Dynamic diversity of SARS-CoV-2 genetic mutations in a lung transplantation patient with persistent COVID-19.

Numerous SARS-CoV-2 variant strains with altered characteristics have emerged since the onset of the COVID-19 pandemic. Remdesivir (RDV), a ribonucleotide analogue inhibitor of viral RNA polymerase, has become a valuable therapeutic agent. However, immunosuppressed hosts may respond inadequately to RDV and develop chronic persistent infections. A patient with respiratory failure caused by interstitial pneumonia, who had undergone transplantation of the left lung, developed COVID-19 caused by Omicron BA.5 strain with persistent chronic viral shedding, showing viral fusogenicity. Genome-wide sequencing analyses revealed the occurrence of several viral mutations after RDV treatment, followed by dynamic changes in the viral populations. The C799F mutation in nsp12 was found to play a pivotal role in conferring RDV resistance, preventing RDV-triphosphate from entering the active site of RNA-dependent RNA polymerase. The occurrence of diverse mutations is a characteristic of SARS-CoV-2, which mutates frequently. Herein, we describe the clinical case of an immunosuppressed host in whom inadequate treatment resulted in highly diverse SARS-CoV-2 mutations that threatened the patient's health due to the development of drug-resistant variants.

PKR-NF-κB Pathway Upstream of IFN-ß Induction Is Dysregulated in Oncolytic Sindbis Virus-infected HeLa Cells.

BACKGROUND/AIM: Sindbis virus (SINV) is a naturally occurring oncolytic virus that kills cancer cells and is less harmful to normal cells. In this study, a recombinant SINV, which expressed green and blue fluorescent proteins, was used to precisely analyze SINV infection and replication. MATERIALS AND METHODS: Antiviral responses, including IFN-ß mRNA, protein kinase R (PKR), NF-B, and caspase 3/7, were analyzed in SINV-infected cancerous HeLa cells and normal human fibroblast TIG-1-20 cells. RESULTS: SINV could infect, replicate, and proliferate both in HeLa and TIG-1-20 cells, causing lytic infection only in HeLa cells. SINV grew preferentially in HeLa cells causing remarkable apoptosis. IFN-ß mRNA expression was suppressed in SINV-infected HeLa cells compared to that in TIG-1-20 cells. Further analyses of PKR and NF-B upstream of IFN-ß induction revealed that the compromised response in the PKR-NF-B pathway during early infection coincided with IFN induction suppression in HeLa cells. CONCLUSION: Dysregulation of PKR in HeLa cells is the determinant of SINV oncolysis.

Molecular detection of dengue virus in patients suspected of Ebola virus disease in Ghana.

Dengue fever is known to be one of the most common arthropod-borne viral infectious diseases of public health importance. The disease is now endemic in more than 100 countries in Africa, the Americas, the Eastern Mediterranean, Southeast Asia and the Western Pacific with an estimated two fifths of the world's population being at risk. The notable endemic viral hemorrhagic fevers (VHFs) found in West Africa, including yellow fever, Lassa fever, Rift Valley fever, dengue fever and until recently Ebola have been responsible for most outbreaks with fatal consequences. These VHFs usually produce unclear acute febrile illness, especially in the acute phase of infection. In this study we detected the presence of 2 different serotypes (DENV-2 and DENV-3) of Dengue virus in 4 sera of 150 patients clinically suspected of Ebola virus disease during the Ebola Virus Disease (EVD) outbreak in West Africa with the use of serological and molecular test assays. Sequence data was successfully generated for DENV-3 and phylogenetic analysis of the envelope gene showed that the DENV-3 sequences had close homology with DENV-3 sequences from Senegal and India. This study documents molecular evidence of an indigenous Dengue fever viral infection in Ghana and therefore necessitates the need to have an efficient surveillance system to rapidly detect and control the dissemination of the different serotypes in the population which has the potential to cause outbreaks of dengue hemorrhagic fevers.

[Two research projects on infectious diseases conducted in Noguchi Memorial Institute for Medical Research, University of Ghana by Tokyo Medical and Dental University].

Ghana-Tokyo Medical and Dental University Research Collaboration Center has been established since 2008 when our Program was chosen together with the Program in the Philippines proposed by Tohoku University as an additional small-scale research center of the Overseas Research Program on Emerging and Reemerging Diseases that is funded by the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government and started in 2005. This 5-year government-supported Program has changed its name to develop into a more active world-level program called Japan Initiative for Global Research Network on Infectious Diseases (J-GRID) and entered the second 5-year phase in 2010, and our Program is playing an important role among other research centers located in Asia and Africa. Currently, two research projects are carried out in parallel in Noguchi Memorial Institute for Medical Research by Tokyo Medical and Dental University: one is a J-GRID project and the other is the one of Science and Technology Research Partnership for Sustainable Development (SATREPS) which is a joint project between Japan International Cooperation Agency (JICA) and Japan Science and Technology Agency (JST). This special article is describing what these two projects are all about.

Exposure to SIVmnd-2 in southern Cameroon: public health implications.

Compelling evidence appeared in 2002 of human exposure to a plethora of primate lentiviruses through hunting, handling of bushmeat, and/or animals kept as pets in Cameroon. To determine SIV prevalence in pet animals, an analysis of 28 sera of nonhuman primates found no SIV infection in greater spot-nosed monkeys (0/5) or chimpanzees (0/10), and a prevalence rate of 23.1% (3/13) in mandrills kept as household pets in southern Cameroon. Phylogenetical analysis based on pol-integrase region and mitochondrial cytochrome b gene showed that the newly found SIV from Mandrillus sphinx (SIVmndCM-202, SIVmndCM-211, and SIVmndCM-218) clustered significantly with SIVmnd-2. Questionnaire data were also collected to assess whether owners had experienced bites, scratches, or exposure to blood and/or body fluid. Risk to human health from cross-species transmission of the newly identified SIVmnd-2 to infect humans remains unknown.

Construction and infection of a new simian/human immunodeficiency chimeric virus (SHIV) containing the integrase gene of the human immunodeficiency virus type 1 genome and analysis of its adaptation to monkey cells.

Expanding the HIV-1-derived regions in the SHIV genome may help to clarify the viral restriction factors determining the host range. In this study, we constructed a new SHIV having the reverse transcriptase and integrase-encoding regions of HIV-1 in addition to the 3' half genomic region of HIV-1. This SHIV, termed SHIVrti/3rn, could replicate in a monkey CD4+ T cell line, HSC-F, although its replication in monkey PBMCs was very weak. After SHIVrti/3rn was passaged in HSC-F cells for 26weeks, it gradually began to replicate in monkey PBMCs. This monkey-cell-adapted virus, termed SHIVrti/3rnP, could replicate in rhesus macaques. The whole genome of SHIVrti/3rnP was sequenced and was found to differ from SHIVrti/3rn at eleven positions. We constructed a series of mutants having some or all of these mutations and investigated their replication kinetics. The mutational analysis revealed that all of the mutations, but mainly the mutations in env, were responsible for the adaptation in HSC-F cells and were enough to replicate in rhesus PBMCs. Of all the SHIVs reported so far that can infect rhesus monkeys in vivo, SHIVrti/3rnP is the one that is genetically the closest to HIV-1.

Construction of a novel SHIV having an HIV-1-derived protease gene and its infection to rhesus macaques: a useful tool for in vivo efficacy tests of protease inhibitors.

We generated a novel SHIV (termed SHIV-pr) that possesses the HIV-1-derived protease (PR) gene in the corresponding position in the SIVmac genome. SHIV-pr is replication-competent in human and monkey CD4(+) T lymphoid cell lines as well as rhesus macaque PBMCs. The viral growth of SHIV-pr was completely blocked in the presence of a peptide-analog PR inhibitor at the tissue culture level. When SHIV-pr was intravenously inoculated into two rhesus macaques, it resulted in a weak but long-lasting persistent infection in one monkey, whereas the infection of another was only temporary. To enhance the viral growth competence by adaptation, we then passaged the virus in vivo from a monkey up to the fourth generation. The initial peak values of plasma viral loads as well as the setpoint values increased generation by generation and reached those of a parental virus SIVmac. When a medication using the content of Kaletra capsule (a mixture of two PR inhibitors, lopinavir and ritonavir) was orally given to three SHIV-pr-infected monkeys for 4 weeks, plasma viral loads dropped to near or below the detection limit and quickly rebounded after the cessation of medication. The results suggest that SHIV-pr can be used to evaluate PR inhibitors using monkeys.

DNA vaccination of macaques by a full-genome SHIV plasmid that has an IL-2 gene and produces non-infectious virus particles.

We previously reported that a mutant full-sized plasmid DNA vaccine regime in macaques was effective against a homologous challenge [Akahata W, Ido E, Shimada T, Katsuyama K, Yamamoto H, Uesaka H, et al. DNA vaccination of macaques by a full genome HIV-1 plasmid which produces non-infectious virus particles. Virology 2000;275:116-24; Akahata W, Ido E, Akiyama H, Uesaka H, Enose Y, Horiuchi R, et al. DNA vaccination of macaques by a full genome SHIV-1 plasmid that produces non-infectious virus particles. J Gen Virol 2003;84:2237-44]. In this study, to evaluate the DNA vaccination regime against a heterologous challenge, a novel plasmid named pSHIV-ZF1*IL-2 was constructed. Four monkeys were intramuscularly and intradermally injected four times with the pSHIV-ZF1*IL-2. Vaccinated monkeys were intravenously challenged with a highly pathogenic, heterologous SHIV at 11 weeks post vaccination. All the vaccinated monkeys suppressed the challenge virus rapidly under the detectable level by 16 weeks post challenge. One vaccinated monkey was protected from a loss of CD4+ T cells. These results suggest pSHIV-ZF1*IL-2 alone seems partially effective even against a challenge with a heterologous, pathogenic virus.

A novel simian immunodeficiency virus from black mangabey (Lophocebus aterrimus) in the Democratic Republic of Congo.

In order to understand primate lentivirus evolution, characterization of additional simian immunodeficiency virus (SIV) strains is essential. Here, an SIV from a black mangabey (Lophocebus aterrimus) originating from the Democratic Republic of Congo was analysed phylogenetically. The monkey had cross-reactive antibodies against human immunodeficiency virus type 1 (HIV-1) and HIV-2. The viral pol region sequence was amplified by nested PCR and sequence analysis confirmed that it was related to known SIV sequences. This is the first report to characterize genetically an SIV from the monkey genus Lophocebus. Phylogenetic analysis of the pol region revealed that this novel SIV, designated SIVbkm, fell into the SIVsyk and SIVgsn virus group, containing viruses isolated from the genus Cercopithecus, and suggests that cross-species transmission has occurred between species of the genera Lophocebus and Cercopithecus.

A new subtype (subgenotype) Ac (A3) of hepatitis B virus and recombination between genotypes A and E in Cameroon.

Blood samples (n=544) from two different populations (Pygmies and Bantus) in Cameroon, West Africa, were analysed. Serological tests indicated that the anti-hepatitis C virus (HCV) prevalence in Bantus (20.3 %) was higher than that in Pygmies (2.3 %, P<0.0001), whereas the distribution of hepatitis B virus (HBV) serological markers was equally high in both populations: in total, 9.4, 17.3 and 86.8 % for HBsAg, anti-HBs and anti-HBc, respectively. HBV genotype A (HBV/A) and HBV/E were predominant (43.5 % each) in both populations, and HBV/D was found in a minority (13 %). The preS/S region was sequenced in nine cases (five HBV/A and four HBV/E) and the complete genome in six cases (four HBV/A and two HBV/E). Subsequent phylogenetic analysis revealed that the HBV/A strains were distinct from the subtypes (subgenotypes) described previously, Ae (A2) and Aa (A1), and in the preS/S region they clustered with previously reported sequences from Cameroon. Based on the nucleotide difference from Aa (A1) and Ae (A2), more than 4 % in the complete genome, the Cameroonian strains were suggested to represent a new subtype (subgenotype), designated HBV/Ac (A3). A high (3.9 %) nucleotide divergence in HBV/Ac (A3) strains suggested that the subtype (subgenotype) has a long natural history in the population of Cameroon. One of the HBV/Ac (A3) strains was found to be a recombinant with an HBV/E-specific sequence in the polymerase reverse transcriptase domain. Further cohort studies will be required to assess detailed epidemiological, virological and clinical characteristics of HBV/Ac (A3), as well as its recombinant form.

Genetic diversity of HIV type 1 in rural eastern Cameroon.

To monitor the presence of genotypic HIV-1 variants circulating in eastern Cameroon, blood samples from 57 HIV-1-infected individuals attending 3 local health centers in the bordering rural villages with Central African Republic (CAR) were collected and analyzed phylogenetically. Out of the 40 HIV-1 strains with positive polymerase chain reaction (PCR) profile for both gag and env-C2V3,12 (30.0%) had discordant subtype or CRF designation: 2 subtype B/A (gag/env), 1 B/CRF01, 2 B/CRF02, 1 CRF01/CRF01.A, 2 CRF11/CRF01, 1 CRF13/A, 1 CRF13/CRF01, 1 CRF13/CRF11, and 1 G/U (unclassified). Twenty-eight strains (70.0%) had concordant subtypes or CRF designation between gag and env: 27 subtype A and 1 F2. Out of the remaining 17HIV-1 strains negative for PCR with the env-C2V3 primers used, 10 (58.8%) had discordant subtype or CRF, and 7 (41.2%) had concordant one based on gag/pol/env-gp41 analysis. Altogether, a high proportion (22/57, 38.6%) of the isolates were found to be recombinant strains. In addition, an emergence of new forms of HIV-1 strains, such as subtype B/A (gag/env), B/CRF01 and B/CRF02, was identified. The epidemiologic pattern of HIV-1 in eastern Cameroon, relatively low and high prevalence of CRF02 and CRF11, respectively, was more closely related to those of CAR and Chad than that of other regions of Cameroon, where CRF02 is the most predominant HIV-1 strain. These findings strongly suggest that this part of Cameroon is a potential hotspot of HIV-1 recombination, with a likelihood of an active generation of new forms of HIV-1 variants, though epidemiologic significance of new HIV-1 forms is unknown.

Genetic diversity of HIV type 1 in Likasi, southeast of the Democratic Republic of Congo.

To investigate the prevalence of subtypes A and C, and the existence of recombinants of both subtypes in the southeast of the Democratic Republic of Congo (DRC), blood samples were collected from 27 HIV-infected individuals in Likasi, located in an area bordering close to Zambia, and analyzed phylogenetically. Out of the 24 strains with a positive PCR profile for pol-IN and env-C2V3, 15 (62.5%) had a discordant subtype or CRF designation: one subtype A/G (pol/env), four A/U (unclassified), three G/A, one G/CRF01, three H/A, one J/C, one CRF02 (G)/A, and one U/A. Nine (37.5%) strains had a concordant subtype or CRF designation: five subtype A, two C, one D, and one CRF02/G. The remaining three samples negative for PCR with env-C2V3 primers used in this study were further analyzed with env-gp41 primers and revealed the presence of two profiles: two J/J (pol-IN/env-gp41) and one C/G. These data highlight the presence of a high proportion (16/27, 59.3%) of recombinant strains and a low prevalence (4.1 and 7.4%) of subtype C based on env-C2V3 and pol-IN analyses, respectively, in Likasi. In addition, this is the first report that CRF02_AG exists in DRC, though the epidemiological significance of the existence of CRF02_AG in DRC remains unknown.

The impact of highly active antiretroviral therapy by the oral route on the CD8 subset in monkeys infected chronically with SHIV 89.6P.

The objective of this study was to assess the impact of highly active antiretroviral therapy (HAART) by an oral route on the peripheral blood CD8 subset in the monkeys infected persistently with a pathogenic strain, SHIV(89.6P). Two rhesus macaques were inoculated intravenously with SHIV(89.6P), then treated with the combination of AZT, 3TC and Lopinavir/Ritonavir (LPV/RTV) as recommended in humans by the oral route with confectionery continued for 28 days. In one of two chronically infected macaques, MM260, the viral load was maintained in the range of 10(4)-10(5) copies/ml before HAART. The plasma viral load and proviral DNA decreased dramatically during the treatment, and cessation of this therapy the viral load rebounded to the pre-treatment level but the proviral DNA rebound was delayed. The other monkey, MM242, had low viral loads (1.2x10(3)-<5x10(2) copies/ml) both before and after HAART. CD4(+) and CD8(+) T cell counts and proviral DNA level were not significantly changed after the treatment. The percentages of CD8(+)CD45RA(-)Ki67(+)cells increased during (MM260) or after (MM242) HAART and the subset was maintained at a high percentage until 18 weeks post HAART in MM242. These findings suggest that this primate model might serve an important role in testing the virological and immunological efficacy of novel therapeutic strategies combined with HAART.

DNA vaccination of macaques by a full-genome simian/human immunodeficiency virus type 1 plasmid chimera that produces non-infectious virus particles.

A DNA vaccination regime was investigated previously in rhesus macaques using a full-genome human immunodeficiency virus type 1 (HIV-1) plasmid, which, due to mutations in the nucleocapsid (NC) proteins, produced only non-infectious HIV-1 particles (Akahata et al., Virology 275, 116-124, 2000). In that study, four monkeys were injected intramuscularly 14 times with the plasmid. All of them showed immunological responses against HIV-1 and partial protection from challenge with a simian immunodeficiency virus/HIV (SHIV) chimeric virus. To improve this DNA vaccination regime, the plasmid used for vaccination was changed. In the present study, four macaques were injected intramuscularly eight times with a full-genome SHIV plasmid that produces non-infectious SHIV particles. CTL activities were higher than those observed in monkeys vaccinated previously with the HIV-1 plasmid. In all macaques vaccinated, peak plasma virus loads after homologous challenge with SHIV were two to three orders of magnitude lower than those of the naive controls, and virus loads fell below the level of detection at 6 weeks post-challenge. This suggested that the vaccination regime in this study was partially effective and better than the previous regime.

HIV type 1 infection in Pygmy hunter gatherers is from contact with Bantu rather than from nonhuman primates.

To investigate the route of zoonotic transmission of HIV-1, we isolated three and seven HIV-1 strains from 449 Pygmy hunter gatherers and 169 neighboring Bantu, respectively, in southern Cameroon. Phylogenetic analysis based on pol-integrase and env-C2V3 sequences revealed that strains from Pygmies were 1CRF02_AG/CRF02_AG, 1 subtype G/CRF02 AG (pol/env), and 1 CRFll_cpx/CRF11_cpx, and that those from Bantu were 2 CRF02_AG/CRF02_AG, 1 CRF02_AG/CRF01_AE/A, 1 CRF02_AG/subtype A, 1 G/A, 1G/CRF02_AG, and 1 unclassified fH. CRF02_AG and CRF11_cpx have been identified in Cameroon. The results suggest that HIV-1 has been introduced into Pygmies through their neighboring Bantu rather than directly from nonhuman primates.

Construction and in vivo infection of a new simian/human immunodeficiency virus chimera containing the reverse transcriptase gene and the 3' half of the genomic region of human immunodeficiency virus type 1.

A new simian/human immunodeficiency virus (SHIV) chimera with the reverse transcriptase (RT)-encoding region of pol, in addition to the 3' region encoding vpr, vpu, tat, rev, env and nef of HIV-1, on an SIV(mac) (SIV from a macaque monkey) background was constructed. This new SHIV chimera, named SHIVrt/3rn, could replicate in monkey peripheral blood mononuclear cells (PBMCs) as well as in the human and monkey CD4(+) T-cell lines M8166 and HSC-F. Since SHIVrt/3rn contains the RT gene of HIV-1, replication of the virus in M8166 cells was inhibited by an HIV-1-specific non-nucleoside RT inhibitor, MKC-442, with a sensitivity similar to that of HIV-1. To investigate the replication competence of SHIVrt/3rn in vivo, two rhesus monkeys were inoculated intravenously with the virus. At 2 to 4 weeks post-inoculation (p.i.), plasma viral RNA loads of both monkeys showed a peak value of more than 10(4) copies ml(-1). Infectious virus was isolated from the PBMCs of one monkey at 2 and 3 weeks p.i. and from the other at 4 weeks p.i. Moreover, proviral DNA was detected constantly throughout the observation period, starting from 3 weeks p.i. An antibody response, detected first at 3 weeks p.i., was maintained at high titres. These results indicate that SHIVrt/3rn can infect and replicate in vivo. SHIVrt/3rn, having part of HIV-1 pol in addition to the 3' part of the HIV-1 genome is genetically more close to HIV-1 than any of the other monkey-infecting SHIVs reported previously.

Mutational analysis of two zinc-finger motifs in the nucleocapsid protein of simian immunodeficiency virus mac239.

To clarify the physiological function of two zinc-finger (ZF) motifs in the nucleocapsid (NC) protein of simian immunodeficiency virus (SIV), we constructed three mutant viruses with alterations in either or both motifs using a molecular clone of SIVmac (SIVmac239). An immunoblot analysis of the cell lysates transfected with DNA mutated in either the first (ZF1) or second (ZF2) motif showed that the amount of partially processed Gag products (Pr46) was greater than that produced by the wild-type (WT). The genomic RNA contents in the viral particles released from the transfected cells were measured by quantitative RT-PCR. Values for the ZF1 and ZF2 mutants and the double mutant were 26, 20 and 7 % that of the WT, respectively, indicating that the two ZF motifs of SIVmac239 NC protein function almost equivalently with respect to RNA encapsidation and processing of Gag precursors. Despite the presence of some genomic RNA in the mutant viruses, they lost all viral infectivity. To determine the reason for this, we examined (using PCR) to which step viral DNA synthesis proceeded in the mutant viruses. We did not see any block up to the step of minus-strand DNA synthesis. However, plus-strand DNA synthesis after plus-strand transfer did not occur in any of the mutant viruses. These findings indicated that the mutations in the ZF motifs of SIVmac led to a loss of infectivity due partly to impairment of DNA synthesis, in addition to inefficient encapsidation of genomic RNA.

Infection of a chimeric simian and human immunodeficiency virus with CCR5-specific HIV-1 envelope to Rhesus macaques.

Human immunodeficiency virus (HIV) infects lymphocytes and macrophages via CD4 and chemokine receptors. In this study, the infectivity of a chimeric simian and human immunodeficiency virus (SHIV) having a CCR5-specific HIV-1 envelope gene was examined. A SHIV strain termed SHIV-JRFL could enter cells via CD4 with a chemokine receptor CCR5, not CXCR4, and the viral replication was suppressed by recombinant human RANTES, one of beta-chemokines. The intravenous inoculation of SHIV-JRFL into two rhesus macaques resulted in a systemic infection, though it was rather weak. During the early infection, the production of RANTES from Con A-stimulated PBMCs of the infected monkeys increased. These results suggested that beta-chemokine has the potential to limit the infectivity of an R5-type SHIV.

Genetic subtypes of HIV type 1 based on the vpu/env sequences in the Republic of Congo.

To investigate the HIV-1 subtypes prevalent in the Republic of Congo, we isolated 28 HIV-1 strains from Congolese AIDS patients in 1996 and 1997, and analyzed them phylogenetically. Phylogenetic analysis based on part of the 5' tat-env (vpu) and env sequences revealed that only 13 (46.4%) of the 28 isolates belonged to the same subtype in the vpu tree as in the env tree; the remaining 15 (53.6%) strains showed discordant subtypes between vpu and env with 6 different profiles; that is, 1 A/A (vpu/env), 1 D/D, 5 G/G, 4 H/H, 2 unclassified (U)/U, 9 G/A, 2 G/H, 1 G/J, 1 H/G, 1 U/A, and 1 U/J. Thus, 9 of the 15 discordant HIV-1s were of the G/A (vpu/env) type, and did not form any subcluster within the subtype G lineage in the vpu-based phylogenetic tree. In addition, CRF02_AG (IbNG), which is a G/A (vpu/env) type, was not found in the Republic of Congo. These data suggest that the majority of HIV-1 subtypes circulating in the Republic of Congo have mosaic structures and may have been derived from independent recombinational events.