Inactivation technology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is certainly a critical measure to mitigate the spread of coronavirus disease 2019 (COVID-19). A deep ultraviolet light-emitting diode (DUV-LED) would be a promising candidate to inactivate SARS-CoV-2, based on the well-known antiviral effects of DUV on microorganisms and viruses. However, due to variations in the inactivation effects across different viruses, quantitative evaluations of the inactivation profile of SARS-CoV-2 by DUV-LED irradiation need to be performed. In the present study, we quantify the irradiation dose of DUV-LED necessary to inactivate SARS-CoV-2. For this purpose, we determined the culture media suitable for the irradiation of SARS-CoV-2 and optimized the irradiation apparatus using commercially available DUV-LEDs that operate at a center wavelength of 265, 280, or 300 nm. Under these conditions, we successfully analyzed the relationship between SARS-CoV-2 infectivity and the irradiation dose of the DUV-LEDs at each wavelength without irrelevant biological effects. In conclusion, total doses of 1.8 mJ/cm² for 265 nm, 3.0 mJ/cm² for 280 nm, and 23 mJ/cm² for 300 nm are required to inactivate 99.9% of SARS-CoV-2. Our results provide quantitative antiviral effects of DUV irradiation on SARS-CoV-2, serving as basic knowledge of inactivation technologies against SARS-CoV-2.

One of the most important and outstanding characteristics of viruses is their cellular and host tropism (Levine and Enquist, 2007). As parasitic entities, viruses have to compromise with numbers of positive and negative factors present in target cells for their survival. In the absence of an appropriate interaction with cells, they do not replicate at all. Viral tropism therefore can be determined at each replication step, beginning with the entry into cells and ending with the progeny production from cells. There are two major types of viral tropism, that is, the receptor-dependent and -independent tropisms. Restriction of viral replication occurs on the cell surface (receptor-dependent viral entry step) and/or intracellularly (receptor-independent post-entry replication steps). In this Research Topic, a number of basic studies on both types of animal virus tropism have been published as either reviews, mini-reviews, or an original research article. Kajitani et al. (2012) have efficiently summarized a unique and complex lifecycle of human papilloma viruses (double-stranded DNA virus). Ohka et al. (2012) have concisely described the receptor-dependent and -independent tropism of poliovirus (positive sense single-stranded RNA virus). Ramadhany et al. (2012) have presented an original study on the mutations in hemagglutinin gene of influenza virus (negative sense single-stranded and segmented RNA virus) and have discussed their effects on the viral tropism. Multiple cellular receptors for measles virus (negative sense single-stranded and segmented RNA virus) have been clearly described by Sato et al. (2012). Takada (2012) has proposed models of filovirus (ebola and Marburg viruses; negative sense single-stranded RNA virus) entry into cells. Yasuda (2012) has discussed the interaction of ebolavirus and anti-viral cellular factor tetherin/BST-2. Species tropism of human and simian immunodeficiency viruses (HIV and SIVs; positive sense single-stranded RNA viruses containing reverse transcriptase), a representative of the receptor-independent tropism, has been systematically summarized by Nakayama and Shioda (2012). Sakuma and Takeuchi (2012) has provided insight into the mechanism for species-specific SIV replication. Nomaguchi et al. (2012) have focused on the function of viral accessory proteins, and discussed the bases for HIV-1 species tropism. Tani et al. (2011) have described the use of vesicular stomatitis virus (negative sense single-stranded RNA virus) as tools in various research and medical fields. Finally, Uchiyama (2012) has reviewed the rickettsia tropism as an example of non-viral microbes (obligate intracellular parasitic bacterium). The authors in this Research Topic have highlighted the importance of viral tropism by presenting biological phenomena and their underpinning host cellular and molecular bases. The biologically unique phenomenon of viral tropism is not only of interest to virologists to bring progress to their basic science but also highly relevant to clinical studies with the goal to design new anti-viral strategies. Accordingly, “Viral Tropism” must be considered a sibling to another Research Topic in Frontiers in Virology entitled “Receptor usage and pathogenesis in acute and chronic viral infection.” Kajitani, N., Satsuka, A., Kawate, A., and Sakai, H. (2012). Productive life cycle of human papillomaviruses that depends upon squamous epithelial differentiation. Front. Microbiol. 3:152. doi: 10.3389/fmicb.2012.00152 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Levine, A. J., and Enquist, L. W. (2007). “History of virology,” in Fields Virology, 5th Edn, eds D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus (Philadelphia, PA: Lippincott Williams & Wilkins), 3–23. Nakayama, E. E., and Shioda, T. (2012). TRIM5α and species tropism of HIV/SIV. Front. Microbiol. 3:13. doi: 10.3389/fmicb.2012.00013 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Nomaguchi, M., Doi, N., Matsumoto, Y., Sakai, Y., Fujiwara, S., and Adachi, A. (2012). Species tropism of HIV-1 modulated by viral accessory proteins. Front. Microbiol. 3:267. doi: 10.3389/fmicb.2012.00267 CrossRef Full Text Ohka, S., Nihei, C., Yamazaki, M., and Nomoto, A. (2012). Poliovirus trafficking toward central nervous system via human poliovirus receptor-dependent and -independent pathway. Front. Microbiol. 3:147. doi: 10.3389/fmicb.2012.00147 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Ramadhany, R., Yasugi, M., Nakamura, S., Daidoji, T., Watanabe, Y., Takahashi, K., Ikuta, K., and Nakaya, T. (2012). Tropism of pandemic 2009 H1N1 influenza A virus. Front. Microbiol. 3:128. doi: 10.3389/fmicb.2012.00128 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Sakuma, R., and Takeuchi, H. (2012). SIV replication in human cells. Front. Microbiol. 3:162. doi: 10.3389/fmicb.2012.00162 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Sato, H., Yoneda, M., Honda, T., and Kai, C. (2012). Morbillivirus receptors and tropism: multiple pathways for infection. Front. Microbiol. 3:75. doi: 10.3389/fmicb.2012.0075 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Takada, A. (2012). Filovirus tropism: cellular molecules for viral entry. Front. Microbiol. 3:34. doi: 10.3389/fmicb.2012.00034 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Tani, H., Morikawa, S., and Matsuura, Y. (2011). Development and application of VSV vectors based on cell tropism. Front. Microbiol. 2:272. doi: 10.3389/fmicb.2011.00272 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Uchiyama, T. (2012). Tropism and pathogenicity of rickettsiae. Front. Microbiol. 3:230. doi: 10.3389/fmicb.2012.00230 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Yasuda, J. (2012). Ebolavirus replication and tetherin/BST-2. Front. Microbiol. 3:111. doi: 10.3389/fmicb.2012.00111 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Citation: Nomaguchi M, Fujita M, Miyazaki Y and Adachi A (2012) Viral tropism. Front. Microbio. 3:281. doi: 10.3389/fmicb.2012.00281 Received: 12 July 2012; Accepted: 18 July 2012; Published online: 03 August 2012. Edited by: Reviewed by: Copyright: © 2012 Nomaguchi, Fujita, Miyazaki and Adachi. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. *Correspondence: adachi@basic.med.tokushima-u.ac.jp

Retroviruses can cause diseases such as AIDS, leukemia, and tumors, but are also used as vectors for human gene therapy. All retroviruses, except foamy viruses, package two copies of unspliced genomic RNA into their progeny viruses. Understanding the molecular mechanisms of retroviral genome packaging will aid the design of new anti-retroviral drugs targeting the packaging process and improve the efficacy of retroviral vectors. Retroviral genomes have to be specifically recognized by the cognate nucleocapsid domain of the Gag polyprotein from among an excess of cellular and spliced viral mRNA. Extensive virological and structural studies have revealed how retroviral genomic RNA is selectively packaged into the viral particles. The genomic area responsible for the packaging is generally located in the 5′ untranslated region (5′ UTR), and contains dimerization site(s). Recent studies have shown that retroviral genome packaging is modulated by structural changes of RNA at the 5′ UTR accompanied by the dimerization. In this review, we focus on three representative retroviruses, Moloney murine leukemia virus, human immunodeficiency virus type 1 and 2, and describe the molecular mechanism of retroviral genome packaging.

The retroviral Gag capsid (Gag-CA) interdomain linker is an unstructured peptide segment connecting structured N-terminal and C-terminal domains. Although the region is reported to play roles in virion morphogenesis and infectivity, underlying molecular mechanisms remain unexplored. To address this issue, we determined biological and molecular phenotypes of HIV-1 CA linker mutants by experimental and in silico approaches. Among the nine linker mutants tested, eight exhibited attenuation of viral particle production to various extents mostly in parallel with a reduction in viral infectivity. Sucrose density gradient, confocal microscopy, and live-cell protein interaction analyses indicated that the defect is accompanied by attenuation of Gag-Gag interactions following Gag plasma membrane targeting in the cells. In silico analyses revealed distinct distributions of interaction-prone hydrophobic patches between immature and mature CA proteins. Molecular dynamics simulations predicted that the linker mutations can allosterically alter structural fluctuations, including the interaction surfaces apart from the mutation sites in both the immature and mature CA proteins. These results suggest that the HIV-1 CA interdomain linker is a cis-modulator of the CA interaction surfaces to optimize efficiency of Gag assembly, virion production, and viral infectivity. IMPORTANCE HIV-1 particle production and infection are highly ordered processes. Viral Gag proteins play a central role in the assembly and disassembly of viral molecules. Of these, capsid protein (CA) is a major contributor to the Gag-Gag interactions. CA consists of two structured domains, i.e., N-terminal (NTD) and C-terminal (CTD) domains, connected by an unstructured domain named the interdomain linker. While multiple regions in the NTD and CTD are reported to play roles in virion morphogenesis and infectivity, the roles of the linker region in Gag assembly and virus particle formation remain elusive. In this study, we showed by biological and molecular analyses that the linker region functions as an intramolecular modulator to tune Gag assembly, virion production, and viral infectivity. Our study thus illustrates a hitherto-unrecognized mechanism, an allosteric regulation of CA structure by the disordered protein element, for HIV-1 replication.

Varieties of in vitro systems have been used to study biochemical properties of human immunodeficiency virus Gag-capsid protein (HIV Gag-CA). Recently, we have comparatively characterized HIV-1 and HIV-2 Gag-CA proteins using such technology, and have demonstrated that the NaCl-initiated CA-polymerization in vitro and the stability of CA N-terminal domain (NTD) as judged by differential scanning fluorimetry (DSF) are inversely correlated. In this study, we found that ZnCl2 works as a competent initiator of the in vitro HIV-1 CA-polymerization at much lower concentrations than those of NaCl frequently used for the polymerization initiation. We also showed by DSF assays that ZnCl2 highly destabilize HIV-1 CA. Furthermore, PF74, a well-known inducer of premature HIV-1 uncoating in infected cells, was demonstrated to unusually promote the HIV-1 CA-disassembly in the presence of ZnCl2 as revealed by DSF assays. Taken together, we conclude that the DSF method may be useful as an efficient monitoring system to screen anti-HIV-1 CA molecules.

HIV-1 Env protein functions in the entry process and is the target of neutralizing antibodies. Its intrinsically high mutation rate is certainly one of driving forces for persistence/survival in hosts. For optimal replication in various environments, HIV-1 Env must continue to adapt and evolve through balancing sometimes incompatible function, replication fitness, and neutralization sensitivity. We have previously reported that adapted viruses emerge in repeated and prolonged cultures of cells originally infected with a macaque-tropic HIV-1_NL4-3 derivative. We have also shown that the adapted viral clones exhibit enhanced growth potentials both in macaque PBMCs and individuals, and that three single-amino acid mutations are present in their Env V1/C2/C4 domains. In this study, we investigated how lab-adapted and highly neutralization-sensitive HIV-1_NL4-3 adapts its Env to macaque cells with strongly replication-restrictive nature for HIV-1. While a single and two mutations gave a significantly enhanced replication phenotype in a macaque cell line and also in human cell lines that stably express either human CD4 or macaque CD4, the virus simultaneously carrying the three adaptive mutations always grew best. Entry kinetics of parental and triple mutant viruses were similar, whereas the mutant was significantly more readily inhibited for its infectivity by soluble CD4 than parental virus. Furthermore, molecular dynamics simulations of the Env ectodomain (gp120 and gp41 ectodomain) bound with CD4 suggest that the three mutations increase binding affinity of Env for CD4 in solution. Thus, it is quite likely that the affinity for CD4 of the mutant Env is enhanced relative to the parental Env. Neutralization sensitivity of the triple mutant to CD4 binding site antibodies was not significantly different from that of parental virus, whereas the mutant exhibited a considerably higher resistance against neutralization by a CD4-induced epitope antibody and Env trimer-targeting V1/V2 antibodies. These results suggest that the three adaptive mutations cooperatively promote viral growth via increased CD4 affinity, and also that they enhance viral resistance to several neutralization antibodies by changing the Env-trimer conformation. In total, we have verified here an HIV-1 adaptation pathway in host cells and individuals involving Env derived from a lab-adapted and highly neutralization-sensitive clone.