Asian Strains Research Articles

Correlation analysis of gastric mucosal lesions with Helicobacter pylori infection and its virulence genotype in Guiyang, Guizhou province, China.

Helicobacter Pylori (H. pylori) infection is the most important factor affecting clinical outcome in patients with gastric mucosal lesions. This study aimed to investigate H. pylori infection in patients with gastric mucosal lesions and their virulence genotype in Guiyang, China. Pathological examinations of 1,364 biopsies from patients with upper gastrointestinal symptoms and H. pylori infection were analyzed according to different pathological types. The bacterial genome DNA was extracted from H. pylori strains isolated from gastric biopsies, and the cagA, vacA, and iceA virulence genes were detected and typed to analyze the correlation of their genotypes between different pathological lesions. The positive rate of H. pylori infection was approximately 19.9% (272/1,364), as determined by histopathological examination (HPE). It was more frequently detected in men than in women. A total of 85 H. pylori isolates were obtained from 280 clinical samples (positive rate 30.4%, 85/280). Of these 85 strains, cagA, vacA, and iceA genes were identified in 85.9%, 100%, and 83.5% of samples, respectively. Approximately 74.1% of strains were cagA East Asian type (cagA-ABD), and 11.8% of were cagA Western strains (cagA-AB, cagA-ABC), only present in patients with chronic non-atrophic gastritis. Gastric intraepithelial neoplasia and gastric cancer harbored both Asian strains. A total of 7 combinations of vacA genotypes were noted, among which s1c/m1b (30.6%) and s1c/m2 (41.2%) were the dominant genotypes. The predominant iceA genotype was iceA1 (64.7%). We observed that the positive rate of H. pylori infection was related to the pathological type of patients' gastric mucosal lesions. Isolated H. pylori strains showed a unique genotype, mainly East Asian type cagA (ABD), vacA s1c/m2 genotype, and iceA1. These results provide an important reference for further studies of H. pylori in Guizhou province, China.

Prevalence and Characteristics of Canine Parvovirus Type 2 in Henan Province, China.

To investigate the epidemic profile and genetic diversity of canine parvovirus type 2 (CPV-2), a total of 111 clinical samples collected from dogs suspected of CPV-2 infection in 10 cities of Henan province of China during 2020 to 2021 were screened by PCR. The results showed a CPV-2-positive rate of 88.29% (98/111). Nearly full-length genomes of 98 CPV-2 strains were sequenced and analyzed. CPV-2c strains (91.84%, 90/98) were significantly higher than that of new CPV-2a strains (8.16%, 8/98) in Henan province without detecting other CPV genotypes, indicating that CPV-2c has become the dominant genotype in Henan province. A phylogenetic analysis of NS1 and VP2 amino acids grouped the strains in this study with Asian strains, which clustered into an identical branch. Based on the CPV-2 VP2 sequences in this study and available in the NCBI database, the adaptation analyses showed that 17 positive selection sites and 10 parallel evolution sites were identified in the VP2 protein of CPV-2, of which three sites (sites 5, 370, and 426) were both under positive selection pressure and parallel evolution. Interestingly, two amino acid mutations (A5G and Q370R) were also observed in the VP2 proteins of 82 CPV-2c strains in this study, which differed from the earlier CPV-2c strain (GU380303) in China. In addition, a unique mutation (I447M) was observed in the VP2 protein of five CPV-2c strains, which was first reported in China. This study provides powerful insight to further our understanding of the epidemic status and evolution of CPV-2 in China. IMPORTANCE CPV-2 was the original virus strain identified in dogs, which cause an acute and lethal disease in dogs. Subsequently, the original CPV-2 was replaced throughout the world by novel antigenic variants (e.g., CPV-2a, CPV-2b, new CPV-2a, new CPV-2b, and CPV-2c). Currently, the epidemiological characteristics of CPV-2 in Henan province of China is still unclear. In our study, a total of 98 nearly full-length genomes of CPV-2 strains were obtained to explore prevalence and genetic evolution of CPV-2 in Henan Province. Moreover, the epidemiological and genetic evolution of CPV-2 in China since its discovery was also investigated. The results of this study will provide valuable information regarding the evolution of CPV-2 strains in China.

ToLCNDV-ES infection in tomato is enhanced by TYLCV: Evidence from field survey and agroinoculation.

The tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus (family Geminiviridae), poses a significant threat to various horticultural crops in many Asian and Mediterranean countries. Since its identification, the Asian strain of this virus has exhibited severe infectivity and caused high yield loss in tomato and cucurbit production in the Indian subcontinent and other parts of Asia. ToLCNDV-ES, a different strain of ToLCNDV, emerged recently in the Mediterranean Basin and caused significant outbreaks in Cucurbitaceae species but has shown low adaptation to tomatoes. In a field survey, tomato plants infected with this Mediterranean strain were not discovered. Nevertheless, the same field survey revealed that ToLCNDV-ES occurred in natural double infection with tomato yellow leaf curl virus (TYLCV) in tomato plants with an infection ratio of up to 50%. Moreover, results obtained from experiments where tomato plants agro-inoculated simultaneously with infectious clones of ToLCNDV-ES and TYLCV showed that ToLCNDV-ES was detected in tomatoes while synergized with TYLCV with infection ratios similar to those found under field conditions. Quantitative PCR data indicated the highest amount of ToLCNDV in co-infected plants and no significant change in TYLCV titers among the different mixed infections. Moreover, it was ascertained that not all begomoviruses can enhance the infectivity of Mediterranean ToLCNDV isolates in tomato plants. Our study reports a new finding regarding the ToLCNDV-ES response in tomato while synergized with TYLCV with evidence from both field and laboratory conditions.

Complete genome analysis reveals evolutionary history and temporal dynamics of Marek's disease virus.

Marek's disease has caused enormous losses in poultry production worldwide. However, the evolutionary process and molecular mechanisms underlying Marek's disease virus (MDV) remain largely unknown. Using complete genomic sequences spanning an unprecedented diversity of MDVs, we explored the evolutionary history and major patterns in viruses sampled from 1964 to 2018. We found that the evolution of MDV strains had obvious geographical features, with the Eurasian and North American strains having independent evolutionary paths, especially for Asian strains. The evolution of MDVs generally followed a clock-like structure with a relatively high evolutionary rate. Asian strains had evolved at a faster rate than European strains, with most genetic mutations occurring in Asian strains. Our results showed that all recombination events occurred in the UL and US subregions. We found direct evidence of a closer correlation between Eurasian strains, related to a series of reorganization events represented by the European strain ATE2539. We also discovered that the vaccine strains had recombined with the wild virulent strains. Base substitution and recombination were found to be the two main mechanisms of MDV evolution. Our study offers novel insights into the evolution of MDVs that could facilitate predicting the spread of infections, and hence their control.

Influence of Zika virus 3′-end sequence and nonstructural protein evolution on the viral replication competence and virulence

ABSTRACT Zika virus (ZIKV) has been circulating in human networks over 70 years since its first appearance in Africa, yet little is known about whether the viral 3′-terminal sequence and nonstructural (NS) protein diverged genetically from ancient ZIKV have different effects on viral replication and virulence in currently prevailing Asian lineage ZIKV. Here we show, by a reverse genetics approach using an infectious cDNA clone for a consensus sequence (Con1) of ZIKV, which represents Asian ZIKV strains, and another clone derived from the MR766 strain isolated in Uganda, Africa in 1947, that the 3′-end sequence –UUUCU-3′ homogeneously present in MR766 genome and the –GUCU-3′ sequence strictly conserved in Asian ZIKV isolates are functionally equivalent in viral replication and gene expression. By gene swapping experiments using the two infectious cDNA clones, we show that the NS1–5 proteins of MR766 enhance replication competence of ZIKV Con1. The Con1, which was less virulent than MR766, acquired severe bilateral hindlimb paralysis when its NS1–5 genes were replaced by the counterparts of MR766 in type I interferon receptor (IFNAR1)-deficient A129 mice. Moreover, MR766 NS5 RNA-dependent RNA polymerase (RdRp) alone also rendered the Con1 virulent, despite there being no difference in RdRp activity between MR766 and Con1 NS5 proteins. By contrast, the Con1 derivatives expressing MR766 Nsps, like Con1, did not develop severe disease in wild-type mice treated with an IFNAR1 blocking antibody. Together, our findings uncover an unprecedented role for ZIKV NS proteins in determining viral pathogenicity in immunocompromised hosts.

A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients.

SettingTuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi.ObjectivesWe aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital.Patients and methodsGenotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed.ResultsA total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance.ConclusionThe Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.

Molecular Analysis of Ndm-1 Positive Klebsiella pneumoniae Strains Isolated From Patients With Bacteremia Due to Urinary System Infection

Introduction: Health concerns about Klebsiella pneumoniae, which causes urinary tract infections (UTIs) and sepsis, are increasing worldwide. In addition, New Delhi metallo-ß-lactamase (NDM) carrier K. pneumoniae and other Gram-negative bacteria appear to cause serious clinical problems. This study aimed to reveal NDM-1 positive K. pneumoniae carrier status, molecular properties, and antibiotic resistance differences of patients who have bacteremia due to urinary system infections. Methods: Blood culture, biochemical tests, Vitek2, polymerase chain reaction, sequencing, phylogenetic analysis, and multilocus sequence typing (MLST) methods were used for the microbiological analysis of K. pneumoniae strains. Results: Overall, 146 K. pneumoniae strains were obtained from the cultures, 16 of which were found to be NDM-1 positive. Although these strains were discovered to have resistance to the authorized antibiotics, they were sensitive to gentamicin (CN), colistin (CT), and trimethoprim/sulfamethoxazole (SXT). Furthermore, it was found that the resistance rates of carbapenem (ertapenem (Etp), imipenem (Ipm), and meropenem (Mem)) were high. All K. pneumoniae strains represented extended-spectrum beta-lactam resistance. It was found that the phylogenetic affinities of K. pneumoniae strains were higher with Asian strains. Five and eleven K. pneumoniae isolates were determined to be ST17 and ST147 type variations, respectively, as a conclusion of the MLST study. Conclusions: It was observed that the presence of NDM-1-positive K. pneumoniae may pose a serious problem in patients with bacteremia caused by UTI. It has been demonstrated that it is important to develop preventive and control measures in the hospital by considering NDM-1-positive K. pneumoniae strains with multi-drug resistance.

Identification and Molecular Characterization of a Divergent Asian-like Canine Parvovirus Type 2b (CPV-2b) Strain in Southern Italy.

Canine parvovirus type 2 (CPV-2) is an infectious agent relevant to domestic and wild carnivorans. Recent studies documented the introduction and spread of CPV-2c strains of Asian origin in the Italian canine population. We investigated tissue samples from a puppy collected during necropsy for the presence of viral enteropathogens and all samples tested positive only for CPV-2. The full coding sequence of a CPV-2b (VP2 426Asp) strain was obtained. This virus was related to CPV-2c strains of Asian origin and unrelated to European CPV-2b strains. The sequence had genetic signatures typical of Asian strains (NS1: 60Val, 545Val, 630Pro; VP2: 5Gly, 267Tyr, 324Ile) and mutations rarely reported in Asian CPV-2b strains (NS1: 588N; VP2: 370Arg). Phylogenetic analyses placed this strain in well-supported clades, including Asian CPV-2c-like strains, but always as a basal, single-sequence long branch. No recombination was observed for this strain, and we speculate that it could have originated from an Asian CPV-2c-like strain that acquired the 426Asp mutation. This study reports the first evidence of an Asian-like CPV-2b strain in Italy, confirming the occurrence of continuous changes in the global CPV-2 spread. Since positive convergent mutations complicate data interpretation, a combination of phylogenetic and mutation pattern analyses is crucial in studying the origin and evolution of CPV-2 strains.

Immune profiles in mouse brain and testes infected by Zika virus with variable pathogenicity.

The Zika virus is responsible for neurological diseases such as microcephaly, Guillain-Barré syndrome, neuropathy, and myelitis in human adults and children. Previous studies have shown that the Zika virus can infect nerve progenitor cells and interfere with neural development. However, it is unclear how the immune system responds to infection with Zika viruses with variable pathogenicity. Here, we used two Zika strains with relatively different pathogenicity, the Asian ancestral strain CAM/2010 and the America pandemic strain GZ01/2016, to infect the brains of mice. We found that both strains elicited a strong immune response. Notably, the strain with relatively high pathogenicity, GZ01/2016, caused more intense immune regulation, with stronger CD8+ T cell and macrophage activation at 14 days post infection (dpi), as well as a greater immune gene disturbance. Notably, several TNF family genes were upregulated at 14 dpi, including Tnfrsf9, Tnfsf13, Tnfrsf8, Cd40, and Tnfsf10. It was notable that GZ01/2016 could maintain the survival of nerve cells at 7dpi but caused neurological disorders at 14dpi. These results indicate that Zika viruses with high pathogenicity may induce sustained activation of the immune system leading to nerve tissue damage.

A Reverse Mutation E143K within the PrM Protein of Zika Virus Asian Lineage Natal RGN Strain Increases Infectivity and Cytopathicity.

Zika virus (ZIKV) is a positive-sense single-stranded RNA virus in the Flaviviridae, which is classified into two different lineages Asian and African. The outbreak of ZIKV Asian lineage isolates in 2015–2016 is associated with the increase in cases with prenatal microcephaly and Guillain–Barré syndrome, and has sparked attention throughout the world. Genome sequence alignment and the analysis of Asian and African lineage isolates indicate that amino acid changes, particular in positively charged amino acid substitutions in the pr region of prM protein might involve a phenotypic change that links with the global outbreak of ZIKV Asian-lineage. The study generated and characterized the virological properties of wild type and mutants of single-round infectious particles (SRIPs) and infectious clones (i.c.s) of ZIKV Asian-lineage Natal RGN strain, and then identified the function of amino acid substitutions at the positions 139 [Asn139→Ser139 (N139S)] and 143 [Glu143→Lys143 (E143K)] in ZIKV polyproteins (located within the pr region of prM protein) in the infectivity and cytopathogenicity. The E143K SRIP and i.c. of Natal RGN strain exhibited relatively higher levels of cytopathic effect, EGFP reporter, viral RNA and protein synthesis, and virus yield in three types of human cell lines, TE617, SF268 and HMC3, compared to wild type (WT), N139S SRIPs and i.c.s, which displayed more efficiency in replication kinetics. Additionally, E143K Natal RGN i.c. had greater activities of virus attachment and entry, yielded higher titers of intracellular and extracellular virions, and assembled the E proteins near to the plasma membrane in infected cells than the other i.c.s. The results indicate that the positively charged amino acid residue Lys143, a conserved residue in the pr region of prM of ZIKV African lineages, plays a crucial role in viral replication kinetics, including viral attachment, entry, assembly and egress. Thus, the negatively charged amino acid residue Glu143 within the pr region of prM leads to an alteration of the phenotypes, in particular, a lower replication efficiency of ZIKV Asian-lineage isolates with the attenuation of infectivity and cytopathicity.

Bartha-K61 vaccine protects nursery pigs against challenge with novel european and asian strains of suid herpesvirus 1

The present study investigates the pathogenicity of two recently isolated strains of Suid herpesvirus 1 (SuHV1), the Greek strain Hercules and the Chinese strain HeN1, in unvaccinated pigs and in pigs vaccinated with a Bartha-K61 strain. In an experiment performed in negative pressure kiosks (isolators), 45-day old seronegative pigs previously oronasally /intramuscularly vaccinated with the Bartha-K61 vaccine strain, along with unvaccinated controls, were challenged either with the Hercules strain or the HeN1 strain of SuHV1. All animals were observed daily for clinical signs and body temperature and nasal swabs, faeces, blood and bodyweight were collected up to a maximum period of 20 days post-challenge (dpc). The results showed that, in the unvaccinated pigs, HeN1 strain was more virulent than the Hercules strain, with increased mortality, shorter time to death and higher group clinical score (p < 0.05). However, after vaccination with the Bartha-K61 vaccine, there was a drastic reduction in morbidity, mortality, bodyweight loss and virus excretion to almost a similar extent in both strains (p < 0.05). No significant differences were seen among the pigs of the two vaccinated groups compared to unvaccinated unchallenged controls, except a slight elevation in body temperature and in clinical score in the HeN1 vaccinees at 2 and 3 dpc, while bodyweight gain was similar to that of the negative control pigs. Our study showed that despite differences in virulence, the standard vaccination scheme with the Bartha-K61 strain could equally protect nursery pigs against both the European and Chinese strains.

Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains

Porcine Parvovirus Type 1 (PPV1) contributes to important losses in the swine industry worldwide. During a PPV1 infection, embryos and fetuses are targeted, resulting in stillbirth, mummification, embryonic death, and infertility (SMEDI syndrome). Even though vaccination is common in gilts and sows, strains mainly belonging to the 27a-like group have been spreading in Europe since early 2000s, resulting in SMEDI problems and requiring in-depth studies into the molecular epidemiology and vaccination efficacy of commercial vaccines. Here, we show that PPV1 has evolved since 1855 [1737, 1933] at a rate of 4.71 × 10−5 nucleotide substitutions per site per year. Extensive sequencing allowed evaluating and reassessing the current PPV1 VP1-based classifications, providing evidence for the existence of four relevant phylogenetic groups. While most European strains belong to the PPV1a (G1) or PPV1b (G2 or 27a-like) group, most Asian and American G2 strains and some European strains were divided into virulent PPV1c (e.g. NADL-8) and attenuated PPV1d (e.g. NADL-2) groups. The increase in the swine population, vaccination degree, and health management (vaccination and biosafety) influenced the spread of PPV1. The reactivity of anti-PPV1 antibodies from sows vaccinated with Porcilis© Parvo, Eryseng© Parvo, or ReproCyc© ParvoFLEX against different PPV1 field strains was the highest upon vaccination with ReproCyc© ParvoFLEX, followed by Eryseng© Parvo, and Porcilis© Parvo. Our findings contribute to the evaluation of the immunogenicity of existing vaccines and support the development of new vaccine candidates. Finally, the potential roles of cluster-specific hallmark amino acids in elevated pathogenicity and viral entry are discussed.

Isolation, identification and phylogenetic analysis of lumpy skin disease virus strain of outbreak in Guangdong, China.

In August 2019, lumpy skin disease occurred for the first time in Xinjiang, China, and then quickly spread to many provinces in China. Here, the virus was isolated from the skin scabs of affected cattle during June 2020 in Guangdong, China. Virus isolation, transmission electron microscopy and polymerase chain reaction identified lumpy skin disease virus (LSDV) in the skin crusts of sick cattle. For the isolation of LSDV, the most sensitive cell line is primary cattle testicular (PCT) cells, while Vero cells cannot be used for the isolation of LSDV. In addition, we evaluated the growth characteristics of LSDV in vitro. Compared with MDBK and Vero cells, LSDV produced higher virus titters in PCT cells at 72 h. Phylogenetic analysis based on second-generation sequencing of the LSDV whole genome showed that the isolated virus (LSDV/MZGD/2020) is closely related to Asian strains and formed a new branch. LSDV/MZGD/2020 is also a vaccine recombinant strain that is distinct from the recombinant strain found in Russia. Through Recombination Detection Program (RDP), Simplot and phylogenetic analyses, strong evidence for recombination events was found in Chinese field LSDV strains. The China LSDV/MZGD/2020 strain may be the result of multiple recombination events between the Neethling 2490 and Neethling vaccine LW 1959 strains. This study expands our knowledge of the genetic diversity and evolution of LSDV.

Exploring potential anti-chikungunya virus activity of phytocompounds: Computational docking and in vitro studies

ObjectiveThis study aimed to identify phytocompounds that possess anti-chikungunya virus activity using computational docking and in vitro studies. MethodsA total of 6050 phytocompounds were retrieved from PubChem and other online databases. Compounds were virtually screened against E (3N42) and nsP2 (3TRK) proteins of CHIKV using iGEMDOCK. Molecular docking was performed for the screened compounds using the Maestro Glide module. Finally, screened lead compounds were studied for their in vitro antiviral activity against the Asian and African strains of CHIKV. ResultsAmong the three lead phytocompounds screened, astragaloside II showed the highest binding energy value of −10.603 kcal/mol, followed by astragaloside IV (-9.007 kcal/mol) and astragaloside III (-6.197 kcal/mol) against the 3TRK target protein whereas astragaloside II showed the highest binding energy value of −10.603 kcal/mol, followed by astragaloside IV (-10.548 kcal/mol) and astragaloside III (-9.539 kcal/mol) against the 3N42 target protein. ADMET analysis revealed that all three lead compounds have non-mutagenic and non-carcinogenic properties. Antiviral studies showed that astragaloside II exhibited antiviral activity at 1.56 µg/mL and 3.12 µg/mL, astragaloside IV at 3.12 µg/mL and 6.25 µg/mL, and astragaloside III at 3.12 µg/mL and 12.5 µg/mL against Asian and African strains of CHIKV, respectively. ConclusionFrom the findings of this study, it is concluded that the phytocompounds such as astragaloside II, astragaloside III, and astragaloside IV possess promising in vitro antiviral activity against Asian and African strains of CHIKV.

Human Neutrophils Present Mild Activation by Zika Virus But Reduce the Infection of Susceptible Cells.

The emergence of the Zika virus (ZIKV) has highlighted the need for a deeper understanding of virus-host interactions in order to pave the way for the development of antiviral therapies. The present work aimed to address the response of neutrophils during ZIKV infection. Neutrophils are important effector cells in innate immunity implicated in the host’s response to neurotropic arboviruses. Our results indicate that human neutrophils were not permissive to Asian or African ZIKV strain replication. In fact, after stimulation with ZIKV, neutrophils were mild primed against the virus as evaluated through CD11b and CD62L modulation, secretion of inflammatory cytokines and granule content, production of reactive oxygen species, and neutrophil extracellular traps formation. Overall, neutrophils did not affect ZIKV infectivity. Moreover, in vitro ZIKV infection of primary innate immune cells did not trigger neutrophil migration. However, neutrophils co-cultured with ZIKV susceptible cell lineages resulted in lower cell infection frequencies, possibly due to cell-to-cell contact. In vivo, neutrophil depletion in immunocompetent mice did not affect ZIKV spreading to the draining lymph nodes. The data suggest that human neutrophils do not play an antiviral role against ZIKV per se, but these cells might participate in an infected environment shaping the ZIKV infection in other target cells.

Characterization of m6 A modifications in the contemporary Zika virus genome and host cellular transcripts.

Zika virus (ZIKV) suddenly evolved from a neglected arthropod-borne flavivirus into a pandemic pathogen during 2015-2016. A panel of amino acid mutations has been shown to be responsible for the enhanced neurovirulence and transmissibility of ZIKV. Recent studies have demonstrated that ZIKV genomic RNA is modified by host N6-methyladenosine (m6 A) machinery during viral replication in host cells, and the m6 A profiles vary among different isolates and different host cells. In the present study, using a contemporary Asian ZIKV strain isolated in 2019 (SZ1901) as a model, we profiled m6 A modifications on both the viral genome RNA and cellular transcripts from the ZIKV-infected human hepatocarcinoma cell line Huh7. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified a unique m6 A map in the genome of ZIKV strain SZ1901 that is different from all previous isolates. Meanwhile, ZIKV infection induced m6 A upregulation in the CDS regions but downregulation in the 3' untranslated region of host RNA transcripts. The m6 A peak intensity in the majority of host genes was downregulated, including ISG-related genes. Overall, our study describes unique viral and host m6 A profiles in contemporary ZIKV-infected Huh7 cells, highlighting the complexity and importance of m6 A modification during viral infection.

Evolution, geographic spreading, and demographic distribution of Enterovirus D68.

Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. We collected samples from several European countries during the 2018 outbreak and determined 53 near full-length genome ('whole genome') sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences. In 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68 season. EV-D68 displays strong signs of continuous antigenic evolution and all 2018 A2 strains had novel patterns in the putative neutralizing epitopes in the BC- and DE-loops. The pattern in the BC-loop of the USA B3 subgroup had not been detected on that continent before. Patients with EV-D68 in subclade A2 were significantly older than patients with a B3 subclade virus. In contrast to other subclades, the age distribution of A2 is distinctly bimodal and was found primarily among children and in the elderly. We hypothesize that EV-D68's rapid evolution of surface proteins, extensive diversity, and high rate of geographic mixing could be explained by substantial reinfection of adults. Better understanding of evolution and immunity across diverse viral pathogens, including EV-D68 and SARS-CoV-2, is critical to pandemic preparedness in the future.

Helicobacter pylori genomes reveal Paleolithic human migration to the east end of Asia

SummaryA virulence bacterium, Helicobacter pylori, evolved parallel to its host human, therefore, can work as a marker for tracing the human migration. We found H. pylori strains indigenous in the southernmost islands of Japanese Archipelago, Okinawa, and defined them as hspOkinawa and hpRyukyu. Genome data of the strains revealed that hspOkinawa diverged from other East Asian strains about 20,000 years ago, and that hpRyukyu diverged about 45,000 years ago. The closest strains of hpRyukyu were found from Afghanistan, Punjab, and Nepal, which suggest this strain originated in the central Asia and traveled across the Eurasian continent during Paleolithic era. The divergence date of hpRyukyu corresponds with human fossil records in Okinawa. Although it is controversial from human DNA analyses whether descendants of the Paleolithic migrants remain in the modern Japanese population, this study reveals that the bacterium of Paleolithic origin remains in the stomachs of current Japanese.

Molecular characteristics and genetic evolutionary analyses of circulating parvoviruses derived from cats in Beijing

BackgroundFeline parvovirus (FPV) is a member of the family Parvoviridae, which is a major enteric pathogen of cats worldwide. This study aimed to investigate the prevalence of feline parvovirus in Beijing of China and analyze the genetic features of detected viruses.ResultsIn this study, a total of 60 (8.5%) parvovirus-positive samples were detected from 702 cat fecal samples using parvovirus-specific PCR. The complete VP2 genes were amplified from all these samples. Among them, 55 (91.7%) sequences were characterized as FPV, and the other five (8.3%) were typed as canine parvovirus type 2 (CPV-2) variants, comprised of four CPV-2c and a new CPV-2b strain. In order to investigate the origin of CPV-2 variants in cats, we amplified full-length VP2 genes from seven fecal samples of dogs infected with CPV-2, which were further classified as CPV-2c. The sequences of new CPV-2b/MT270586 and CPV-2c/MT270587 detected from feline samples shared 100% identity with previous canine isolates KT156833 and MF467242 respectively, suggesting the CPV-2 variants circulating in cats might be derived from dogs. Sequence analysis indicated new mutations, Ala91Ser and Ser192Phe, in the FPV sequences, while obtained CPV-2c carried mutations reported in Asian CPV variants, showing they share a common evolutionary pattern with the Asian 2c strains. Interestingly, the FPV sequence (MT270571), displaying four CPV-specific residues, was found to be a putative recombinant sequence between CPV-2c and FPV. Phylogenetic analysis of the VP2 gene showed that amino acid and nucleotide mutations promoted the evolution of FPV and CPV lineages.ConclusionsOur findings will be helpful to further understand the circulation and evolution of feline and canine parvovirus in Beijing.

Recombination, and Then What? How Zika Virus Hybrids Improve Their Fitness

Zika virus (ZIKV) is an emerging flavivirus primarily transmitted through the bite of Aedesmosquitoes. It spread explosively around the tropics in the 21st century, and still presents a threat to human health. There is a need to better understand the drivers of emergence of ZIKV and likely consequences of its future evolution. RNA recombination is a process of genetic exchange which occurs in positive-sense RNA viruses and contributes to virus evolution. We have developed a recombinant-specific PCR assay for detection of ZIKV recombinants in mammalian and insect cell co-infections. Using this system, we demonstrated the ability of distinct geographic and genetic isolates to recombine and tested their viability in tissue culture. Initial ZIKV recombinants produce plaques with a significantly smaller diameter than either parental strain. Recombinant large-plaque variants were isolated through serial passage and plaque purification, and the genome analysed for adaptive mutations. A single nucleotide coding mutation in NS1 was detected in several independent large-plaque variants. The role of this mutation in virus replication was investigated through reverse genetics to assess whether it gave the recombinant a replicative advantage. Understanding the genetic changes that arise during, and following recombination is important in the context of virus evolution. It is particularly relevant for ZIKV, as co-circulation of the African and Asian strains of ZIKV in nature has already occurred in parts of Latin America and Africa. Current and future studies will focus on the phenotype of recombinant ZIKV, their replication in mammalian and insect cell lines, and in mosquitoes.