Copper-Mediated and Palladium-Catalyzed Cross-Coupling of Indoles and N-Methylpyridinium Salts: A Practical Way to Prepare 3-(Pyridin-2-yl)indoles.

Herein, a Pd/Cu bimetallic-catalyzed direct C-H heteroarylation of pyridines via the traceless protecting group strategy is described. A series of N-methyl-activated pyridines and 1-methylindoles are coupled with high regioselectivity to produce the corresponding 3-(pyridin-2-yl)indoles in moderate to good yields, wherein related electron-rich heterocycles (e.g., indole, 1-methylpyrrole, benzofuran, benzo[b]thiophene) are also applicable. Streamlined operation, good functional group tolerance, and late-stage modifications make this twofold C-H activation protocol an attractive route for the synthesis of 3-(pyridin-2-yl)indole derivatives.

Avian influenza A virus H7N9 in China, a role reversal from reassortment receptor to the donator.

Reassortment can introduce one or more gene segments of influenza A viruses (IAVs) into another, resulting in novel subtypes. Since 2013, a new outbreak of human highly pathogenic avian influenza has emerged in the Yangtze River Delta (YRD) and South-Central regions of China. In this study, using Anhui province as an example, we discuss the possible impact of H7N9 IAVs on future influenza epidemics through a series of gene reassortment events. Sixty-one human H7N9 isolates were obtained from five outbreaks in Anhui province from 2013 to 2019. Bioinformatics analyses revealed that all of them were characterized by low pathogenicity and high human or mammalian tropism and had introduced novel avian influenza A virus (AIV) subtypes such as H7N2, H7N6, H9N9, H5N6, H6N6, and H10N6 through gene reassortment. In reassortment events, Anhui isolates may donate one or more segments of HA, NA, and the six internal protein-coding genes for the novel subtype AIVs. Our study revealed that H7N9, H9N2, and H5N1 can serve as stable and persistent gene pools for AIVs in the YRD and South-Central regions of China. Novel AIV subtypes might be generated continuously by reassortment. These AIVs may have obtained human-type receptor-binding abilities from their donors and prefer binding to them, which can cause human epidemics through accidental spillover infections. Facing the continual threat of emerging avian influenza, constant monitoring of AIVs should be conducted closely for agricultural and public health.

Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection.

Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.

Rapid and simultaneous visual screening of SARS-CoV-2 and influenza virufses with customized isothermal amplification integrated lateral flow strip.

Due to the similar clinical symptoms of influenza (Flu) and coronavirus disease 2019 (COVID-19), there is a looming infection threat of concurrent Flu viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this work, we introduce a customized isothermal amplification integrated lateral flow strip (LFS) that is capable performing duplex reverse transcription-recombinase polymerase amplification (RT-RPA) and colorimetric LFS in a sequential manner. With customized amplification primer sets targeted to SARS-CoV-2 (opening reading frame 1a/b and nucleoprotein genes) and Flu viruses (Flu A and Flu B), the platform allows the rapid and simultaneous visual screening of SARS-CoV-2 and Flu viruses (Flu A and Flu B) without cross reactivity, false positives, and false negatives. Moreover, it maximally eases the detection, reduces the detection time (1 h), and improves the assay performance to detect as low as 10 copies of the viral RNA. Its clinical application is powerfully demonstrated with 100% accuracy for evaluating 15 SARS-CoV-2-positive clinical samples, 10 Flu viruses-positive clinical samples, and 5 negative clinical samples, which were pre-confirmed by standard qRT-PCR. We envision this portable device can meet the increasing need of online monitoring the serious infectious diseases that substantially affects health care systems worldwide.

TLR3 polymorphisms are associated with the severity of hand, foot, and mouth disease caused by enterovirus A71 in a Chinese children population.

Hand, foot, and mouth disease (HFMD) caused by enterovirus A71 (EV-A71) is a contagious viral disease, and toll-like receptors (TLRs) play essential roles in resisting the pathogen. The aim of this study was to assess the potential relationship between several TLRs polymorphisms and the HFMD severity in a Chinese children population. A total of 328 Chinese children with HFMD were included in the present study. The polymorphisms of TLR3 (rs3775290, rs3775291, rs3775296, rs1879026, rs5743312, rs5743313, rs5743303, rs13126816, and rs3775292), TLR4 (rs4986790, rs4986791, rs2149356, rs11536889, and rs41426344), TLR7 (rs179009, rs179010, rs179016, rs3853839, rs2302267, rs1634323, and rs5741880), and TLR8 (rs3764880, rs2159377, rs2407992, rs5744080, rs3747414, rs3764879, and rs5744069) genes were selected. The study indicated that individuals with the GG genotype of TLR3 single-nucleotide polymorphism rs1879026 had a higher risk of developing severe cases (GG vs. GT: OR = 1.875; 95% CI, 1.183-2.971; p = .007). Meanwhile, TLR3 rs3775290 CC genotype and C allele were associated with lower disease severity in females (CC vs. CT: OR = 0.350; 95% CI, 0.163-0.751; p = .006; C vs. T: OR = 0.566; 95% CI, 0.332-0.965; p = .036). TLR3 rs3775291 CC genotype showed 2.537 folds higher risk of developing severe cases in females (CC vs. CT: OR = 2.537; 95% CI, 1.108-5.806; p = .026). Moreover, TLR3 rs1879026 GG genotype was found to be related to increased risk of severe cases in males (GG vs. GT: OR = 2.076; 95% CI, 1.144-3.768; p = .016). The current findings show that the genetic variants of TLR3 rs1879026, rs3775290, and rs3775291 are associated with the severity of EV-A71-associated HFMD in a Chinese children population.

Digital PCR assay for the effective detection of COVID-19 patients with SARS-CoV-2 low viral load.

OBJECTIVE: Viral nucleic acid detection by real-time reverse transcription polymerase chain reaction (qPCR) is the current standard method for diagnosis of SARS-CoV-2 infection. However, due to low viral load in some COVID-19 patients, false negative results from this method have been repeatedly reported. METHOD: In this study, we compared the sensitivity and specificity of digital PCR (dPCR) in simulated samples and clinical samples with qPCR assay through a series of vigorous tests. RESULTS: The results showed that dPCR was more sensitive than qPCR especially for samples with low viral load (≤3 copies). In addition, dPCR had similar specificity as qPCR and could effectively distinguish other human coronaviruses and influenza virus from SARS-CoV-2. More importantly, dPCR was more sensitive than qPCR in detecting the virus in the "negative" samples from recurrent COVID-19 patients. CONCLUSIONS: In summary, dPCR could serve as a powerful complement to the current qPCR method for SARS-CoV-2 detection, especially for the samples with extremely low viral load, such as recurrent COVID-19 patients.

Molecular epidemiology of SARS-CoV-2 clusters caused by asymptomatic cases in Anhui Province, China.

BACKGROUND: COVID-19 is a newly emerging disease caused by a novel coronavirus (SARS-CoV-2), which spread globally in early 2020. Asymptomatic carriers of the virus contribute to the propagation of this disease, and the existence of asymptomatic infection has caused widespread fear and concern in the control of this pandemic. METHODS: In this study, we investigated the origin and transmission route of SARS-CoV-2 in Anhui's two clusters, analyzed the role and infectiousness of asymptomatic patients in disease transmission, and characterized the complete spike gene sequences in the Anhui strains. RESULTS: We conducted an epidemiological investigation of two clusters caused by asymptomatic infections sequenced the spike gene of viruses isolated from 12 patients. All cases of the two clusters we investigated had clear contact histories, both from Wuhan, Hubei province. The viruses isolated from two outbreaks in Anhui were found to show a genetically close link to the virus from Wuhan. In addition, new single nucleotide variations were discovered in the spike gene. CONCLUSIONS: Both clusters may have resulted from close contact and droplet-spreading and asymptomatic infections were identified as the initial cause. We also analyzed the infectiousness of asymptomatic cases and the challenges to the current epidemic to provided information for the development of control strategies.

Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000-18.

Hand, foot, and mouth disease (HFMD), which is a frequently reported and concerning disease worldwide, is a severe burden on societies globally, especially in the countries of East and Southeast Asia. Coxsackievirus A16 (CV-A16) is one of the most important causes of HFMD and a severe threat to human health, especially in children under 5 years of age. To investigate the epidemiological characteristics, spread dynamics, recombinant forms (RFs), and other features of CV-A16, we leveraged the continuous surveillance data of CV-A16-related HFMD cases collected over an 18-year period. With the advent of the EV-A71 vaccine since 2016, which targeted the EV-A71-related HFMD cases, EV-A71-related HFMD cases decreased dramatically, whereas the CV-A16-related HFMD cases showed an upward trend from 2017 to October 2019. The CV-A16 strains observed in this study were genetically related and widely distributed in the mainland of China. Our results show that three clusters (B1a-B1c) existed in the mainland of China and that the cluster of B1b dominates the diffusion of CV-A16 in China. We found that eastern China played a decisive role in seeding the diffusion of CV-A16 in China, with a more complex and variant transmission trend. Although EV-A71 vaccine was launched in China in 2016, it did not affect the genetic diversity of CV-A16, and its genetic diversity did not decline, which confirmed the epidemiological surveillance trend of CV-A16. Two discontinuous clusters (2000-13 and 2014-18) were observed in the full-length genome and arranged along the time gradient, which revealed the reason why the relative genetic diversity of CV-A16 increased and experienced more complex fluctuation model after 2014. In addition, the switch from RFs B (RF-B) and RF-C co-circulation to RF-D contributes to the prevalence of B1b cluster in China after 2008. The correlation between genotype and RFs partially explained the current prevalence of B1b. This study provides unprecedented full-length genomic sequences of CV-A16 in China, with a wider geographic distribution and a long-term time scale. The study presents valuable information about CV-A16, aimed at developing effective control strategies, as well as a call for a more robust surveillance system, especially in the Asia-Pacific region.

Sporadic occurrence of H9N2 avian influenza infections in human in Anhui province, eastern China: A notable problem.

H9N2 viruses can cause great economic losses to the domestic poultry industry when co-infected with other influenza viruses or pathogens. . To better understand the molecular characteristics of H9N2 avian influenza viruses (AIVs) and analyze the genetic evolutionary relationship, we isolated three H9N2 subtypes AIVs from nasopharyngeal swab specimens from the three cases reported in Anhui province since 2015, and systematically reviewed the genome-wide data of 21 poultry--isolated H9N2 viruses during 1998-2017. The six internal genes of three human-isolated viruses and recent poultry-isolated viruses (since 2014) in Anhui province presented high gene homologies with HPAI H7N9, even including H10N8 and H5N6. The three human-isolated H9N2 AIVs and poultry-isolated viruses (since 2008) in Anhui province were highly similar, and classified into genotype S. Seven N-linked potential glycosylation sites in the HA protein were detected in the three human-isolated viruses, which also appeared in poultry-isolated H9N2 AIVs. None of the human-isolated H9N2 AIVs had the I368V mutation in PB1 protein, but all the poultry-isolated H9N2 viruses in 2017 carried this mutation. Multidisciplinary, cross-regional and cross-sectoral approaches are warranted to address complex public health challenges and achieve the goal of 'one health'.

Japanese Spotted Fever in Eastern China, 2013.

We isolated Rickettsia japonica from a febrile patient in Lu'an City, China, in 2013. Subsequently, we found an R. japonica seroprevalence of 54.8% (494/902) in the rural population of Anhui Province and an R. japonica prevalence in Haemaphysalis longicornis ticks of 0.5% (5/935). R. japonica and its tick vector exist in China.

Orientia tsutsugamushi infection in rodents in Anhui Province of China.

We conducted an investigation of Orientia tsutsugamushi infection among rodents in non-endemic areas in Anhui Province. Fifty-six (56) rodents including 44 Apodemus agrarius and 12 Niviventer niviventer were trapped and captured in autumn in the fields of three counties in Anhui Province. DNA samples were amplified and sequenced for the 56kDa protein gene of Orientia tsutsugamushi. The overall infection rate in the rodents was 23.2%(13/56). The rate of detection of O. tsutsugamushi in Apodemus agrarius and Niviventer niviventer were 27.3% and 8.3% respectively. Moreover, we identified two genotypes (Karp and Gilliam strains) of Orientia tsutsugamushi in rodents. Our study demonstrated that Apodemus agrarius is the main host for O. tsutsugamushi pathogen and this is the first report of Karp and Gilliam strains in these non-endemic areas in Anhui Province.

[Phylogenetic Analysis of the VP1 Region of Coxsackievirus A16 Strains Isolated in Anhui Province, 2014].

To study on the phylogenetic characterization of the VP1 genes of coxsackievirus A16 (CVA16) causing hand-food-mouth disease (HFMD) isolated from Anhui province in 2014. A total of 413 throat swab specimens from HFMD patients were collected during January to November, 2014 for the isolation and identification of enteroviruses using real-time RT-PCR assays. The VP1 regions of CVA16 isolates were amplified using RT-PCR and sequenced. And the phylogenetic tree was constructed among the VP1 regions of those isolates, the different genotypes and sub-genotypes of CVA16 strains. A total of 97 enteroviruses were isolated from 413 samples, the positive rate was 23.49% (97/413), including seventeen CVA16, seventy six HEV71 and four other enteroviruses. The results of the phylogenetic tree showed that 17.CVA16 strains isolated from Anhui in 2014 clustered within B1b evolution branch of B1 genotype. The nucleotide and amino acid sequence identities were 95.30%-100% and 98.70%-100% among the isolates, respectively, but within B1b branch of 17 strains formed several small transmission chains. The nucleotide acid of 17 CVA16 isolates in Anhui province were closed to the strains isolated from Yunnan, Hunan, Guangdong, Tibet and Jiangsu, especially from Hunan in 2013 and from Shenzhen of Guangdong in 2014, the identity were 96.40%-99.70%. The CVA16 strains isolated from Anhui in 2014 were all belong to genetic subtype B1b of B1 genotype was dominant, and among those isolates, several small virus transmission chains had formed with co-circulating and evolution.

Rural residents in China are at increased risk of exposure to tick-borne pathogens Anaplasma phagocytophilum and Ehrlichia chaffeensis.

As emerging tick born rickettsial diseases caused by A. phagocytophilum and E. chaffeensis, anaplasmosis and ehrlichiosis have become a serious threat to human and animal health throughout the world. In particular, in China, an unusual transmission of nosocomial cases of human granulocytic anaplasmosis occurred in Anhui Province in 2006 and more recent coinfection case of A. phagocytophilum and E. chaffeensis was documented in Shandong Province. Although the seroprevalence of human granulocytic anaplasmosis (former human granulocytic ehrlichiosis, HGE) has been documented in several studies, these data existed on local investigations, and also little data was reported on the seroprevalence of human monocytic ehrlichiosis (HME) in China. In this cross-sectional epidemiological study, indirect immunofluorescence antibody assay (IFA) proposed by WHO was used to detect A. phagocytophilum and E. chaffeensis IgG antibodies for 7,322 serum samples from agrarian residents from 9 provinces/cities and 819 urban residents from 2 provinces. Our data showed that farmers were at substantially increased risk of exposure. However, even among urban residents, risk was considerable. Seroprevalence of HGA and HME occurred in diverse regions of the country and tended to be the highest in young adults. Many species of ticks were confirmed carrying A. phagocytophilum organisms in China while several kinds of domestic animals including dog, goats, sheep, cattle, horse, wild rabbit, and some small wild rodents were proposed to be the reservoir hosts of A. phagocytophilum. The broad distribution of vector and hosts of the A. phagocytophilum and E. chaffeensis, especially the relationship between the generalized susceptibility of vectors and reservoirs and the severity of the disease's clinical manifestations and the genetic variation of Chinese HGA isolates in China, is urgently needed to be further investigated.

Molecular epidemiology of coxsackievirus A16: intratype and prevalent intertype recombination identified.

Coxsackievirus A16 (CVA16) is responsible for nearly 50% of all the confirmed hand, foot, and mouth disease (HFMD) cases in mainland China, sometimes it could also cause severe complications, and even death. To clarify the genetic characteristics and the epidemic patterns of CVA16 in mainland China, comprehensive bioinfomatics analyses were performed by using 35 CVA16 whole genome sequences from 1998 to 2011, 593 complete CVA16 VP1 sequences from 1981 to 2011, and prototype strains of human enterovirus species A (EV-A). Analysis on complete VP1 sequences revealed that subgenotypes B1a and B1b were prevalent strains and have been co-circulating in many Asian countries since 2000, especially in mainland China for at least 13 years. While the prevalence of subgenotype B1c (totally 20 strains) was much limited, only found in Malaysia from 2005 to 2007 and in France in 2010. Genotype B2 only caused epidemic in Japan and Malaysia from 1981 to 2000. Both subgenotypes B1a and B1b were potential recombinant viruses containing sequences from other EV-A donors in the 5'-untranslated region and P2, P3 non-structural protein encoding regions.

Biological features of novel avian influenza A (H7N9) virus.

Human infection associated with a novel reassortant avian influenza H7N9 virus has recently been identified in China. A total of 132 confirmed cases and 39 deaths have been reported. Most patients presented with severe pneumonia and acute respiratory distress syndrome. Although the first epidemic has subsided, the presence of a natural reservoir and the disease severity highlight the need to evaluate its risk on human public health and to understand the possible pathogenesis mechanism. Here we show that the emerging H7N9 avian influenza virus poses a potentially high risk to humans. We discover that the H7N9 virus can bind to both avian-type (α2,3-linked sialic acid) and human-type (α2,6-linked sialic acid) receptors. It can invade epithelial cells in the human lower respiratory tract and type II pneumonocytes in alveoli, and replicated efficiently in ex vivo lung and trachea explant culture and several mammalian cell lines. In acute serum samples of H7N9-infected patients, increased levels of the chemokines and cytokines IP-10, MIG, MIP-1ß, MCP-1, IL-6, IL-8 and IFN-α were detected. We note that the human population is naive to the H7N9 virus, and current seasonal vaccination could not provide protection.

Anaplasma phagocytophilum infection in domestic animals in ten provinces/cities of China.

A nationwide epidemiologic investigation of domestic animal infections has been conducted in nine provinces and one city during 2007-2010. Serum samples from a total of 707 goats, 433 cattle, and 219 dogs were collected for detecting Anaplasma phagocytophilum IgG antibody by immunofluorescence assays and the average seroprevalences were 10.05% for dogs, 3.82% for goats, and 0.69% for cattle, respectively. A total of 472 goats, 201 cattle, 102 dog blood clots, and 1,580 ticks were collected for polymerase chain reaction (PCR) amplifying A. phagocytophilum 16S rRNA genes and the PCR-positive rates were 26.69% for goats, 23.38% for cattle, and 10.89% for dogs. Six species were identified and the average PCR-positive rates were 58.3% for Dermacentor silvarum, 43.9% for Haemaphysalis longicornis, 12.5% for Ixodes persulcatus, 7.5% (3 of 40) for Boophilus microplus, and 5.2% for Rhipicephalus sanguineus, respectively. The evidence in the study indicated the zoonotic Rickettsia is highly prevalent in China.

Co-remediation of cadmium-polluted soil using stainless steel slag and ammonium humate.

INTRODUCTION AND METHODS: This study investigated the remediation of cadmium-polluted soil using a combination of stainless steel slag and ammonium humate. These remedial agents were added to an artificially polluted garden soil to inhabit cadmium toxicity in soil by changing the physical and chemical properties of soil in a pot experiment. RESULTS AND CONCLUSIONS: The results showed that the co-application of ammonium humate and stainless steel slag significantly decreased the total and available soil cadmium concentrations, with maximum decreases of 16.30% and 58.04%, respectively. The co-application of an adequate dose of these remedial agents can significantly increase soil pH. The soil organic matter and cation exchange capacity, as well as the amount of soil aggregates, were also significantly increased by the addition ammonium humate, but not stainless steel slag.