The dissimilar nature of the movement of the flap tip of both monomers is evident from the dynamic cross-correlation map. The protein structural network analysis displays that mutation causes structural rearrangements and changes the communication path between residues. Overall, we believe our study may help explore and accelerate the development of novel HIV-1/HIV-2 protease inhibitors with better potency.
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Affiliation(s)
- M F Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - S Haridev
- Department of Physics, Indian Institute of Technology Indore, Indore, India
| | - R Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - P Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Ceccarelli G, Giovanetti M, Sagnelli C, Ciccozzi A, d’Ettorre G, Angeletti S, Borsetti A, Ciccozzi M. Human Immunodeficiency Virus Type 2: The Neglected Threat. Pathogens 2021; 10:pathogens10111377. [PMID: 34832533 PMCID: PMC8621479 DOI: 10.3390/pathogens10111377] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/15/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
West Africa has the highest prevalence of human immunodeficiency virus (HIV)-2 infection in the world, but a high number of cases has been recognized in Europe, India, and the United States. The virus is less transmissible than HIV-1, with sexual contacts being the most frequent route of acquisition. In the absence of specific antiretroviral therapy, most HIV-2 carriers will develop AIDS. Although, it requires more time than HIV-1 infection, CD4+ T cell decline occurs more slowly in HIV-2 than in HIV-1 patients. HIV-2 is resistant to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and some protease inhibitors. Misdiagnosis of HIV-2 in patients mistakenly considered HIV-1-positive or in those with dual infections can cause treatment failures with undetectable HIV-1 RNA. In this era of global integration, clinicians must be aware of when to consider the diagnosis of HIV-2 infection and how to test for this virus. Although there is debate regarding when therapy should be initiated and which regimen should be chosen, recent trials have provided important information on treatment options for HIV-2 infection. In this review, we focus mainly on data available and on the insight they offer about molecular epidemiology, clinical presentation, antiretroviral therapy, and diagnostic tests of HIV-2 infection.
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Affiliation(s)
- Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Policlinico Umberto I, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.C.); (G.d.)
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil;
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Caterina Sagnelli
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131 Naples, Italy;
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00100 Rome, Italy;
| | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, Policlinico Umberto I, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.C.); (G.d.)
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, 00100 Rome, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00100 Rome, Italy;
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00100 Rome, Italy;
- Correspondence: ; Tel.: +39-06-22541-9187
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One Health Perspectives on New Emerging Viral Diseases in African Wild Great Apes. Pathogens 2021; 10:pathogens10101283. [PMID: 34684232 PMCID: PMC8539261 DOI: 10.3390/pathogens10101283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
The most recent emerging infectious diseases originated in animals, mainly in wildlife reservoirs. Mutations and recombination events mediate pathogen jumps between host species. The close phylogenetic relationship between humans and non-human primates allows the transmission of pathogens between these species. These pathogens cause severe impacts on public health and impair the conservation of habituated or non-habituated wild-living apes. Constant exposure of great apes to human actions such as hunting, deforestation, the opening of roads, and tourism, for example, contributes to increased interaction between humans and great apes. In spite of several studies emphasizing the risks of pathogen transmission between animals and humans, outbreaks of the reverse transmission of infectious agents threatening wildlife still occur on the African continent. In this context, measures to prevent the emergence of new diseases and conservation of primate species must be based on the One Health concept; that is, they must also ensure the monitoring of the environment and involve political and social aspects. In this article, we review and discuss the anthropological aspects of the transmission of diseases between people and wild primates and discuss new anthropozoonotic diseases in great apes in Africa from studies published between 2016 and 2020. We conclude that the health of great apes also depends on monitoring the health of human populations that interact with these individuals.
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35
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Pires C, Silva IC. Initial review on medicinal preparations of undetermined constitution containing natural materials for the treatment of HIV or AIDS. J Herb Med 2021. [DOI: 10.1016/j.hermed.2021.100477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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36
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Quinn TC. Forty years of AIDS: a retrospective and the way forward. J Clin Invest 2021; 131:e154196. [PMID: 34523618 DOI: 10.1172/jci154196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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37
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Abstract
Over the last few decades, hundreds of human pathogens have emerged at a rate unprecedented in human history. Emerged from where? Mostly from animals. The AIDS virus is blamed on the butchering of primates in the African bushmeat trade, we created mad cow disease when we turned cows into carnivores and cannibals, and SARS and COVID-19 have been traced back to the exotic wild animal trade. Our last pandemic, swine flu in 2009, arose not from some backwater wet market in Asia, however. It was largely made-in-the-USA on pig production operations in the United States. In this new Age of Emerging Diseases, there are now billions of animals overcrowded and intensively confined in filthy factory farms for viruses to incubate and mutate within. Today's industrial farming practices have given viruses billions more spins at pandemic roulette. How can we stop the emergence of pandemic viruses in the first place? Whenever possible, treat the cause. The largest and oldest association of public health professionals in the world, the American Public Health Association, has called for a moratorium on factory farming for nearly two decades. Indeed, factory farms are a public health menace. In addition to discontinuing the intensive confinement practices of animal agriculture, we should continue to research, develop, and invest in innovative plant-based and cultivated meat technologies to move away from raising billions of feathered and curly-tailed test tubes for viruses with pandemic potential to mutate within.
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38
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Kuthyar S, Reese AT. Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome. mSystems 2021; 6:e0056721. [PMID: 34342530 PMCID: PMC8407385 DOI: 10.1128/msystems.00567-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The human gut microbiome varies between populations, largely reflecting ecological differences. One ecological variable that is rarely considered but may contribute substantially to microbiome variation is the multifaceted nature of human-animal interfaces. We present the hypothesis that different interactions with animals contribute to shaping the human microbiome globally. We utilize a One Health framework to explore how changes in microbial exposure from human-animal interfaces shape the microbiome and, in turn, contribute to differential human health across populations, focusing on commensal and pathogen exposure, changes in colonization resistance and immune system training, and the potential for other functional shifts. Although human-animal interfaces are known to underlie human health and particularly infectious disease disparities, since their impact on the human microbiome remains woefully understudied, we propose foci for future research. We believe it will be crucial to understand this critical aspect of biology and its impacts on human health around the globe.
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Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Aspen T. Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
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Sousa JD, Havik PJ, Müller V, Vandamme AM. Newly Discovered Archival Data Show Coincidence of a Peak of Sexually Transmitted Diseases with the Early Epicenter of Pandemic HIV-1. Viruses 2021; 13:v13091701. [PMID: 34578283 PMCID: PMC8472979 DOI: 10.3390/v13091701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022] Open
Abstract
To which extent STDs facilitated HIV-1 adaptation to humans, sparking the pandemic, is still unknown. We searched colonial medical records from 1906–1958 for Leopoldville, Belgian Congo, which was the initial epicenter of pandemic HIV-1, compiling counts of treated STD cases in both Africans and Europeans. Almost all Europeans were being treated, while for Africans, generalized treatment started only in 1929. Treated STD counts in Europeans thus reflect STD infection rates more accurately compared to counts in Africans. In Africans, the highest recorded STD treatment incidence was in 1929–1935, declining to low levels in the 1950s. In Europeans, the recorded treatment incidences were highest during the period 1910–1920, far exceeding those in Africans. Europeans were overwhelmingly male and had frequent sexual contact with African females. Consequently, high STD incidence among Europeans must have coincided with high prevalence and incidence in the city’s African population. The data strongly suggest the worst STD period was 1910–1920 for both Africans and Europeans, which coincides with the estimated origin of pandemic HIV-1. Given the strong effect of STD coinfections on HIV transmission, these new data support our hypothesis of a causal effect of STDs on the epidemic emergence of HIV-1.
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Affiliation(s)
- João Dinis Sousa
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium;
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal;
- Correspondence:
| | - Philip J. Havik
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal;
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium;
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal;
- Institute for the Future, KU Leuven, B-3000 Leuven, Belgium
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Yakimovich A. Machine Learning and Artificial Intelligence for the Prediction of Host-Pathogen Interactions: A Viral Case. Infect Drug Resist 2021; 14:3319-3326. [PMID: 34456575 PMCID: PMC8385421 DOI: 10.2147/idr.s292743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/03/2021] [Indexed: 01/27/2023] Open
Abstract
The research of interactions between the pathogens and their hosts is key for understanding the biology of infection. Commencing on the level of individual molecules, these interactions define the behavior of infectious agents and the outcomes they elicit. Discovery of host-pathogen interactions (HPIs) conventionally involves a stepwise laborious research process. Yet, amid the global pandemic the urge for rapid discovery acceleration through the novel computational methodologies has become ever so poignant. This review explores the challenges of HPI discovery and investigates the efforts currently undertaken to apply the latest machine learning (ML) and artificial intelligence (AI) methodologies to this field. This includes applications to molecular and genetic data, as well as image and language data. Furthermore, a number of breakthroughs, obstacles, along with prospects of AI for host-pathogen interactions (HPI), are discussed.
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Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses. Viruses 2021; 13:v13081509. [PMID: 34452374 PMCID: PMC8402684 DOI: 10.3390/v13081509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?
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42
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Zhao J, Huang H, Lee S, Ragupathy V, Biswas S, Mbondji-wonje C, Wang X, Jiang A, Hewlett I. Identification, Genetic Characterization and Validation of Highly Diverse HIV-1 Viruses for Reference Panel Development. Viruses 2021; 13:v13071417. [PMID: 34372623 PMCID: PMC8310377 DOI: 10.3390/v13071417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/02/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
The continued diversification of HIV poses potentially significant challenges to HIV diagnostics and therapeutics. The dynamic evolution of emerging variants is highlighted in countries such as Cameroon in West Central Africa, where all known subtypes and circulating recombinant forms (CRFs) have been shown to be prevalent. We obtained several hundred HIV-positive plasma and viruses from this region for characterization and identification of highly divergent HIV strains. A total of 163 viral strains were cultured to high titers and high volumes using donor peripheral blood mononuclear cells (PBMCs). Initially, 101 viruses representing 59 strains were well characterized and categorized. Results showed that the viral load (VL) range was 0.36–398.9 × 107 copies/mL, p24 values was 0.2–1134 ng/mL. Phylogenetic analysis of thirty-six near full-length HIV-1 genomic sequences demonstrated that most recombinants were highly diverse CRF02 containing unique recombinant forms (URFs). There were seven viral isolates identified as pure subtype/sub-subtypes (F2, A1, G, and D), six as CRFs (CRF06, CRF18, and CRF22), and ten as URFs. These extensively characterized reagents reflect the current dynamic and complex HIV epidemic in Cameroon and provide valuable insights into the potential phylogenetic evolutionary trend of global HIV molecular epidemiology in the future. These materials may be useful for development of HIV validation and reference panels to evaluate the performance of serologic antigen and nucleic acid assays for their ability to detect and quantitate highly divergent HIV strains.
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Affiliation(s)
- Jiangqin Zhao
- Correspondence: (J.Z.); (I.H.); Tel.: +1-240-402-6746 (J.Z.); +1-240-402-9587 (I.H.)
| | | | | | | | | | | | | | | | - Indira Hewlett
- Correspondence: (J.Z.); (I.H.); Tel.: +1-240-402-6746 (J.Z.); +1-240-402-9587 (I.H.)
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43
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Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San JE, de Oliveira T, Gnanakaran S, Korber B. HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens. Cell Host Microbe 2021; 29:1093-1110. [PMID: 34242582 PMCID: PMC8173590 DOI: 10.1016/j.chom.2021.05.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.
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Affiliation(s)
- Will Fischer
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA
| | - Elena E Giorgi
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA
| | - Srirupa Chakraborty
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Kien Nguyen
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Tanmoy Bhattacharya
- T-2: Nuclear and Particle Physics, Astrophysics and Cosmology, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545 USA
| | - James Theiler
- ISR-3: Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Pablo A Goloboff
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, S. M. de Tucumán, Miguel Lillo 251 4000, Argentina; Research Associate, American Museum of Natural History, New York 10024, USA
| | - Hyejin Yoon
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Werner Abfalterer
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Brian T Foley
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sandrasegaram Gnanakaran
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA.
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Assessment of Associations between Malaria Parasites and Avian Hosts-A Combination of Classic System and Modern Molecular Approach. BIOLOGY 2021; 10:biology10070636. [PMID: 34356491 PMCID: PMC8301060 DOI: 10.3390/biology10070636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/20/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022]
Abstract
Simple Summary Throughout history, frequent outbreaks of diseases in humans have occurred following transmission from animals. While some diseases can jump between birds and mammals, others are stuck to closely related species. Understanding the mechanisms of host–parasite associations will enable us to predict the outbreaks of diseases and will therefore be important to society and ecological health. For decades, scientists have attempted to reveal how host–parasite associations are formed and persist. The key is to assess the ability of the parasite to infect and reproduce within the host without killing the host. Related studies have faced numerous challenges, but technical advances are providing solutions and are gradually broadening our understanding. In this review, I use bird malaria and related blood parasites as a model system and summarize the important advances in techniques and perspectives and how they provide new approaches for understanding the evolution of host–parasite associations to further predict disease outbreaks. Abstract Avian malaria and related haemosporidian parasites are responsible for fitness loss and mortality in susceptible bird species. This group of globally distributed parasites has long been used as a classical system for investigating host–parasite associations. The association between a parasite and its hosts can be assessed by the prevalence in the host population and infection intensity in a host individual, which, respectively, reflect the ability of the parasite to infect the host and reproduce within the host. However, the latter has long been poorly investigated due to numerous challenges, such as lack of general molecular markers and limited sensitivity of traditional methods, especially when analysing naturally infected birds. The recent development of genetic databases, together with novel molecular methodologies, has shed light on this long-standing problem. Real-time quantitative PCR has enabled more accurate quantification of avian haemosporidian parasites, and digital droplet PCR further improved experimental sensitivity and repeatability of quantification. In recent decades, parallel studies have been carried out all over the world, providing great opportunities for exploring the adaptation of haemosporidian parasites to different hosts and the variations across time and space, and further investigating the coevolutionary history between parasites and their hosts. I hereby review the most important milestones in diagnosis techniques of avian haemosporidian parasites and illustrate how they provide new insights for understanding host–parasite associations.
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Jamison DT, Wu KB. The East-West Divide in Response to COVID-19. ENGINEERING (BEIJING, CHINA) 2021; 7:936-947. [PMID: 34150351 PMCID: PMC8196471 DOI: 10.1016/j.eng.2021.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/25/2021] [Accepted: 05/16/2021] [Indexed: 05/03/2023]
Abstract
Coronavirus disease 2019 (COVID-19) deaths per million population in the countries of the West had often exceeded those in the countries of the East by factor of 100 by May 2021. In this paper, we refer to the West as represented by the United States plus the five most populous countries of Western Europe (France, Germany, Italy, Spain, and the United Kingdom), and the East as the 15 countries in East Asia and Oceania that are members of the Regional Comprehensive Economic Partnership, RCEP (Australia, Brunei, Cambodia, China, Indonesia, Japan, the Republic of Korea, Laos, Malaysia, Myanmar, New Zealand, Philippines, Singapore, Thailand, and Vietnam). This paper argues that currently available information points to the factors most responsible for the East-West divide. Warnings by early January 2020 about an atypical viral pneumonia in Wuhan, China, prompted rapid responses in many jurisdictions in East Asia. Publication of the virus's genome on 10 January 2020 provided essential information for making diagnostic tests and launching vaccine development. China's lockdown of Wuhan on 23 January 2020 provided a final, decisive signal of the danger of the new disease. By late March 2020, China had fully controlled its epidemic, and many other RCEP countries had taken early and decisive measures, including restrictions on travel, that aborted serious outcomes. Inaction during the critical month of February 2020 in the United States and most other Western countries allowed the disease to take hold and spread. In both the East and the West, stringent population-wide non-pharmaceutical interventions were widely implemented at great cost to societies, economies, and school systems. Without these measures, the outcomes could have been even worse. Most countries in the East also implemented tightly focused policies to isolate infectious individuals. Even today, most countries in the West allow infectious individuals to mingle with their families, coworkers, and communities. Much of the East-West divide plausibly results from failure in the West to implement the basic public health policies of early action and the isolation of infectious individuals. Widespread immunization in some RCEP and high-income countries will soon attenuate their outbreaks, while the slow rollout of vaccines in lower income countries is replacing the East-West divide in outcomes with a North-South one. The South is thus replacing the West as the breeding ground for more dangerous variants as exemplified by the highly contagious Delta variant, which may undermine hitherto successful control strategies in many countries.
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Affiliation(s)
- Dean T Jamison
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 98158, USA
| | - Kin Bing Wu
- Independent Consultant, Atherton, CA 94027, USA
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Multiple Infiltration and Cross-Species Transmission of Foamy Viruses across the Paleozoic to the Cenozoic Era. J Virol 2021; 95:e0048421. [PMID: 33910951 DOI: 10.1128/jvi.00484-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a coevolutionary pattern with their hosts that could be dated back to the Paleozoic era, while in contrast, frog FVs were much more likely acquired from cross-species (class-level) transmission in the Cenozoic era. In addition, we found that three distinct FV lineages had integrated into the genome of a salamander. Unexpectedly, we identified a lineage of endogenous FVs in caecilians that expressed all complete major genes, demonstrating the potential existence of an exogenous form of FV outside of mammals. Our discovery of rare phenomena in amphibian FVs has significantly increased our understanding of the macroevolution of the complex retrovirus. IMPORTANCE Foamy viruses (FVs) represent, more so than other viruses, the best model of coevolution between a virus and a host. This study represents the largest investigation so far of amphibian FVs and reveals 412 FVs of 6 distinct lineages from three major orders of amphibians. Besides a coevolutionary pattern, cross-species and repeated infections were also observed during the evolution of amphibian FVs. Remarkably, expressed FVs including a potential exogenous form were discovered, suggesting that active FVs might be underestimated in nature. These findings revealed that the multiple origins and complex evolution of amphibian FVs started from the Paleozoic era.
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Ellwanger JH, Chies JAB. Zoonotic spillover: Understanding basic aspects for better prevention. Genet Mol Biol 2021; 44:e20200355. [PMID: 34096963 PMCID: PMC8182890 DOI: 10.1590/1678-4685-gmb-2020-0355] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/05/2021] [Indexed: 01/07/2023] Open
Abstract
The transmission of pathogens from wild animals to humans is called “zoonotic spillover”. Most human infectious diseases (60-75%) are derived from pathogens that originally circulated in non-human animal species. This demonstrates that spillover has a fundamental role in the emergence of new human infectious diseases. Understanding the factors that facilitate the transmission of pathogens from wild animals to humans is essential to establish strategies focused on the reduction of the frequency of spillover events. In this context, this article describes the basic aspects of zoonotic spillover and the main factors involved in spillover events, considering the role of the inter-species interactions, phylogenetic distance between host species, environmental drivers, and specific characteristics of the pathogens, animals, and humans. As an example, the factors involved in the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic are discussed, indicating what can be learned from this public health emergency, and what can be applied to the Brazilian scenario. Finally, this article discusses actions to prevent or reduce the frequency of zoonotic spillover events.
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Affiliation(s)
- Joel Henrique Ellwanger
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
| | - José Artur Bogo Chies
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
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Diener L. [COVID-19 and Its Environment: From a History of Human Medicine Towards an Ecological History of Medicine?]. NTM 2021; 29:203-211. [PMID: 33871662 PMCID: PMC8054680 DOI: 10.1007/s00048-021-00299-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
This paper is part of the Forum COVID-19: Perspectives in the Humanities and Social Sciences. The history of medicine is mostly written as a history of human medicine. COVID-19 and other zoonotic infectious diseases, however, demand a reconsideration of medical history in terms of ecology and the inclusion of non-human actors and diverse environments. This contribution discusses possible approaches for an ecological history of medicine which satisfies the needs of several current and overlapping crises.
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Affiliation(s)
- Leander Diener
- Institut für Biomedizinische Ethik und Medizingeschichte, Universität Zürich, Winterthurerstr. 30, 8006, Zürich, Schweiz.
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Abstract
June 2021 marks the 40th anniversary of the first description of AIDS. On the 30th anniversary, we defined priorities as improving use of existing interventions, clarifying optimal use of HIV testing and antiretroviral therapy for prevention and treatment, continuing research, and ensuring sustainability of the response. Despite scientific and programmatic progress, the end of AIDS is not in sight. Other major epidemics over the past decade have included Ebola, arbovirus infections, and coronavirus disease (COVID-19). A benchmark against which to compare other global interventions is the HIV/AIDS response in terms of funding, coordination, and solidarity. Lessons from Ebola and HIV/AIDS are pertinent to the COVID-19 response. The fifth decade of AIDS will have to position HIV/AIDS in the context of enhanced preparedness and capacity to respond to other potential pandemics and transnational health threats.
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Affiliation(s)
| | | | - James W. Curran
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (K.M. De Cock, H.W. Jaffe)
- Emory University and Emory Center for AIDS Research, Atlanta (J.W. Curran)
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Cagliani R, Mozzi A, Pontremoli C, Sironi M. Evolution and Origin of Human Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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