A New Segmented Virus Associated with Human Febrile Illness in China.

BACKGROUND: In 2017, surveillance for tickborne diseases in China led to the identification of a patient who presented to a hospital in Inner Mongolia with a febrile illness that had an unknown cause. The clinical manifestation of the illness was similar to that of tickborne encephalitis virus (TBEV) infection, but neither TBEV RNA nor antibodies against the virus were detected. METHODS: We obtained a blood specimen from the index patient and attempted to isolate and identify a causative pathogen, using genome sequence analysis and electron microscopy. We also initiated a heightened surveillance program in the same hospital to screen for other patients who presented with fever, headache, and a history of tick bites. We used reverse-transcriptase-polymerase-chain-reaction (RT-PCR) and cell-culture assays to detect the pathogen and immunofluorescence and neutralization assays to determine the levels of virus-specific antibodies in serum specimens from the patients. RESULTS: We found that the index patient was infected with a previously unknown segmented RNA virus, which we designated Alongshan virus (ALSV) and which belongs to the jingmenvirus group of the family Flaviviridae. ALSV infection was confirmed by RT-PCR assay in 86 patients from Inner Mongolia and Heilongjiang who presented with fever, headache, and a history of tick bites. Serologic assays showed that seroconversion had occurred in all 19 patients for whom specimens were available from the acute phase and the convalescent phase of the illness. CONCLUSIONS: A newly discovered segmented virus was found to be associated with a febrile illness in northeastern China. (Funded by the National Key Research and Development Program of China and the National Natural Science Foundation of China.).

Molecular evolutionary and antigenic characteristics of newly isolated H9N2 avian influenza viruses in Guangdong province, China.

Four new H9N2 avian influenza viruses (AIVs) were isolated from domestic birds in Guangdong between December 2015 and April 2016. Nucleotide sequence comparisons indicated that most of the internal genes of these four strains were highly similar to those of human H7N9 viruses. Amino acid substitutions and deletions found in the HA and NA proteins indicated that all four of these new isolates may have an enhanced ability to infect humans and other mammals. A cross-hemagglutinin-inhibition assay, conducted with two vaccine strains that are broadly used in China, suggested that antisera against vaccine candidates could not provide complete inhibition of the new isolates.

Comparative analysis of MicroRNA expression in dog lungs infected with the H3N2 and H5N1 canine influenza viruses.

MicroRNAs, a class of noncoding RNAs 18 to 23 nucleotides (nt) in length, play critical roles in a wide variety of biological processes. The objective of this study was to examine differences in microRNA expression profiles derived from the lungs of beagle dogs infected with the avian-origin H3N2 canine influenza virus (CIV) or the highly pathogenic avian influenza (HPAI) H5N1 virus (canine-origin isolation strain). After dogs were infected with H3N2 or H5N1, microRNA expression in the lungs was assessed using a deep-sequencing approach. To identify the roles of microRNAs in viral pathogenicity and the host immune response, microRNA target genes were predicted, and their functions were analyzed using bioinformatics software. A total of 229 microRNAs were upregulated in the H5N1 infection group compared with those in the H3N2 infection group, and 166 microRNAs were downregulated. MicroRNA target genes in the H5N1 group were more significantly involved in metabolic pathways, such as glycerolipid metabolism and glycerophospholipid metabolism, than those in the H3N2 group. The inhibition of metabolic pathways may lead to appetite loss, weight loss and weakened immunity. Moreover, miR-485, miR-144, miR-133b, miR-4859-5p, miR-6902-3p, miR-7638, miR-1307-3p and miR-1346 were significantly altered microRNAs that potentially led to the inhibition of innate immune pathways and the heightened pathogenicity of H5N1 compared with that of H3N2 in dogs. This study deepens our understanding of the complex relationships among microRNAs, the influenza virus-mediated immune response and immune injury in dogs.

Evidence for subclinical influenza A(H1N1)pdm09 virus infection among dogs in Guangdong Province, China.

During 2012, we identified sampled dogs with elevated levels of antibodies (≥1:40) against A(H1N1)pdm09 virus by using a hemagglutination inhibition (HI) assay (seroprevalence, 24.7%) and a microneutralization (MN) assay (seroprevalence, 10.8%). These high seroprevalences of A(H1N1)pdm09 among dogs without clinical signs of influenza support the premise that dogs may play a role in the human influenza ecology in China.

Identification of four genotypes of H3N2 swine influenza virus in pigs from southern China.

In 2011, four H3N2 swine influenza viruses (SIVs) were isolated from nasal swabs of four pigs (800 nasal swabs were collected from pigs showing influenza-like symptoms) in Guangdong province, China. Four different genotypes of H3N2 appeared among pigs in southern China, including wholly human-like H3N2 viruses, intermediate (1975) double-reassortant human H3N2 viruses (resulting from reassortment between an early human lineage and a recent human lineage), recent double-reassortant human H3N2 viruses, and avian-like H3N2 viruses. Because pigs can support the reassortment of human and avian influenza viruses, our surveillance should be enhanced as a part of an overall pandemic preparedness plan.

Seroepidemiological evidence of avian influenza A virus transmission to pigs in southern China.

Recently, three novel avian-origin swine influenza viruses (SIVs) were first isolated from pigs in Guangdong Province, southern China, yet little is known about the seroprevalence of avian influenza viruses among pigs in southern China. Here, we report for the first time the seroprevalence of avian H3, H4, and H6 influenza viruses in swine populations and the lack of seroepidemiological evidence of avian H5 influenza virus transmission to pigs in China.

Complete genome sequence of duck Tembusu virus, isolated from Muscovy ducks in southern China.

We report here the complete genomic sequence of the duck Tembusu virus (DTMUV) WJ-1 strain, isolated from Muscovy ducks. This is the first complete genome sequence of DTMUV reported in southern China. Compared with the other strains (TA, GH-2, YY5, and ZJ-407) that were previously found in eastern China, WJ-1 bears a few differences in the nucleotide and amino acid sequences. We found that there are 47 mutations of amino acids encoded by the whole open reading frame (ORF) among these five strains. The whole-genome sequence of DTMUV will help in understanding the epidemiology and molecular characteristics of duck Tembusu virus in southern China.

Complete genome sequence of a novel field strain of rearranged porcine circovirus type 2 in southern China.

We report here the complete genomic sequence of a novel porcine circovirus type 2 (PCV2) strain, which is supposed to be the result of natural genetic recombination between the ORF1 gene of genotype PCV2b-1B and the ORF2 gene of PCV2b-1C. Further analyses revealed that this novel PCV2 strain arose from recombination between PCV2a and PCV2b strains within the ORF2 gene. To our knowledge, this is the first report of both inter- and intragenotype PCV2 gene rearrangement in the field, and it will help in understanding the epidemiology and molecular characteristics of porcine circovirus type 2(PCV2) in southern China.

Complete genome sequence of an avian-like H4N8 swine influenza virus discovered in southern China.

We report here the complete genomic sequence of an avian-like H4N8 swine influenza virus containing an H5N1 avian influenza virus segment from swine in southern China. Phylogenetic analyses of the sequences of all eight viral RNA segments demonstrated that these are wholly avian influenza viruses of the Asia lineage. To our knowledge, this is the first report of interspecies transmission of an avian H4N8 influenza virus to domestic pigs under natural conditions.

Complete genome sequence of an avian-origin H3N2 canine influenza A virus isolated in farmed dogs in southern China.

We report here the complete genomic sequence of an avian-origin H3N2 canine influenza A virus containing multiple mutations in farmed dogs in southern China. Phylogenetic analyses of the sequences of all eight viral RNA segments demonstrated that these are wholly avian influenza viruses of the Asia lineage. To our knowledge, this is the first report of interspecies transmission of an avian H3N2 influenza virus to domestic farm dogs under natural conditions in Southern China. The amino acid information provided herein suggests that continued study is required to determine if this virus could be established in the farm dog population and pose potential threats to public health.

Complete Genome Sequence of a Novel Avian-Like H3N2 Swine Influenza Virus Discovered in Southern China.

We report here the complete genomic sequence of a novel avian-like H3N2 swine influenza virus containing an H5N1 highly pathogenic avian influenza virus segment that was obtained from swine in southern China. Phylogenetic analysis indicated that this virus might originate from domestic aquatic birds. The sequence information provided herein suggests that continuing study is required to determine if this virus can be established in the swine population and pose potential threats to public health.

Complete genome sequence of a novel duck hepatitis A virus discovered in southern China.

We report here the complete genomic sequence of a novel duck hepatitis A virus (DHAV) isolated from mixed infections with DHAV type 1 (DHAV-1) and DHAV-3 in ducklings in Southern China. The whole nucleotide sequence had the highest homology with the sequence of DHAV-3 (GenBank accession number DQ812093) (96.2%). To our knowledge, this is the first report of gene rearrangement between DHAV-1 and DHAV-3, and it will help to understand the epidemiology and molecular characteristics of duck hepatitis A virus in Southern China.

Short communication: isolation and phylogenetic analysis of an avian-origin H3N2 canine influenza virus in dog shelter, China.

A H3N2 canine influenza virus, A/canine/Guangdong/3/2011 (H3N2), was isolated from roaming dogs in rural China. Sequence and phylogenetic analysis of eight gene segments revealed that the A/canine/Guangdong/3/2011 (H3N2) was most similar to a recent H3N2 canine influenza virus isolated in cats from South Korea, which originated from an avian strain. To our knowledge, this is the first report of an avian-origin H3N2 CIV which was isolated from roaming dogs in China. The epidemiologic information provided herein suggests that continued study is required to determine if this virus could be established in the roaming dog population in rural China and pose potential threats to public health.

Microbiological identification and analysis of Swine lungs collected from carcasses in Swine farms, china.

The primary objective of this 3 years study was to determine the prevalence of porcine pathogens of the lungs of swine in swine farms in southern China. A total of 5,420 samples were collected from 200 swine farms. The bacterium that was most commonly isolated was Streptococcus suis, with 10.24 % of the samples being positive, 114 lungs (2.1 %) were positive for pseudorabies virus and 263 (4.85 %) were positive for classical swine fever virus; much lower than positive for PRRSV (15.1 %, p = 0.023) and PCV2 (13.8 %, p = 0.038). lungs that were positive for PRRSV and/or PCV-2 have significantly increased odds of being positive for any of the S. suis (9.79 vs. 0.44 %, p = 0.003).

Advances in Development and Application of Influenza Vaccines.

Influenza A virus is one of the most important zoonotic pathogens that can cause severe symptoms and has the potential to cause high number of deaths and great economic loss. Vaccination is still the best option to prevent influenza virus infection. Different types of influenza vaccines, including live attenuated virus vaccines, inactivated whole virus vaccines, virosome vaccines, split-virion vaccines and subunit vaccines have been developed. However, they have several limitations, such as the relatively high manufacturing cost and long production time, moderate efficacy of some of the vaccines in certain populations, and lack of cross-reactivity. These are some of the problems that need to be solved. Here, we summarized recent advances in the development and application of different types of influenza vaccines, including the recent development of viral vectored influenza vaccines. We also described the construction of other vaccines that are based on recombinant influenza viruses as viral vectors. Information provided in this review article might lead to the development of safe and highly effective novel influenza vaccines.

The Prevalence, Coinfection, and Evolutionary and Molecular Characteristics of Prevalent Goose Circovirus in Guangdong, China.

To understand the prevalence, coinfection with other viruses, underlying genetic evolution, recombination, and molecular biological characteristics of goose circovirus (GoCV) in Guangdong, China, from December 2019 to August 2020, 310 tissue samples of geese showing stunted growth and feather disorder syndrome were collected from this region and analyzed. GoCV, Tembusu virus, waterfowl paramyxovirus, avian influenza virus, fowl adenovirus type 4, and duck plague virus were detected with PCR or real-time PCR. Thirty-one complete GoCV viral genomes were obtained from 164 PCR-verified GoCV nucleotide-positive samples and subjected to phylogenetic analysis, gene recombination analysis, and genome secondary structure prediction. The results showed that more than half of the samples were GoCV positive, and 31.1% of the GoCV-positive samples were from coinfections with at least one of the other viruses. The phylogenetic analysis showed that the GoCVs could be divided into three genome types. The genes of most main epidemic strains now circulating in Guangdong belonged to the Ia subtype, and some strains gradually formed a new Ib subtype. The secondary structure of the viral genome was similar to that of other known circoviruses. Furthermore, B cell linear epitope prediction and protein structure homology modeling of the viral capsid protein were performed based on the viral amino acid sequences. The results showed that the spatial structure of the capsid protein of the 31 sequenced strains was similar to that of duck circovirus and consisted of two ß-sandwich conformations. A total of five B cell linear epitopes were predicted, and four of them were mapped on the predicted model of the capsid protein of GoCVs. This report provides a reference for the epidemiology of GoCV in Guangdong, understanding the elemental composition of the virus genes and proteins, selecting representative vaccine strains, constructing targeted immune preparations for GoCV, and strengthening prevention and control of the disease.

Prevalencia, coinfección y características evolutivas y moleculares del circovirus del ganso prevalente en Guangdong, China. Para comprender la prevalencia, la coinfección con otros virus, su evolución genética subyacente, la recombinación y las características biológicas moleculares del circovirus del ganso (GoCV) en Guangdong, China, de diciembre de 2019 a agosto de 2020, 310 se recolectaron muestras de tejido de gansos que presentaban retraso en el crecimiento y síndrome del trastorno de las plumas en esta región y fueron analizadas. Se detectaron mediante PCR o por PCR en tiempo real el circovirus del ganso, el virus Tembusu (TMUV), el paramixovirus de aves acuáticas (WFPV), el virus de la influenza aviar (AIV), el adenovirus del pollo tipo 4 (Fadv-4) y el virus de la enteritis viral del pato (DPV). Se obtuvieron 31 genomas virales completos del circovirus del ganso de 164 muestras positivas de nucleótidos de circovirus del ganso verificadas por PCR y se sometieron a análisis filogenético, a análisis de recombinación de genes y predicción de la estructura secundaria del genoma. Los resultados mostraron que más de la mitad de las muestras eran positivas para circovirus del ganso y el 31.1% de las muestras positivas para circovirus del ganso eran de coinfecciones con al menos uno de los otros virus. El análisis filogenético mostró que los circovirus del ganso podrían dividirse en tres tipos de genomas. Los genes de la mayoría de las principales cepas epidémicas que ahora circulan en Guangdong pertenecían al subtipo Ia, y algunas cepas formaron gradualmente un nuevo subtipo Ib. La estructura secundaria del genoma viral era similar a la de otros circovirus conocidos. Además, la predicción del epítope lineal de células B y el modelo de la homología de la estructura de la proteína de la cápside viral se realizaron basándose en las secuencias de aminoácidos virales. Los resultados mostraron que la estructura espacial de la proteína de la cápside de las 31 cepas secuenciadas era similar a la del circovirus de pato y consistía de dos conformaciones de tipo sándwich ß. Se predijo un total de cinco epítopes lineales de células B y cuatro de ellos se mapearon en el modelo predicho de la proteína de la cápside del circovirus del ganso. Este informe proporciona una referencia para la epidemiología de circovirus del ganso en Guangdong, entendiendo la composición elemental de los genes y proteínas del virus, seleccionando cepas de vacunas representativas, construyendo preparaciones de blancos inmunitarios para circovirus del ganso y fortaleciendo la prevención y el control de la enfermedad.

The NS1 protein of H5N6 feline influenza virus inhibits feline beta interferon response by preventing NF-κB and IRF3 activation.

Despite the apparent lack of a feline influenza virus lineage, cats are susceptible to infection by influenza A viruses. Here, we characterized in vitro A/feline/Guangdong/1/2015, an H5N6 avian influenza virus recently isolated from cats. A/feline/Guangdong/1/2015 replicated to high titers and caused CPE in feline kidney cells. We determined that infection with A/feline/Guangdong/1/2015 did not activate the IFN-ß promoter, but inhibited it by blocking the activation of NF-κB and IRF3. We also determined that the viral NS1 protein mediated the block, and that the dsRNA binding domain of NS1 was essential to perform this function. In contrast to treatment after infection, cells pretreated with IFN-ß suppressed viral replication. Our findings provide an example of an H5N6 influenza virus suppressing IFN production, which might be associated with interspecies transmission of avian influenza viruses to cats.

First genome report and analysis of chicken H7N9 influenza viruses with poly-basic amino acids insertion in the hemagglutinin cleavage site.

We report the full-length sequence of two chicken source influenza A (H7N9) viruses found in Guangdong live poultry market (LPM) during the most recent wave of human infections (from October 2016 to the present time). These viruses carry insertion of poly-basic amino acids (KGKRTAR/G) at the protease cleavage site of the HA protein, which were previously found in the highly pathogenic (HP) human influenza A (H7N9) [IAV(H7N9)] strains. Phylogenetic analysis of these two novel avian influenza viruses (AIVs) suggested that their genomes reassorted between the Yangtze River Delta (YRD) and Pearl River Delta (PRD) clades. Molecular clock analysis indicated that they emerged several months before the HP human strains. Collectively, our results suggest that IAV(H7N9) viruses evolve in chickens through antigenic drift to include a signature HP sequence in the HA gene, which highlights challenges in risk assessment and public health management of IAV(H7N9) infections at the human-animal interface.

Live poultry market workers are susceptible to both avian and swine influenza viruses, Guangdong Province, China.

Guangdong Province is recognized for dense populations of humans, pigs, poultry and pets. In order to evaluate the threat of viral infection faced by those working with animals, a cross-sectional, sero-epidemiological study was conducted in Guangdong between December 2013 and January 2014. Individuals working with swine, at poultry farms, or live poultry markets (LPM), and veterinarians, and controls not exposed to animals were enrolled in this study and 11 (4 human, 3 swine, 3 avian, and 1 canine) influenza A viruses were used in hemagglutination inhibition (HI) assays (7 strains) and the cross-reactivity test (9 strains) in which 5 strains were used in both tests. Univariate analysis was performed to identify which variables were significantly associated with seropositivity. Odds ratios (OR) revealed that swine workers had a significantly higher risk of elevated antibodies against A/swine/Guangdong/L6/2009(H1N1), a classical swine virus, and A/swine/Guangdong/SS1/2012(H1N1), a Eurasian avian-like swine virus than non-exposed controls. Poultry farm workers were at a higher risk of infection with avian influenza H7N9 and H9N2. LPM workers were at a higher risk of infection with 3 subtypes of avian influenza, H5N1, H7N9, and H9N2. Interestingly, the OR also indicated that LPM workers were at risk of H1N1 swine influenza virus infection, perhaps due to the presence of pigs in the LPM. While partial confounding by cross-reactive antibodies against human viruses or vaccines cannot be ruled out, our data suggests that animal exposed people as are more likely to have antibodies against animal influenza viruses.