Molecular evolution of Azagny virus, a newfound hantavirus harbored by the West African pygmy shrew (Crocidura obscurior) in Côte d'Ivoire

<p>Abstract</p> <p>Background</p> <p>Tanganya virus (TGNV), the only shrew-associated hantavirus reported to date from sub-Saharan Africa, is harbored by the Therese's shrew (<it>Crocidura theresae</it>), and is phylogenetically distinct from Thottapalayam virus (TPMV) in the Asian house shrew (<it>Suncus murinus</it>) and Imjin virus (MJNV) in the Ussuri white-toothed shrew (<it>Crocidura lasiura</it>). The existence of myriad soricid-borne hantaviruses in Eurasia and North America would predict the presence of additional hantaviruses in sub-Saharan Africa, where multiple shrew lineages have evolved and diversified.</p> <p>Methods</p> <p>Lung tissues, collected in RNAlater^®, from 39 Buettikofer's shrews (<it>Crocidura buettikoferi</it>), 5 Jouvenet's shrews (<it>Crocidura jouvenetae</it>), 9 West African pygmy shrews (<it>Crocidura obscurior</it>) and 21 African giant shrews (<it>Crocidura olivieri</it>) captured in Côte d'Ivoire during 2009, were systematically examined for hantavirus RNA by RT-PCR.</p> <p>Results</p> <p>A genetically distinct hantavirus, designated Azagny virus (AZGV), was detected in the West African pygmy shrew. Phylogenetic analysis of the S, M and L segments, using maximum-likelihood and Bayesian methods, under the GTR+I+Γ model of evolution, showed that AZGV shared a common ancestry with TGNV and was more closely related to hantaviruses harbored by soricine shrews than to TPMV and MJNV. That is, AZGV in the West African pygmy shrew, like TGNV in the Therese's shrew, did not form a monophyletic group with TPMV and MJNV, which were deeply divergent and basal to other rodent- and soricomorph-borne hantaviruses. Ancestral distributions of each hantavirus lineage, reconstructed using Mesquite 2.74, suggested that the common ancestor of all hantaviruses was most likely of Eurasian, not African, origin.</p> <p>Conclusions</p> <p>Genome-wide analysis of many more hantaviruses from sub-Saharan Africa are required to better understand how the biogeographic origin and radiation of African shrews might have contributed to, or have resulted from, the evolution of hantaviruses.</p

Thottapalayam Virus, a Prototype Shrewborne Hantavirus

This virus is antigenically and phylogenetically distinct from rodent-borne hantaviruses

Genetic diversity and phylogeography of Seewis virus in the Eurasian common shrew in Finland and Hungary

Recent identification of a newfound hantavirus, designated Seewis virus (SWSV), in the Eurasian common shrew (Sorex araneus), captured in Switzerland, corroborates decades-old reports of hantaviral antigens in this shrew species from Russia. To ascertain the spatial or geographic variation of SWSV, archival liver tissues from 88 Eurasian common shrews, trapped in Finland in 1982 and in Hungary during 1997, 1999 and 2000, were analyzed for hantavirus RNAs by reverse transcription-polymerase chain reaction. SWSV RNAs were detected in 12 of 22 (54.5%) and 13 of 66 (19.7%) Eurasian common shrews from Finland and Hungary, respectively. Phylogenetic analyses of S- and L-segment sequences of SWSV strains, using maximum likelihood and Bayesian methods, revealed geographic-specific genetic variation, similar to the phylogeography of rodent-borne hantaviruses, suggesting long-standing hantavirus-host co-evolutionary adaptation

Seewis virus, a genetically distinct hantavirus in the Eurasian common shrew (Sorex araneus)

More than 20 years ago, hantaviral antigens were reported in tissues of the Eurasian common shrew (Sorex araneus), Eurasian water shrew (Neomys fodiens) and common mole (Talpa europea), suggesting that insectivores, or soricomorphs, might serve as reservoirs of unique hantaviruses. Using RT-PCR, sequences of a genetically distinct hantavirus, designated Seewis virus (SWSV), were amplified from lung tissue of a Eurasian common shrew, captured in October 2006 in Graubünden, Switzerland. Pair-wise analysis of the full-length S and partial M and L segments of SWSV indicated approximately 55%–72% similarity with hantaviruses harbored by Murinae, Arvicolinae, Neotominae and Sigmodontinae rodents. Phylogenetically, SWSV grouped with other recently identified shrew-borne hantaviruses. Intensified efforts are underway to clarify the genetic diversity of SWSV throughout the geographic range of the Eurasian common shrew, as well as to determine its relevance to human health

Evidence for a Founder Effect among HIV-infected injection drug users (IDUs) in Pakistan.

Background: We have previously reported a HIV-1 subtype A infection in a community of injection drug users (IDUs) in Karachi, Pakistan. We now show that this infection among the IDUs may have originated from a single source. Methods: Phylogenetic analysis was performed of partial gag sequences, generated using PCR, from 26 HIV-positive IDU samples. Results: Our results showed formation of a tight monophyletic group with an intra-sequence identity of \u3c 98% indicating a founder effect . Our data indicate that the HIV-1 epidemic in this community of IDUs may have been transmitted by an HIV positive overseas contract worker who admitted to having contact with commercial sex workers during stay abroad. Conclusion: Specific measures need to implemented to control transmission of HIV infection in Pakistan through infected migrant workers

Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d'Ivoire

Recently identified hantaviruses harbored by shrews and moles (order Soricomorpha) suggest that other mammals having shared ancestry may serve as reservoirs. To investigate this possibility, archival tissues from 213 insectivorous bats (order Chiroptera) were analyzed for hantavirus RNA by RT-PCR. Following numerous failed attempts, hantavirus RNA was detected in ethanol-fixed liver tissue from two banana pipistrelles (Neoromicia nanus), captured near Mouyassué village in Côte d'Ivoire, West Africa, in June 2011. Phylogenetic analysis of partial L-segment sequences using maximum-likelihood and Bayesian methods revealed that the newfound hantavirus, designated Mouyassué virus (MOUV), was highly divergent and basal to all other rodent- and soricomorph-borne hantaviruses, except for Nova virus in the European common mole (Talpa europaea). Full genome sequencing of MOUV and further surveys of other bat species for hantaviruses, now underway, will provide critical insights into the evolution and diversification of hantaviruses

Genetic diversity of Imjin virus in the Ussuri white-toothed shrew (Crocidura lasiura) in the Republic of Korea, 2004-2010

Recently, Imjin virus (MJNV), a genetically distinct hantavirus, was isolated from lung tissues of the Ussuri white-toothed shrew (Crocidura lasiura) captured near the demilitarized zone in the Republic of Korea. To clarify the genetic diversity of MJNV, partial M- and L-segment sequences were amplified from lung tissues of 12 of 37 (32.4%) anti-MJNV IgG antibody-positive Ussuri white-toothed shrews captured between 2004 and 2010. A 531-nucleotide region of the M segment (coordinates 2,255 to 2,785) revealed that the 12 MJNV strains differed by 0-12.2% and 0-2.3% at the nucleotide and amino acid levels, respectively. A similar degree of nucleotide (0.2-11.9%) and amino acid (0-3.8%) difference was found in a 632-nucleotide length of the L segment (coordinates 962 to 1,593) of nine MJNV strains. Phylogenetic analyses, based on the partial M and L segments of MJNV strains generated by the neighbor-joining and maximum likelihood methods, showed geographic-specific clustering, akin to the phylogeography of rodent-borne hantaviruses

Academic response to storm-related natural disasters—lessons learned

On 30 October 2017, selected faculty and administrators from Research Centers in Minority Institutions (RCMI) grantee institutions gathered to share first-hand accounts of the devastating impact of Hurricanes Harvey, Irma, and Maria, which had interrupted academic activities, including research, education, and training in Puerto Rico, Florida, and Texas. The presenters reviewed emergency response measures taken by their institutions to maintain community health care access and delivery, the storm-related impact on clinical and research infrastructure, and strategies to retain locally grown clinical expertise and translational science research talent in the aftermath of natural disasters. A longer-term perspective was provided through a comparative review of lessons learned by one New Orleans-based institution (now more than a decade post-storm) in the aftermath of Hurricane Katrina. Caring for the internal and external communities associated with each institution and addressing the health disparities exacerbated by storm-related events is one key strategy that will pay long-term dividends in the survival of the academic institutions and the communities they serve

Evolutionary Insights from a Genetically Divergent Hantavirus Harbored by the European Common Mole (Talpa europaea)

BACKGROUND:The discovery of genetically distinct hantaviruses in shrews (Order Soricomorpha, Family Soricidae) from widely separated geographic regions challenges the hypothesis that rodents (Order Rodentia, Family Muridae and Cricetidae) are the primordial reservoir hosts of hantaviruses and also predicts that other soricomorphs harbor hantaviruses. Recently, novel hantavirus genomes have been detected in moles of the Family Talpidae, including the Japanese shrew mole (Urotrichus talpoides) and American shrew mole (Neurotrichus gibbsii). We present new insights into the evolutionary history of hantaviruses gained from a highly divergent hantavirus, designated Nova virus (NVAV), identified in the European common mole (Talpa europaea) captured in Hungary. METHODOLOGY/PRINCIPAL FINDINGS:Pair-wise alignment and comparison of the full-length S- and L-genomic segments indicated moderately low sequence similarity of 54-65% and 46-63% at the nucleotide and amino acid levels, respectively, between NVAV and representative rodent- and soricid-borne hantaviruses. Despite the high degree of sequence divergence, the predicted secondary structure of the NVAV nucleocapsid protein exhibited the characteristic coiled-coil domains at the amino-terminal end, and the L-segment motifs, typically found in hantaviruses, were well conserved. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that NVAV formed a distinct clade that was evolutionarily distant from all other hantaviruses. CONCLUSIONS:Newly identified hantaviruses harbored by shrews and moles support long-standing virus-host relationships and suggest that ancestral soricomorphs, rather than rodents, may have been the early or original mammalian hosts

Sequence analysis of human T cell lymphotropic virus type I strains from southern India: gene amplification and direct sequencing from whole blood blotted onto filter paper

Human T cell lymphotropic virus type I (HTLV-I) infection in India has been found to be associated with adult T cell leukaemia/lymphoma (ATLL) and HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP) among life-long residents of southern India. To examine the heterogeneity of HTLV-I strains from southern India and to determine their relationship with the sequence variants of HTLV-I from Melanesia, 1149 nucleotides spanning selected regions of the HTLV-I gag, pol, env and pX genes were amplified and directly sequenced from DNA extracted from whole blood blotted onto filter paper and from peripheral blood mononuclear cells, obtained from one patient with HAM/TSP, two with ATLL and eight asymptomatic carriers from Andhra Pradesh, Kerala and Tamil Nadu. Sequence alignments and comparisons indicated that the 11 HTLV-I strains from southern India were 99.2% to 100% identical among themselves and 98.7% to 100% identical to the Japanese prototype HTLV-I ATK. The majority of base substitutions were transitions and silent. No frameshifts, insertions, deletions or possibly disease-specific base changes were found in the regions sequenced. The observed clustering of the Indian HTLV-I strains with those from Japan, as determined by the maximum parsimony method, suggested a common source of HTLV-I infection with subsequent parallel evolution. Amplification of DNA from blood specimens collected on filter paper may be useful for the study of other blood-borne pathogens