This page has only limited features, please log in for full access.
Family clusters have contributed significantly to the onward spread of SARS-CoV-2. However, the dynamics of viral transmission in this setting remain incompletely understood. We describe the clinical and viral-phylogenetic characteristics of a family cluster of SARS-CoV-2 infections with a high attack rate, and explore how whole-genome sequencing (WGS) can inform outbreak investigations in this context. In this cluster, the first symptomatic case was a 22-month-old infant who developed rhinorrhoea and sneezing 2 days prior to attending a family gathering. Subsequently, seven family members in attendance at this event were diagnosed with SARS-CoV-2 infections, including the infant described. WGS revealed indistinguishable SARS-CoV-2 genomes recovered from the adults at the gathering, which were closely related genetically to B.1 lineage viruses circulating in the local community. However, a divergent viral sub-lineage was recovered from the infant and another child, each harbouring a distinguishing spike substitution (N30S). This suggested that the infant was unlikely to be the primary case, despite displaying symptoms first, and additional analysis of her nasopharyngeal swab revealed a picornavirus co-infection to account for her early symptoms. Our findings demonstrate how WGS can elucidate the transmission dynamics of SARS-CoV-2 infections within household clusters and provide useful information to support outbreak investigations. Additionally, our description of SARS-CoV-2 viral lineages and notable variants circulating in Ireland to date provides an important genomic-epidemiological baseline in the context of vaccine introduction.
Daniel Hare; Gabriel Gonzalez; Jonathan Dean; Kathleen McDonnell; Michael J. Carr; Cillian F. De Gascun. Genomic epidemiological analysis of SARS-CoV-2 household transmission. Access Microbiology 2021, 3, 000252 .
AMA StyleDaniel Hare, Gabriel Gonzalez, Jonathan Dean, Kathleen McDonnell, Michael J. Carr, Cillian F. De Gascun. Genomic epidemiological analysis of SARS-CoV-2 household transmission. Access Microbiology. 2021; 3 (7):000252.
Chicago/Turabian StyleDaniel Hare; Gabriel Gonzalez; Jonathan Dean; Kathleen McDonnell; Michael J. Carr; Cillian F. De Gascun. 2021. "Genomic epidemiological analysis of SARS-CoV-2 household transmission." Access Microbiology 3, no. 7: 000252.
Background: Human adenovirus (HAdV)-D56 was first described in 2011 by genomics analysis of a strain isolated in France in 2008 from a fatal case of neonatal infection. Since then, it has been reported in cases of keratoconjunctivitis and male urethritis. Three epidemiologically unrelated fatal cases of neonatal sepsis associated with infection by HAdV-D strains with a similar genetic makeup were documented in the United States between 2014 and 2020. Methods: Whole genome sequences were obtained for the isolated strains, and genomics analyses were conducted to compare them to phylogenetically related HAdV-D genomic sequences available in GenBank. Results: The three new US strains were indistinguishable by in silico restriction enzyme analysis. Their genome sequences were 99.9% identical to one another and to the prototype strain isolated in 2008 from a similar context of disease. The phylogenetic reconstruction revealed a highly supported clustering of all HAdV-D56 strains isolated in various countries since 1982. Our comparison to serologically intermediate strains 15/H9 described in the literature indicated that HAdV-D56-like viruses have circulated worldwide since the late 1950s. Conclusion: As with other HAdV-D genotypes with the ability to infect ocular and genital mucosae, the risk of severe prenatal or perinatal HAdV-D56 infection must be considered.
William Otto; Daryl Lamson; Gabriel Gonzalez; Geoffrey Weinberg; Nicole Pecora; Brian Fisher; Kirsten St. George; Adriana Kajon. Fatal Neonatal Sepsis Associated with Human Adenovirus Type 56 Infection: Genomic Analysis of Three Recent Cases Detected in the United States. Viruses 2021, 13, 1105 .
AMA StyleWilliam Otto, Daryl Lamson, Gabriel Gonzalez, Geoffrey Weinberg, Nicole Pecora, Brian Fisher, Kirsten St. George, Adriana Kajon. Fatal Neonatal Sepsis Associated with Human Adenovirus Type 56 Infection: Genomic Analysis of Three Recent Cases Detected in the United States. Viruses. 2021; 13 (6):1105.
Chicago/Turabian StyleWilliam Otto; Daryl Lamson; Gabriel Gonzalez; Geoffrey Weinberg; Nicole Pecora; Brian Fisher; Kirsten St. George; Adriana Kajon. 2021. "Fatal Neonatal Sepsis Associated with Human Adenovirus Type 56 Infection: Genomic Analysis of Three Recent Cases Detected in the United States." Viruses 13, no. 6: 1105.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), employs host-cell angiotensin-converting enzyme 2 (ACE2) for cell entry. Genetic analyses of ACE2 have identified several single-nucleotide polymorphisms (SNPs) specific to different human populations. Molecular dynamics simulations have indicated that several of these SNPs could affect interactions between SARS-CoV-2 and ACE2, thereby providing a partial explanation for the regional differences observed in SARS-CoV-2 infectivity and severity. However, the significance of population-specific ACE2 SNPs in SARS-CoV-2 infectivity is unknown, as no in vitro validation studies have been performed. Here, we analyzed the impact of eight SNPs found in specific populations on receptor binding and cell entry in vitro. Except for a SNP causing a nonsense mutation that reduced ACE2 expression, none of the selected SNPs markedly altered the interaction between ACE2 and the SARS-CoV-2 spike protein (SARS-2-S), which is responsible for receptor recognition and cell entry, or the efficiency of viral cell entry mediated by SARS-2-S. Our findings indicate that ACE2 polymorphisms have limited impact on the ACE2-dependent cell entry of SARS-CoV-2 and underscore the importance of future studies on the involvement of population-specific SNPs of other host genes in susceptibility toward SARS-CoV-2 infection.
Mei Hashizume; Gabriel Gonzalez; Chikako Ono; Ayako Takashima; Masaharu Iwasaki. Population-Specific ACE2 Single-Nucleotide Polymorphisms Have Limited Impact on SARS-CoV-2 Infectivity In Vitro. Viruses 2021, 13, 67 .
AMA StyleMei Hashizume, Gabriel Gonzalez, Chikako Ono, Ayako Takashima, Masaharu Iwasaki. Population-Specific ACE2 Single-Nucleotide Polymorphisms Have Limited Impact on SARS-CoV-2 Infectivity In Vitro. Viruses. 2021; 13 (1):67.
Chicago/Turabian StyleMei Hashizume; Gabriel Gonzalez; Chikako Ono; Ayako Takashima; Masaharu Iwasaki. 2021. "Population-Specific ACE2 Single-Nucleotide Polymorphisms Have Limited Impact on SARS-CoV-2 Infectivity In Vitro." Viruses 13, no. 1: 67.
Human adenovirus type 4 (HAdV-E4) is the only type (and serotype) classified within species Human mastadenovirus E that has been isolated from a human host to the present. Recent phylogenetic analysis of whole genome sequences of strains representing the spectrum of intratypic genetic diversity described to date identified two major evolutionary lineages designated phylogroups (PG) I, and II, and validated the early clustering of HAdV-E4 genomic variants into two major groups by low resolution restriction fragment length polymorphism analysis. In this study we expanded our original analysis of intra- and inter-PG genetic variability, and used a panel of viruses representative of the spectrum of genetic diversity described for HAdV-E4 to examine the magnitude of inter- and intra-PG phenotypic diversity using an array of cell-based assays and a cotton rat model of HAdV respiratory infection. Our proteotyping of HAdV-E strains using concatenated protein sequences in selected coding regions including E1A, E1B-19K and −55K, DNA polymerase, L4-100K, various E3 proteins, and E4-34K confirmed that the two clades encode distinct variants/proteotypes at most of these loci. Our in vitro and in vivo studies demonstrated that PG I and PG II differ in their growth, spread, and cell killing phenotypes in cell culture and in their pulmonary pathogenic phenotypes. Surprisingly, the differences in replicative fitness documented in vitro between PGs did not correlate with the differences in virulence observed in the cotton rat model. This body of work is the first reporting phenotypic correlates of naturally occurring intratypic genetic variability for HAdV-E4.IMPORTANCEHuman adenovirus type 4 (HAdV-E4) is a prevalent causative agent of acute respiratory illness of variable severity and of conjunctivitis and comprises two major phylogroups that carry distinct coding variations in proteins involved in viral replication and modulation of host responses to infection. Our data show that PG I and PG II are intrinsically different regarding their ability to grow and spread in culture and to cause pulmonary disease in cotton rats.This is the first report of phenotypic divergence among naturally occurring known genetic variants of a HAdV type of medical importance. This research reveals readily detectable phenotypic differences between strains representing phylogroups I and II, and it introduces a unique experimental system for the elucidation of the genetic basis of adenovirus fitness and virulence and thus for increasing our understanding of the implications of intratypic genetic diversity in the presentation and course of HAdV-E4-associated disease.
Camden R. Bair; Wei Zhang; Gabriel Gonzalez; Arash Kamali; Daniel Stylos; Jorge C. G. Blanco; Adriana E. Kajon. HUMAN ADENOVIRUS TYPE 4 COMPRISES TWO MAJOR PHYLOGROUPS WITH DISTINCT REPLICATIVE FITNESS AND VIRULENCE PHENOTYPES. 2020, 1 .
AMA StyleCamden R. Bair, Wei Zhang, Gabriel Gonzalez, Arash Kamali, Daniel Stylos, Jorge C. G. Blanco, Adriana E. Kajon. HUMAN ADENOVIRUS TYPE 4 COMPRISES TWO MAJOR PHYLOGROUPS WITH DISTINCT REPLICATIVE FITNESS AND VIRULENCE PHENOTYPES. . 2020; ():1.
Chicago/Turabian StyleCamden R. Bair; Wei Zhang; Gabriel Gonzalez; Arash Kamali; Daniel Stylos; Jorge C. G. Blanco; Adriana E. Kajon. 2020. "HUMAN ADENOVIRUS TYPE 4 COMPRISES TWO MAJOR PHYLOGROUPS WITH DISTINCT REPLICATIVE FITNESS AND VIRULENCE PHENOTYPES." , no. : 1.
The extensive sequence data generated from SARS-CoV-2 during the 2020 pandemic has facilitated the study of viral genome evolution over a brief period of time. This has highlighted instances of directional mutation pressures exerted on the SARS-CoV-2 genome from host antiviral defense systems. In this brief review we describe three such human defense mechanisms, the apolipoprotein B mRNA editing catalytic polypeptide-like proteins (APOBEC), adenosine deaminase acting on RNA proteins (ADAR), and reactive oxygen species (ROS), and discuss their potential implications on SARS-CoV-2 evolution.
Tobias Mourier; Mukhtar Sadykov; Michael J. Carr; Gabriel Gonzalez; William W. Hall; Arnab Pain. Host-directed editing of the SARS-CoV-2 genome. Biochemical and Biophysical Research Communications 2020, 538, 35 -39.
AMA StyleTobias Mourier, Mukhtar Sadykov, Michael J. Carr, Gabriel Gonzalez, William W. Hall, Arnab Pain. Host-directed editing of the SARS-CoV-2 genome. Biochemical and Biophysical Research Communications. 2020; 538 ():35-39.
Chicago/Turabian StyleTobias Mourier; Mukhtar Sadykov; Michael J. Carr; Gabriel Gonzalez; William W. Hall; Arnab Pain. 2020. "Host-directed editing of the SARS-CoV-2 genome." Biochemical and Biophysical Research Communications 538, no. : 35-39.
Mammalian orthoreovirus (MRV) has been identified in humans, livestock and wild animals; this wide host range allows individual MRV to transmit into multiple species. Although several interspecies transmission and genetic reassortment events of MRVs among humans, livestock and wildlife have been reported, the genetic diversity and geographic distribution of MRVs in Africa are poorly understood. In this study, we report the first isolation and characterization of MRVs circulating in a pig population in Zambia. In our screening, MRV genomes were detected in 19.7 % (29/147) of faecal samples collected from pigs by reverse transcription PCR. Three infectious MRV strains (MRV-85, MRV-96 and MRV-117) were successfully isolated, and their complete genomes were sequenced. Recombination analyses based on the complete genome sequences of the isolated MRVs demonstrated that MRV-96 shared the S3 segment with a different MRV isolated from bats, and that the L1 and M3 segments of MRV-117 originated from bat and human MRVs, respectively. Our results suggest that the isolated MRVs emerged through genetic reassortment events with interspecies transmission. Given the lack of information regarding MRVs in Africa, further surveillance of MRVs circulating among humans, domestic animals and wildlife is required to assess potential risk for humans and animals.
Hayato Harima; Michihito Sasaki; Masahiro Kajihara; Gabriel Gonzalez; Edgar Simulundu; Eugene C. Bwalya; Yongjin Qiu; Kosuke Okuya; Mao Isono; Yasuko Orba; Ayato Takada; Bernard M. Hang’Ombe; Aaron S. Mweene; Hirofumi Sawa. Characterization of mammalian orthoreoviruses isolated from faeces of pigs in Zambia. Journal of General Virology 2020, 101, 1027 -1036.
AMA StyleHayato Harima, Michihito Sasaki, Masahiro Kajihara, Gabriel Gonzalez, Edgar Simulundu, Eugene C. Bwalya, Yongjin Qiu, Kosuke Okuya, Mao Isono, Yasuko Orba, Ayato Takada, Bernard M. Hang’Ombe, Aaron S. Mweene, Hirofumi Sawa. Characterization of mammalian orthoreoviruses isolated from faeces of pigs in Zambia. Journal of General Virology. 2020; 101 (10):1027-1036.
Chicago/Turabian StyleHayato Harima; Michihito Sasaki; Masahiro Kajihara; Gabriel Gonzalez; Edgar Simulundu; Eugene C. Bwalya; Yongjin Qiu; Kosuke Okuya; Mao Isono; Yasuko Orba; Ayato Takada; Bernard M. Hang’Ombe; Aaron S. Mweene; Hirofumi Sawa. 2020. "Characterization of mammalian orthoreoviruses isolated from faeces of pigs in Zambia." Journal of General Virology 101, no. 10: 1027-1036.
Polyomaviruses (PyVs) are small, circular dsDNA viruses carried by diverse vertebrates, including bats. Although previous studies have reported several horseshoe bat PyVs collected in Zambia and China, it is still unclear how PyVs evolved in this group of widely dispersed mammals. Horseshoe bats (genus Rhinolophus) are distributed across the Old World and are natural reservoirs of numerous pathogenic viruses. Herein, non-invasive bat samples from European horseshoe bat species were collected in Hungary for PyV identification and novel PyVs with complete genomes were successfully recovered from two different European horseshoe bat species. Genomic and phylogenetic analysis of the Hungarian horseshoe bat PyVs supported their classification into the genera Alphapolyomavirus and Betapolyomavirus. Notably, despite the significant geographical distances between the corresponding sampling locations, Hungarian PyVs exhibited high genetic relatedness with previously described Zambian and Chinese horseshoe bat PyVs, and phylogenetically clustered with these viruses in each PyV genus. Correlation and virus–host relationship analysis suggested that these PyVs co-diverged with their European, African and Asian horseshoe bat hosts distributed on different continents during their evolutionary history. Additionally, assessment of selective pressures over the major capsid protein (VP1) of horseshoe bat PyVs showed sites under positive selection located in motifs exposed to the exterior of the capsid. In summary, our findings revealed a pattern of stable intrahost divergence of horseshoe bat PyVs with their mammalian hosts on the African and Eurasian continents over evolutionary time.
Márton Z. Vidovszky; Zhizhou Tan; Michael J. Carr; Sándor Boldogh; Balázs Harrach; Gabriel Gonzalez. Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents. Journal of General Virology 2020, 101, 1119 -1130.
AMA StyleMárton Z. Vidovszky, Zhizhou Tan, Michael J. Carr, Sándor Boldogh, Balázs Harrach, Gabriel Gonzalez. Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents. Journal of General Virology. 2020; 101 (10):1119-1130.
Chicago/Turabian StyleMárton Z. Vidovszky; Zhizhou Tan; Michael J. Carr; Sándor Boldogh; Balázs Harrach; Gabriel Gonzalez. 2020. "Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents." Journal of General Virology 101, no. 10: 1119-1130.
Bluetongue (BT) is an arthropod-borne viral disease of ruminants with serious trade and socio-economic implications. Although the disease has been reported in a number of countries in sub-Saharan Africa, there is currently no information on circulating serotypes and disease distribution in Zambia. Following surveillance for BT in domestic and wild ruminants in Zambia, BT virus (BTV) nucleic acid and antibodies were detected in eight of the 10 provinces of the country. About 40% (87/215) of pooled blood samples from cattle and goats were positive for BTV nucleic acid, while one hartebeest pool (1/43) was positive among wildlife samples. Sequence analysis of segment 2 revealed presence of serotypes 3, 5, 7, 12 and 15, with five nucleotypes (B, E, F, G and J) being identified. Segment 10 phylogeny showed Zambian BTV sequences clustering with Western topotype strains from South Africa, intimating likely transboundary spread of BTV in Southern Africa. Interestingly, two Zambian viruses and one isolate from Israel formed a novel clade, which we designated as Western topotype 4. The high seroprevalence (96.2%) in cattle from Lusaka and Central provinces and co-circulation of multiple serotypes showed that BT is widespread, underscoring the need for prevention and control strategies.
Herman M. Chambaro; Michihito Sasaki; Edgar Simulundu; Isaac Silwamba; Yona Sinkala; Gabriel Gonzalez; David Squarre; Paul Fandamu; Caesar H. Lubaba; Musso Munyeme; Alikhadio Maseko; Choopa Chimvwele; Liywalii Mataa; Lynnfield E. Mooya; Andrew N. Mukubesa; Hayato Harima; Kenny L. Samui; Hetron M. Munang’Andu; Martin Simuunza; King S. Nalubamba; Yongjin Qiu; Michael J. Carr; William W. Hall; Yuki Eshita; Hirofumi Sawa; Yasuko Orba. Co-Circulation of Multiple Serotypes of Bluetongue Virus in Zambia. Viruses 2020, 12, 963 .
AMA StyleHerman M. Chambaro, Michihito Sasaki, Edgar Simulundu, Isaac Silwamba, Yona Sinkala, Gabriel Gonzalez, David Squarre, Paul Fandamu, Caesar H. Lubaba, Musso Munyeme, Alikhadio Maseko, Choopa Chimvwele, Liywalii Mataa, Lynnfield E. Mooya, Andrew N. Mukubesa, Hayato Harima, Kenny L. Samui, Hetron M. Munang’Andu, Martin Simuunza, King S. Nalubamba, Yongjin Qiu, Michael J. Carr, William W. Hall, Yuki Eshita, Hirofumi Sawa, Yasuko Orba. Co-Circulation of Multiple Serotypes of Bluetongue Virus in Zambia. Viruses. 2020; 12 (9):963.
Chicago/Turabian StyleHerman M. Chambaro; Michihito Sasaki; Edgar Simulundu; Isaac Silwamba; Yona Sinkala; Gabriel Gonzalez; David Squarre; Paul Fandamu; Caesar H. Lubaba; Musso Munyeme; Alikhadio Maseko; Choopa Chimvwele; Liywalii Mataa; Lynnfield E. Mooya; Andrew N. Mukubesa; Hayato Harima; Kenny L. Samui; Hetron M. Munang’Andu; Martin Simuunza; King S. Nalubamba; Yongjin Qiu; Michael J. Carr; William W. Hall; Yuki Eshita; Hirofumi Sawa; Yasuko Orba. 2020. "Co-Circulation of Multiple Serotypes of Bluetongue Virus in Zambia." Viruses 12, no. 9: 963.
Porcine sapelovirus (PSV) has been detected worldwide in pig populations. Although PSV causes various symptoms such as encephalomyelitis, diarrhea, and pneumonia in pigs, the economic impact of PSV infection remains to be determined. However, information on the distribution and genetic diversity of PSV is quite limited, particularly in Africa. In this study, we investigated the prevalence of PSV infection in Zambia and characterized the isolated PSVs genetically and biologically. We screened 147 fecal samples collected in 2018 and found that the prevalences of PSV infection in suckling pigs and fattening pigs were high (36.2% and 94.0%, respectively). Phylogenetic analyses revealed that the Zambian PSVs were divided into three different lineages (Lineages 1–3) in the clade consisting of Chinese strains. The Zambian PSVs belonging to Lineages 2 and 3 replicated more efficiently than those belonging to Lineage 1 in Vero E6 and BHK cells. Bioinformatic analyses revealed that genetic recombination events had occurred and the recombination breakpoints were located in the L and 2A genes. Our results indicated that at least two biologically distinct PSVs could be circulating in the Zambian pig population and that genetic recombination played a role in the evolution of PSVs.
Hayato Harima; Masahiro Kajihara; Edgar Simulundu; Eugene Bwalya; Yongjin Qiu; Mao Isono; Kosuke Okuya; Gabriel Gonzalez; Junya Yamagishi; Bernard M. Hang’Ombe; Hirofumi Sawa; Aaron S. Mweene; Ayato Takada. Genetic and Biological Diversity of Porcine Sapeloviruses Prevailing in Zambia. Viruses 2020, 12, 180 .
AMA StyleHayato Harima, Masahiro Kajihara, Edgar Simulundu, Eugene Bwalya, Yongjin Qiu, Mao Isono, Kosuke Okuya, Gabriel Gonzalez, Junya Yamagishi, Bernard M. Hang’Ombe, Hirofumi Sawa, Aaron S. Mweene, Ayato Takada. Genetic and Biological Diversity of Porcine Sapeloviruses Prevailing in Zambia. Viruses. 2020; 12 (2):180.
Chicago/Turabian StyleHayato Harima; Masahiro Kajihara; Edgar Simulundu; Eugene Bwalya; Yongjin Qiu; Mao Isono; Kosuke Okuya; Gabriel Gonzalez; Junya Yamagishi; Bernard M. Hang’Ombe; Hirofumi Sawa; Aaron S. Mweene; Ayato Takada. 2020. "Genetic and Biological Diversity of Porcine Sapeloviruses Prevailing in Zambia." Viruses 12, no. 2: 180.
Between 2011 and 2018, 518 respiratory adenovirus infections were diagnosed in a pediatric clinic in Shizuoka, Japan. Detection and typing were performed by partial sequencing of both hexon- and fiber-coding regions which identified: adenovirus type 1 (Ad-1, n = 85), Ad-2 (n = 160), Ad-3 (n = 193), Ad-4 (n = 18), Ad-5 (n = 27), Ad-11 (n = 2), Ad-54 (n = 3), and Ad-56 (n = 1). Considering previous reports of the circulation of an endemic recombinant Ad-2, e.g., Ad-89, 100 samples typed as Ad-2 were randomly selected for further molecular typing by sequencing the penton base-coding region. Despite the high nucleotide sequence conservation in the penton base- coding region, 27 samples showed 98% identity to Ad-2. Furthermore, 14 samples showed 97.7% identity to Ad-2 and 99.8% identity to Ad-89, while the remaining 13 samples showed an average 98% pairwise identity to other Ad-C types and clustered with Ad-5. The samples typed as Ad-89 (n = 14) and as a recombinant Ad type (P5H2F2) (n = 13) represented 27% of cases originally diagnosed as Ad-2, and were detected sporadically. Therefore, two previously uncharacterized types in Japan, Ad-89 and a recombinant Ad-C, were shown to circulate in children. This study creates a precedent to evaluate the epidemiology and divergence among Ad-C types by comprehensively considering the type classification of adenoviruses.
Kenichiro Takahashi; Gabriel Gonzalez; Masaaki Kobayashi; Nozomu Hanaoka; Michael J. Carr; Masami Konagaya; Naomi Nojiri; Miki Ogi; Tsuguto Fujimoto. Pediatric Infections by Human mastadenovirus C Types 2, 89, and a Recombinant Type Detected in Japan between 2011 and 2018. Viruses 2019, 11, 1131 .
AMA StyleKenichiro Takahashi, Gabriel Gonzalez, Masaaki Kobayashi, Nozomu Hanaoka, Michael J. Carr, Masami Konagaya, Naomi Nojiri, Miki Ogi, Tsuguto Fujimoto. Pediatric Infections by Human mastadenovirus C Types 2, 89, and a Recombinant Type Detected in Japan between 2011 and 2018. Viruses. 2019; 11 (12):1131.
Chicago/Turabian StyleKenichiro Takahashi; Gabriel Gonzalez; Masaaki Kobayashi; Nozomu Hanaoka; Michael J. Carr; Masami Konagaya; Naomi Nojiri; Miki Ogi; Tsuguto Fujimoto. 2019. "Pediatric Infections by Human mastadenovirus C Types 2, 89, and a Recombinant Type Detected in Japan between 2011 and 2018." Viruses 11, no. 12: 1131.
After analyzing 27 new genomes from fowl adenovirus (FAdV) field isolates and so-far unsequenced prototypes, we report the first evidence for recombination in FAdVs. Recombination was confined to species FAdV-D and FAdV-E, accommodating the largest number of, and the intraspecies-wise most differentiated, types. The majority of detected events occurred in FAdV-E, involving segments with parental origin of all constitutive types. Together with the diversity of breakpoints, this suggests widespread recombination in this species. With possible constraints through species-specific genes and diversification patterns, the recombinogenic potential of FAdVs attains particular interest for inclusion body hepatitis (IBH), an important disease in chickens, caused by types from the recombination-prone species. Autonomously evolving, recombinant segments were associated with major sites under positive selection, among them the capsid protein hexon and fiber genes, the right-terminal ORFs 19, 25, and the ORF20/20A family. The observed mosaicism in genes indicated as targets of adaptive pressures points toward an immune evasion strategy. Intertypic hexon/fiber-recombinants demonstrated hybrid neutralization profiles, retrospectively explaining reported controversies on reference strains B3-A, T8-A, and X11-A. Furthermore, cross-neutralization supported sequence-based evidence for interdomain recombination in fiber and contributed to a tentatively new type. Overall, our findings challenge the purported uniformity of types responsible for IBH, urging more complete identification strategies for FAdVs. Finally, important consequences arise for in vivo studies investigating cross-protection against IBH.
Anna Schachner; Gabriel Gonzalez; Lukas Endler; Kimihito Ito; Michael Hess. Fowl Adenovirus (FAdV) Recombination with Intertypic Crossovers in Genomes of FAdV-D and FAdV-E, Displaying Hybrid Serological Phenotypes. Viruses 2019, 11, 1094 .
AMA StyleAnna Schachner, Gabriel Gonzalez, Lukas Endler, Kimihito Ito, Michael Hess. Fowl Adenovirus (FAdV) Recombination with Intertypic Crossovers in Genomes of FAdV-D and FAdV-E, Displaying Hybrid Serological Phenotypes. Viruses. 2019; 11 (12):1094.
Chicago/Turabian StyleAnna Schachner; Gabriel Gonzalez; Lukas Endler; Kimihito Ito; Michael Hess. 2019. "Fowl Adenovirus (FAdV) Recombination with Intertypic Crossovers in Genomes of FAdV-D and FAdV-E, Displaying Hybrid Serological Phenotypes." Viruses 11, no. 12: 1094.
Enteroviruses (EVs) are responsible for extremely large-scale, periodic epidemics in pediatric cohorts, particularly in East and Southeast Asia. Clinical presentation includes a diverse disease spectrum, including hand-foot and mouth disease (HFMD), aseptic meningitis, encephalitis, acute flaccid paralysis, and acute flaccid myelitis. HFMD is predominantly attributable to EV-A types, including the major pathogen EV-A71, and coxsackieviruses, particularly CV-A6, CV-A16, and CV-A10. There have been multiple EV-A71 outbreaks associated with a profound burden of neurological disease and fatal outcomes in Asia since the early 1980s. Efficacious vaccines against EV-A71 have been developed in China but widespread pediatric vaccination programs have not been introduced in other countries. Encephalitis, as a consequence of complications arising from HFMD infection, leads to damage to the thalamus and medulla oblongata. Studies in Vietnam suggest that myoclonus is a significant indicator of central nervous system (CNS) complications in EV-A71-associated HFMD cases. Rapid response in HFMD cases in children is imperative to prevent the progression to a CNS infection; however, prophylactic and therapeutic agents have not been well established internationally, therefore surveillance and functional studies including development of antivirals and multivalent vaccines is critically important to reduce disease burden in pediatric populations.
Gabriel Gonzalez; Michael J. Carr; Masaaki Kobayashi; Nozomu Hanaoka; Tsuguto Fujimoto. Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World. International Journal of Molecular Sciences 2019, 20, 5201 .
AMA StyleGabriel Gonzalez, Michael J. Carr, Masaaki Kobayashi, Nozomu Hanaoka, Tsuguto Fujimoto. Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World. International Journal of Molecular Sciences. 2019; 20 (20):5201.
Chicago/Turabian StyleGabriel Gonzalez; Michael J. Carr; Masaaki Kobayashi; Nozomu Hanaoka; Tsuguto Fujimoto. 2019. "Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World." International Journal of Molecular Sciences 20, no. 20: 5201.
Species Human mastadenovirus E (HAdV-E) comprises several simian types and a single human type: HAdV-E4, a respiratory and ocular pathogen. RFLP analysis for the characterization of intratypic genetic variability has previously distinguished two HAdV-E4 clusters: prototype (p)-like and a-like. Our analysis of whole genome sequences confirmed two distinct lineages, which we refer to as phylogroups (PGs). PGs I and II comprise the p- and a-like genomes, respectively, and differ significantly in their G + C content (57.7% ± 0.013 vs 56.3% ± 0.015). Sequence differences distinguishing the two clades map to several regions of the genome including E3 and ITR. Bayesian analyses showed that the two phylogroups diverged approximately 602 years before the present. A relatively faster evolutionary rate was identified for PG II. Our data provide a rationale for the incorporation of phylogroup identity to HAdV-E4 strain designation to reflect the identified unique genetic characteristics that distinguish PGs I and II.
Gabriel Gonzalez; Camden R. Bair; Daryl M. Lamson; Hidemi Watanabe; Laura Panto; Michael Carr; Adriana E. Kajon. Genomic characterization of human adenovirus type 4 strains isolated worldwide since 1953 identifies two separable phylogroups evolving at different rates from their most recent common ancestor. Virology 2019, 538, 11 -23.
AMA StyleGabriel Gonzalez, Camden R. Bair, Daryl M. Lamson, Hidemi Watanabe, Laura Panto, Michael Carr, Adriana E. Kajon. Genomic characterization of human adenovirus type 4 strains isolated worldwide since 1953 identifies two separable phylogroups evolving at different rates from their most recent common ancestor. Virology. 2019; 538 ():11-23.
Chicago/Turabian StyleGabriel Gonzalez; Camden R. Bair; Daryl M. Lamson; Hidemi Watanabe; Laura Panto; Michael Carr; Adriana E. Kajon. 2019. "Genomic characterization of human adenovirus type 4 strains isolated worldwide since 1953 identifies two separable phylogroups evolving at different rates from their most recent common ancestor." Virology 538, no. : 11-23.
Adriana E Kajon; Xiaoxin Li; Gabriel Gonzalez; Susan Core; Helga Hofmann-Sieber; Shuguang Leng. Isolation and initial propagation of guinea pig adenovirus (GPAdV) in Cavia porcellus cell lines. 2019, 8, 1597 .
AMA StyleAdriana E Kajon, Xiaoxin Li, Gabriel Gonzalez, Susan Core, Helga Hofmann-Sieber, Shuguang Leng. Isolation and initial propagation of guinea pig adenovirus (GPAdV) in Cavia porcellus cell lines. . 2019; 8 ():1597.
Chicago/Turabian StyleAdriana E Kajon; Xiaoxin Li; Gabriel Gonzalez; Susan Core; Helga Hofmann-Sieber; Shuguang Leng. 2019. "Isolation and initial propagation of guinea pig adenovirus (GPAdV) in Cavia porcellus cell lines." 8, no. : 1597.
Japanese encephalitis virus (JEV) exerts a profound burden of viral encephalitis. We have investigated the differentially expressed transcripts in the neuronal transcriptome during JEV infection by RNA sequencing (RNA-Seq) of virus-infected SH-SY5Y human neuroblastoma cells. Gene ontology analysis revealed significant enrichment from two main pathways: endoplasmic reticulum (ER)-nucleus signaling (P value: 5.75E−18; false discovery rate [FDR] 3.11E−15) and the ER unfolded protein response (P value: 7.58E−18; FDR 3.11E−15). qPCR validation showed significant upregulation and differential expression (P < 0.01) of ER stress-signaling transcripts (SESN2, TRIB3, DDIT3, DDIT4, XBP1, and ATF4) at 24 h post-infection for both low (LN) and high (HN) neurovirulence JEV strains. Immunoblot analysis following JEV infection of SH-SY5Y cells showed an increase in levels of SESN2 protein following JEV infection. Similarly, Zika virus (MR766) infection of SH-SY5Y showed a titer-dependent increase in ER stress-signaling transcripts; however, this was absent or diminished for DDIT4 and ATF4, respectively, suggestive of differences in the induction of stress-response transcripts between flaviviruses. Interestingly, SLC7A11 and SLC3A2 mRNA were also both deregulated in JEV-infected SH-SY5Y cells and encode the two constituent subunits of the plasma membrane xCT amino acid antiporter that relieves oxidative stress by export of glutamate and import of cystine. Infection of SH-SY5Y and HEK293T cells by the JEV HN strain Sw/Mie/40/2004 lead to significant upregulation of the SLC7A11 mRNA to levels comparable to DDIT3. Our findings suggest upregulation of antioxidants including SESN2 and, also, the xCT antiporter occurs to counteract the oxidative stress elicited by JEV infection.
Michael Carr; Gabriel Gonzalez; Axel Martinelli; Christida Estu Wastika; Kimihito Ito; Yasuko Orba; Michihito Sasaki; William W. Hall; Hirofumi Sawa. Upregulated expression of the antioxidant sestrin 2 identified by transcriptomic analysis of Japanese encephalitis virus-infected SH-SY5Y neuroblastoma cells. Virus Genes 2019, 55, 630 -642.
AMA StyleMichael Carr, Gabriel Gonzalez, Axel Martinelli, Christida Estu Wastika, Kimihito Ito, Yasuko Orba, Michihito Sasaki, William W. Hall, Hirofumi Sawa. Upregulated expression of the antioxidant sestrin 2 identified by transcriptomic analysis of Japanese encephalitis virus-infected SH-SY5Y neuroblastoma cells. Virus Genes. 2019; 55 (5):630-642.
Chicago/Turabian StyleMichael Carr; Gabriel Gonzalez; Axel Martinelli; Christida Estu Wastika; Kimihito Ito; Yasuko Orba; Michihito Sasaki; William W. Hall; Hirofumi Sawa. 2019. "Upregulated expression of the antioxidant sestrin 2 identified by transcriptomic analysis of Japanese encephalitis virus-infected SH-SY5Y neuroblastoma cells." Virus Genes 55, no. 5: 630-642.
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Paulina Duhita Anindita; Michihito Sasaki; Gabriel Gonzalez; Wallaya Phongphaew; Michael Carr; Bernard M. Hang’Ombe; Aaron S. Mweene; Kimihito Ito; Yasuko Orba; Hirofumi Sawa. Publisher Correction: Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates. Scientific Reports 2019, 9, 8502 .
AMA StylePaulina Duhita Anindita, Michihito Sasaki, Gabriel Gonzalez, Wallaya Phongphaew, Michael Carr, Bernard M. Hang’Ombe, Aaron S. Mweene, Kimihito Ito, Yasuko Orba, Hirofumi Sawa. Publisher Correction: Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates. Scientific Reports. 2019; 9 (1):8502.
Chicago/Turabian StylePaulina Duhita Anindita; Michihito Sasaki; Gabriel Gonzalez; Wallaya Phongphaew; Michael Carr; Bernard M. Hang’Ombe; Aaron S. Mweene; Kimihito Ito; Yasuko Orba; Hirofumi Sawa. 2019. "Publisher Correction: Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates." Scientific Reports 9, no. 1: 8502.
Polyomaviruses (PyVs) are small, double-stranded DNA tumor viruses carried by diverse vertebrates. PyVs have previously been considered highly host restricted in mammalian hosts, with host-switching events thought rare or nonexistent. Prior investigations have revealed short-range host-switching events of PyVs in two different African bat species within the horseshoe bat genusRhinolophus. Herein, we have conducted a systematic investigation of PyVs in 1,083 archived bat samples collected from five provinces across China, and identified 192 PyVs from 186 bats from 15 host species within 6 families (Rhinolophidae, Vespertilionidae, Hipposideridae, Emballonuridae, Miniopteridae and Pteropodidae) representing 28 newly-described PyVs, indicative of extensive genetic diversity of bat PyVs. Surprisingly, two PyVs were identified in multiple bat species from different families, and another PyV clustered phylogenetically with PyVs carried by bats from a different host family, indicative of three inter-family PyV host-switching events. The time to most recent common ancestor (tMRCA) of the three events was estimated at 0.02-11.6 million years ago (MYA), which is inconsistent with the estimated tMRCA of their respective bat hosts (36.3-66.7 MYA), and is most parsimoniously explained by host-switching events. PyVs identified from geographically separated Chinese horseshoe bat species in the present study showed close genetic identities, and clustered with each other and with PyVs from African horseshoe bats, allowing assessment of the effects of positive selection in VP1 within the horseshoe bat family Rhinolophidae. Correlation analysis indicated that co-evolution with their hosts contributed much more to evolutionary divergence of PyV than geographic distance. In conclusion, our findings provide the first evidence of inter-family host-switching events of PyV in mammals and challenge the prevailing evolutionary paradigm for strict host restriction of mammalian PyVs.Author summarySince the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered both genetically stable and highly host-restricted in their mammalian hosts. In this study, we have identified multiple cases of host-switching events of PyVs by large scale surveillance in diverse bat species collected in China. These host-switching events occurred between bat families living in the same colony, indicating that a large population with frequent contacts between different bat species may represent an ecological niche facilitating PyV host-switching. The cases studied involved members of bats from several families, including horseshoe bats, which were previously found to harbor a number of highly virulent viruses to both humans and domestic animals. Our findings have provided evidence that even highly host-specific DNA viruses can transmit between bats of different species and indicate an increased propensity for spillover events involving horseshoe bats. We propose an evolutionary scheme for bat-borne PyVs in which intra-host divergence and host-switching has generated the diverse PyVs in present day bats. This scheme provides a useful model to study the evolution of PyVs in other hosts and, potentially, the modeling of bat zoonoses and the transmission of other DNA viruses in other mammals, including humans.
Zhizhou Tan; Gabriel Gonzalez; Jinliang Sheng; Jianmin Wu; Fuqiang Zhang; Lin Xu; Peisheng Zhang; Aiwei Zhu; Yonggang Qu; Changchun Tu; Michael J. Carr; Biao He. Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events. 2019, 627158 .
AMA StyleZhizhou Tan, Gabriel Gonzalez, Jinliang Sheng, Jianmin Wu, Fuqiang Zhang, Lin Xu, Peisheng Zhang, Aiwei Zhu, Yonggang Qu, Changchun Tu, Michael J. Carr, Biao He. Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events. . 2019; ():627158.
Chicago/Turabian StyleZhizhou Tan; Gabriel Gonzalez; Jinliang Sheng; Jianmin Wu; Fuqiang Zhang; Lin Xu; Peisheng Zhang; Aiwei Zhu; Yonggang Qu; Changchun Tu; Michael J. Carr; Biao He. 2019. "Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events." , no. : 627158.
The Smacoviridae has recently been classified as a family of small circular single-stranded DNA viruses. An increasing number of smacovirus genomes have been identified exclusively in faecal matter of various vertebrate species and from insect body parts. However, the genetic diversity and host range of smacoviruses remains to be fully elucidated. Herein, we report the genetic characterization of eleven circular replication-associated protein (Rep) encoding single-stranded (CRESS) DNA viruses detected in the faeces of Zambian non-human primates. Based on pairwise genome-wide and amino acid identities with reference smacovirus species, ten of the identified CRESS DNA viruses are assigned to the genera Porprismacovirus and Huchismacovirus of the family Smacoviridae, which bidirectionally encode two major open reading frames (ORFs): Rep and capsid protein (CP) characteristic of a type IV genome organization. The remaining unclassified CRESS DNA virus was related to smacoviruses but possessed a genome harbouring a unidirectionally oriented CP and Rep, assigned as a type V genome organization. Moreover, phylogenetic and recombination analyses provided evidence for recombination events encompassing the 3'-end of the Rep ORF in the unclassified CRESS DNA virus. Our findings increase the knowledge of the known genetic diversity of smacoviruses and highlight African non-human primates as carrier animals.
Paulina D. Anindita; Michihito Sasaki; Gabriel Gonzalez; Wallaya Phongphaew; Michael Carr; Bernard M. Hang’Ombe; Aaron S. Mweene; Kimihito Ito; Yasuko Orba; Hirofumi Sawa. Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates. Scientific Reports 2019, 9, 5045 .
AMA StylePaulina D. Anindita, Michihito Sasaki, Gabriel Gonzalez, Wallaya Phongphaew, Michael Carr, Bernard M. Hang’Ombe, Aaron S. Mweene, Kimihito Ito, Yasuko Orba, Hirofumi Sawa. Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates. Scientific Reports. 2019; 9 (1):5045.
Chicago/Turabian StylePaulina D. Anindita; Michihito Sasaki; Gabriel Gonzalez; Wallaya Phongphaew; Michael Carr; Bernard M. Hang’Ombe; Aaron S. Mweene; Kimihito Ito; Yasuko Orba; Hirofumi Sawa. 2019. "Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates." Scientific Reports 9, no. 1: 5045.
Adenoviral epidemic keratoconjunctivitis (EKC) presents as severe conjunctival inflammations involving the cornea that can lead to the development of corneal opacities and blurred vision, which can persist for months. EKC is highly contagious and responsible for outbreaks worldwide, therefore accurate diagnosis and rapid containment are imperative. EKC is caused by a number of types within Human adenovirus species D (HAdV-D): 8, 37 and 64 (formerly known as 19a) and these types were considered the major causes of EKC for over fifty years. Nonetheless, recent improved molecular typing methodologies have identified recombinant HAdV-D types 53, 54 and 56, as newly emerging etiologic agents of EKC infections worldwide. EKC cases due to these recombinant types have potentially been underdiagnosed and underestimated as a source of new EKC outbreaks. Recombination events among circulating HAdV-D types represent a source of new infectious disease threats. Also, the growing number of adenoviral types enabled genomic and phenotypic comparisons to determine pathological properties related to EKC. This review covers the clinical features of EKC, current challenges in clinical practice and recent progress in EKC-related HAdV research, which focuses on the development of novel diagnostic and therapeutic approaches.
Gabriel Gonzalez; Nobuyo Yawata; Koki Aoki; Nobuyoshi Kitaichi. Challenges in management of epidemic keratoconjunctivitis with emerging recombinant human adenoviruses. Journal of Clinical Virology 2019, 112, 1 -9.
AMA StyleGabriel Gonzalez, Nobuyo Yawata, Koki Aoki, Nobuyoshi Kitaichi. Challenges in management of epidemic keratoconjunctivitis with emerging recombinant human adenoviruses. Journal of Clinical Virology. 2019; 112 ():1-9.
Chicago/Turabian StyleGabriel Gonzalez; Nobuyo Yawata; Koki Aoki; Nobuyoshi Kitaichi. 2019. "Challenges in management of epidemic keratoconjunctivitis with emerging recombinant human adenoviruses." Journal of Clinical Virology 112, no. : 1-9.
The population structure of Clostridium difficile currently comprises eight major genomic clades. For the highly divergent C-I clade, only two toxigenic strains have been reported, which lack the tcdA and tcdC genes and carry a complete locus for the binary toxin (CDT) next to an atypical TcdB monotoxin pathogenicity locus (PaLoc). As part of a routine surveillance of C. difficile in stool samples from diarrheic human patients, we discovered three isolates that consistently gave negative results in a PCR-based screening for tcdC. Through phenotypic assays, whole-genome sequencing, experiments in cell cultures, and infection biomodels we show that these three isolates (i) escape common laboratory diagnostic procedures, (ii) represent new ribotypes, PFGE-types, and sequence types within the Clade C-I, (iii) carry chromosomal or plasmidal TcdBs that induce classical or variant cytopathic effects (CPE), and (iv) cause different levels of cytotoxicity and hamster mortality rates. These results show that new strains of C. difficile can be detected by more refined techniques and raise questions on the origin, evolution, and distribution of the toxin loci of C. difficile and the mechanisms by which this emerging pathogen causes disease.
Gabriel Ramírez-Vargas; Diana López-Ureña; Adriana Badilla; Josué Orozco-Aguilar; Tatiana Murillo; Priscilla Rojas; Thomas Riedel; Jörg Overmann; Gabriel Gonzalez; Esteban Chaves-Olarte; Carlos Quesada-Gómez; César Rodríguez. Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. Scientific Reports 2018, 8, 1 -11.
AMA StyleGabriel Ramírez-Vargas, Diana López-Ureña, Adriana Badilla, Josué Orozco-Aguilar, Tatiana Murillo, Priscilla Rojas, Thomas Riedel, Jörg Overmann, Gabriel Gonzalez, Esteban Chaves-Olarte, Carlos Quesada-Gómez, César Rodríguez. Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. Scientific Reports. 2018; 8 (1):1-11.
Chicago/Turabian StyleGabriel Ramírez-Vargas; Diana López-Ureña; Adriana Badilla; Josué Orozco-Aguilar; Tatiana Murillo; Priscilla Rojas; Thomas Riedel; Jörg Overmann; Gabriel Gonzalez; Esteban Chaves-Olarte; Carlos Quesada-Gómez; César Rodríguez. 2018. "Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements." Scientific Reports 8, no. 1: 1-11.