Objective:To investigate the distribution and hantavirus (HV) carrying state in host animals of hemorrhagic fever with renal syndrome (HFRS) in Henan Province from 2019 to 2022.Methods:Host animal monitoring was carried out at the monitoring sites of HFRS in Henan Province. The real-time fluorescence quantitative PCR was used to detect hantavirus in rat lungs. The types of hantavirus were analyzed. The positive samples were sequenced and then sequence homology and variation were analyzed.Results:A total of 1 308 rodents were captured from 2019 to 2022, 16 specimens of rat lungs tested positive for hantavirus nucleic acid. The positive rate of HV was 1.22% (16/1 308). According to type, the positive rate of HV in Apodius agrarius was the highest (68.75%, 11/16). According to distribution, the positive rate of HV in field samples was the highest (2.50%, 12/480), and the positive rate of HV in residential samples was 0.53% (4/759). The typing results of 16 positive samples showed that all viruses were hantavirus type Ⅰ (hantaan virus). The positive samples were sequenced and eight S gene fragments (GenBank number: OQ681444-OQ681451) and six M gene fragments (OQ681438-OQ681443) were obtained. The S and M gene fragments were similar to the Shaanxi 84FLi strain and Sichuan SN7 strain. Phylogenetic analysis of S and M gene fragments showed that they all belonged to the hantaan virus-H5 subtype. Amino acid sequence analysis revealed that, compared with the hantaan virus vaccine strain 84FLi, the 74th amino acid encoded by eight S fragments was replaced by aspartamide with serine. Tryptophan was replaced by glycine at the 14th position of Gn region in XC2022047, and isoleucine was replaced by alanine at the 359 position of XC2022022 and XC2022024.Conclusion:The hantavirus carried by host animals in Henan Province from 2019 to 2022 belongs to the type Ⅰ (hantaan virus), and Apodemus agrarius is still the dominant host animal of the hantaan virus. Compared with the vaccine strains, amino acid sites are replaced in the immune epitopes of the S and M gene fragments.

Objective:To analyze the specific immunoglobulin G (IgG) antibodies level in the population after the coronavirus disease 2019 (COVID-19) pandemic in Henan Province.Methods:A total of 5 178 peripheral venous blood samples were collected from 10 districts (counties) in Henan Province according to the national seroepidemiological survey program for COVID-19, and the method of cluster random sampling was adopted from March 6 to 15, 2023. Descriptive analysis was used for the basic data, history of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination, SARS-CoV-2 infection of the respondents. The specific IgG antibody of SARS-CoV-2 was detected using chemiluminescence method. Statistical analysis was performed by using rank sum test, Kruskal Wallis test, and Dunn′s test.Results:The overall positive rate of SARS-CoV-2-specific IgG antibody was 83.35%(4 316/5 178). There were statistically significant differences in the specific IgG antibodies against SARS-CoV-2 produced by people of different sexes, different ages, infected or not, vaccinated or not, and vaccinated with different doses of SARS-CoV-2 vaccine ( Z=3.60, H=195.32, Z=6.10, 18.08, H=382.70, respectively, all P<0.001). The specific IgG antibodies produced by unvaccinated+ uninfected group, unvaccinated+ infected group, vaccinated+ uninfected group, and vaccinated+ infected group were 3.54(0.98, 11.00), 60.65(2.33, 84.80), 133.00(59.80, 173.00), and 142.00(98.30, 176.00), respectively. And the difference was statistically significant( H=354.62, P<0.001). The specific IgG antibodies of uninfected people increased with the increase of inoculum times( H=287.00 and 98.48, both P<0.001). The specific IgG antibodies of people who were not infected with SARS-CoV-2 in the groups of whose interval from the last inoculation of SARS-CoV-2 vaccine to blood collection was less than three months, three to six months and more than six months were 171.86(156.04, 196.57), 71.71(17.08, 110.38) and 132.14(57.59, 172.25), respectively, and the difference was statistically significant ( H=19.93, P<0.001). Among them, the absolute difference between the less than three months group and the three to six months group was statistically significant ( Z=3.67, P<0.001), and the absolute difference between the less than three months group and the more than six months group was statistically significant ( Z=3.47, P<0.001). The specific IgG antibodies level in the less than three months group was the highest. Conclusions:There is a certain correlation between the number of SARS-CoV-2 vaccine doses and the specific IgG antibodies level in uninfected people. The specific IgG antibodies could maintain a high level for three months after immunization.

Objective:To analyze the genus, drug resistance/virulence and phylogenetic characteristics of Brucella strains isolated from brucellosis surveillance sentinels in Henan Province from 2013 to 2022, and provide baseline data for the surveillance, early warning and outbreak tracing of brucellosis. Methods:Blood samples were collected from patients with Brucella infection for strain isolation, culture and species identification, drug susceptibility test, whole genome sequencing, splicing and assembly, functional/virulence/resistance gene prediction analysis and phylogenetic tree drawing based on single nucleotide polymorphism (SNP). Results:In 36 brucellosis patients, the majority were men (86.11%, 31/36), young adults aged 18-50 (88.89%, 32/36) and farmers/herdsmen (72.22%, 26/36). A total of 36 strains of Brucella melitensis were isolated, and average 1 305 functional proteins of 21 categories were predicted by strain genome; all the strains carried four main virulence factors (pmm, VirB group, BtpA/BtpB, BvrS/BvrR). The drug sensitivity rate was 100.00% to six types of antibiotics including levofloxacin, rifampicin, doxycycline, streptomycin, tetracycline and gentamicin, they showed different resistances to three antibiotics including compound trimethoprim-sulfamethoxazole, ciprofloxacin and ampicillin. The strains carried four types of resistance genes and two clusters of resistance genes, with four combinations of genotypes, the resistance mechanisms included antibiotic degradation/modification enzymes, resistant nodular cell differentiation (RND) efflux pumps, 16S/23S ribosomal rRNA binding site mutations, etc. The number of SNP differed in the genomes of 36 Brucellamelitensis strains ranged from 0 to 454 and phylogenetic tree was divided into three major branches, with relative branch distances between 0.000 0 and 0.498 6 for each strain. Conclusions:Human Brucellamelitensis strains isolated from surveillance sentinels in Henan from 2013 to 2022 carried multiple virulence and antibiotic resistance genes and had different drug resistance phenotypes. Single nucleotide polymorphism analysis and phylogenetic tree analysis showed significant differences in phylogenetic relationships among different strains.

Objective:To analyze the genetic evolution and molecular characteristics of H7N9 avian influenza virus (AIV) isolated in a live poultry market.Methods:Samples such as poultry feces, sewage, and hair removal machine and chopping board swabs were collected. Real-time fluorescent quantitative PCR was used to detect influenza A virus and H7N9 AIV in the samples. The whole genome of H7N9 AIV was amplified with influenza A virus universal primers and sequenced. BLAST and MEGA X were used for sequence alignment, phylogenetic analysis and molecular characterization.Results:Seven poultry-related environment samples were collected in the live poultry market in Xuchang city in February 2023, and four were positive for H7N9 AIV. The whole genome sequences of three H7N9 AIV isolates were successfully obtained, and the isolates shared high nucleotide identity in different genes (98.37%-100.00%). BLAST analysis showed they were highly identical to H7N9 strains isolated from domestic poultry in China from 2020 to 2021. Genetic evolution analysis showed that the three isolates clustered in the same branch and were closer to the recent environmental isolates than to the recent strains isolated from human or avian. Through comparison with the sequences of the representative strains in different periods, it was found that the isolated strains in this study showed high avian pathogenicity with four amino acids KRAA inserted at the cleavage site; the hemagglutinin receptor-binding site was QSG, which was an avian binding receptor; there was a G186I mutation in hemagglutinin. Mammalian-adaptive mutation E627K was not detected in polymerase basic protein 2. Mutations (R292K and I38T) associated with drug resistance to neuraminidase inhibitor (oseltamivir) and polymerase acidic protein inhibitor (baloshavir) were not detected, suggesting that these isolates remained susceptible to these drugs. A S31N mutation was found in M2 protein, indicating they were resistant to alkamines.Conclusions:The three H7N9 AIV strains isolated in the live poultry market have high avian pathogenicity, but there are no significant increase in mutations related to the binding ability to human receptors, mammalian pathogenicity, viral transmissibility, or drug resistance as compared with previous representative strains causing human or avian infection.

Objective:To analyze the reinfection rates in people previously infected with SARS-CoV-2 in Zhengzhou and Yuzhou cities (first infected with Delta/B.1.617.2 variant), and Anyang city (first infected with Omicron/BA.1.1 variant) in January 2022 and the population characteristics, and compare the differences in antibody levels among different populations.Methods:Serum samples were collected from 371 previously infected, 134 reinfected and 19 uninfected people for IgG antibody detection. Among them, serum samples from 45 previously infected, 44 reinfected and 19 uninfected people were tested with different novel coronavirus variants (early original strain, BA.5.2 variant, XBB.1.5 variant) for neutralizing antibody detection.Results:The rate of reinfection was 32.82% (85/259) in Zhengzhou and Yuzhou cities, and 19.92% (49/246) in Anyang city. The IgG antibody level in reinfected people was higher than that in previously infected and uninfected people ( P<0.05). The IgG antibody level in uninfected group was higher in people vaccinated within three months than in those vaccinated six months ago ( P<0.05). The IgG antibody level in the group receiving four doses of vaccine was higher than that in the group receiving three doses of vaccine ( P<0.05). The results of true virus neutralization antibody detection showed that in the Zhengzhou and Yuzhou cases, the level of neutralization antibody against the early original strain was higher than those against the BA.5.2 variant and the XBB.1.5 variant ( P<0.05), and the level of neutralizing antibody against BA.5.2 variant was higher than that against XBB.1.5 variant ( P<0.05). In Anyang city cases, the level of neutralizing antibody against the early original strain was higher than those against BA.5.2 variant and XBB.1.5 variant ( P<0.05); in the reinfected population, the level of neutralizing antibody against the early original strain was higher than that against the XBB.1.5 variant ( P<0.05). In addition, the levels of all neutralizing antibodies in both previously infected and reinfected people were higher than those in uninfected people ( P<0.05). The level of neutralizing antibody in the infected population in Zhengzhou and Yuzhou cities was higher than that in the infected population in Anyang city and in uninfected population ( P<0.05). The levels of antibodies against BA.5.2 and anti-XBB.1.5 variants in infected people in Zhengzhou and Yuzhou cities were higher than those in uninfected people ( P<0.05). The level of neutralizing antibody against BA.5.2 variants in the previously infected population in Anyang city was higher than that in the uninfected population ( P<0.05), and the level of neutralizing antibody against XBB.1.5 variants in the infected population in Anyang city was higher than that in the uninfected population ( P<0.05). Conclusions:After infection with SARS-CoV-2, the neutralizing antibodies produced in the human body have a certain cross-protection effect on other variants, but the antibody level will gradually decrease over time. Protection from a previous early SARS-CoV-2 variants infection against the current main circulating Omicron variants (such as XBB variants) is low, and the immunity conferred by pervious infection or booster vaccination may not be able to provide sufficient protection against new variants.

Objective:To analyze the whole genome of Omicron variants causing the first local Omicron outbreak in Henan Province and to investigate the mutations in the SARS-CoV-2 genome for source tracing.Methods:Respiratory tract samples from COVID-19 cases in the Omicron outbreak in Henan Province from January 7 to 29, 2022 were subjected to whole-genome sequencing and sequence alignment analysis. Whole-genome identity, variations and evolution of the Omicron variants were analyzed.Results:Through high-throughput sequencing, the whole-genome sequences of SARS-CoV-2 were obtained from 120 cases, which accounted for 25.64% (120/468) of all COVID-19 cases in Anyang during the same period. Compared with the genome of Wuhan reference strain (NC_045512.2), there were 57-59 nucleotide mutation sites in the 120 whole genome sequences, and one or two nucleotide mutation sites were added to the shared 57 nucleotide sites. All of the 120 strains were VOC/Omicron (BA.1.1) variants and shared high homology. The whole-genome sequence obtained from the first case A contained 57 nucleotide mutation sites, while apart from the 57 identical nucleotide mutation sites, one specific mutation site (C1594T) was found in the whole-genome sequence obtained from the first case B, suggesting that the two cases were in the same transmission chain. After comparing with the database of domestic and imported cases by the Chinese Center for Disease Control and Prevention and the Henan Provincial Center for Disease Control and Prevention, it was found that the current outbreak was linked with the same transmission chain as the existing local epidemics in other provinces. Moreover, epidemiological investigation showed that on January 2, case A had come into contact with her cousin and his family who returned from an affected area outside the province.Conclusions:Based on the gene sequencing results and epidemiological investigation, the COVID-19 outbreak in Anyang city, Henan Province was a local epidemic and the source of it was a college student who returned to Anyang city from other province on December 28, 2021. These infections were linked to the same transmission chain as the existing local infection in other provinces.

Objective:To report the first case of sever fever with thrombocytopenia syndrome caused by severe fever with thrombocytopenia syndrome virus (SFTSV) in Puyang city, and to study the epidemiological and molecular characteristics of S, M, L fragments of the SFTSV isolate.Methods:The epidemiological characteristics of this case was analyzed with epidemiological methods. SFTSV was isolated from the patient′s serum sample. Nucleic acid of SFTSV was extracted and detected by fluorescent RT-PCR. A multiplex PCR method was constructed to amplify the nucleic acid sequence of the virus. whole-genome sequencing was performed on the next-generation sequencing platform. MEGA11 and DNAStar was used for homology analysis and a phylogenetic tree was constructed.Results:Epidemiological investigation showed that the patient and his close contacts had no history of travel or tick bite within 14 d, but had a history of fieldwork. The patient′s serum sample was positive for SFTSV nucleic acid. Genetic analysis showed that the S, M, L gene fragments of the first SFTSV isolate in Puyang belonged to genotype E. This isolate shared 94.8%-99.6%, 94.0%-99.8% and 95.7%-99.7% nucleotide sequence homology with the representative strains acquired from GeneBank in S, M, L gene fragments, respectively.Conclusions:This case was the first case of SFTSV-caused severe fever with thrombocytopenia syndrome in Puyang. The SFTSV isolate shared a close homology with domestic isolates, but its genotype was significantly different from the SFTSV strains isolated in Henan in recent years, indicating that it might an imported case from other places in Henan Province or Hubei Province. Disease monitoring and professional training for medical personnel should be strengthened and more attention should be paid to the evolution and mutation of SFTSV.

Objective:To analyze the epidemiological characteristics and spatiotemporal characteristics of human brucellosis in Henan Province.Methods:Data of human brucellosis in Henan Province from 2005 to 2021 were collected through the China Disease Prevention and Control Information System, and a descriptive epidemiological method was used to analyze the epidemic profile of brucellosis in Henan Province and the three distribution characteristics. Global and local spatial autocorrelation were used to analyze the spatial distribution and the hot spots of brucellosis in Henan Province, respectively, and spatiotemporal scanning was used to analyze the spatiotemporal clustering regions of brucellosis in Henan Province.Results:A total of 39 862 brucellosis cases were reported in Henan Province from 2005 to 2021, with an average annual incidence of 2.44/100 000, and the number of cases showed an overall increasing trend each year (χ 2trend = 11 127.85, P = 0.001). The onset months were mainly concentrated from March to July, accounting for 59.00% (23 517/39 862), with May as the peak (5 478 cases). Cases of brucellosis were reported in 157 counties (cities, districts) of the province. The ratio of male to female was 2.52∶1.00 (28 542/11 320). Farmers were the main occupation, with 32 985 cases (82.75%). The age of onset was mainly 45 to 65 years old, with 20 226 cases (50.74%). The global spatial autocorrelation analysis showed that the global Moran's I was > 0, Z > 1.96, and P < 0.05 in all years except 2006 - 2008, showing spatial clustering. Further local spatial autocorrelation analysis was performed, and high-high and low-low clustering areas existed in 2012 - 2021 ( P < 0.01). Spatiotemporal scanning analysis showed that there was one spatiotemporal cluster in the high incidence area and two spatiotemporal clusters in the low incidence area. The high incidence cluster was centered in Neixiang County, covering 48 counties (cities, districts) including Song County and Ruzhou City, and the aggregation time was from 2014 to 2021. The two low incidence clusters were centered in Yongcheng City and Boai County, covering 58 and 18 counties (cities, districts), respectively, and the aggregation time was 2016 - 2021 and 2005 - 2012, respectively. Conclusion:The overall incidence of brucellosis in Henan Province is on the rise from 2005 to 2021, with middle-aged and elderly male farmers as the main affected population, and there are spatiotemporal clusters of brucellosis in Henan Province.

Objective:To analyze and summarize the epidemiological and molecular characteristics of SARS-CoV-2 Delta variant, a variant of concern (VOC), in Henan Province in 2021 in order to provide a basis for epidemic prevention and control.Methods:According to the feedback of sequencing results from Chinese Center for Disease Control and Prevention, 111 patients infected with SARS-CoV-2 Delta VOC were selected from the Henan imported and local cases in 2021. Basic patient information was obtained from the pandemic website. The differences in age, gender, vaccination history, the number of vaccine doses and different clinical types were analyzed. Moreover, the differences in RT-qPCR results of ORF1 ab gene and N gene Ct values between cases of different genders and symptoms were analyzed statistically. Sequencing results of the nucleotide and S protein mutation sites were analyzed. Results:There was no significant difference in the gender distribution of 111 cases between different age groups (χ 2=2.217, P=0.529). There was also no significant difference in clinical types between patients with different vaccination history (χ 2=12.074, P=0.209). The Ct values of most SARS-CoV-2 nucleic acid-positive specimens were distributed in the lower range and the viral loads were higher. The difference in the Ct value of ORF1 ab gene between different gender groups was not statistically significant (χ 2=1.646, P=0.439), but were significantly different among asymptomatic, mild, normal, and severe cases (χ 2=13.257, P=0.039). There was no significant difference in N gene Ct value among cases of different genders or different symptoms (all P>0.05). The 111 patients in this study were mainly found through close-contact screening and full-staff nucleic acid screening and accounted for 62.2% (69 cases) of the total. The sequencing length coverage was basically greater than 99% (accounting for 90.1%, 100/111); the total number of nucleotide mutation sites was mostly in the range of 46-50 (86.4%, 89/103); the total number of S protein mutation sites was mostly 12 (82.5%, 85/103). The 103 Delta mutants all contained nine mutation sites, which were T19R, R158G, L452R, T478K, D614G, P681R, D950N, E156del and F157del, with a mutation rate of 100%. Conclusions:People were highly susceptible to the SARS-CoV-2 Delta in Henan Province in 2021. High viral load and increase in the ORF1 ab gene load would aggravate the clinical symptoms.

Objective:To analyze the genome characteristics and variations in nucleotides and amino acids of SARS-CoV-2 causing an outbreak in Henan Province in November 2021 and perform the traceability analysis.Methods:In this study, throat swab specimens from cases in the acute phase were collected and tested for the nucleic acids of SARS-CoV-2 by real-time fluorescent RT-PCR. SARS-CoV-2 nucleic acid-positive samples were subjected to high-throughput genome sequencing and whole-genome alignment analysis.Results:The median Ct values of ORF1ab gene and N gene in 70 positive specimens was 26.41 (15.58 to 39.27) and 24.43 (12.04 to 39.74), respectively. Compared with the sequence of Wuhan-Hu(NC_045512) reference strain, 47 to 49 nucleotide mutations sharing 47 nucleotide mutation and 41 amino acid mutations were found in 63 strains of successfully sequenced SARS-CoV-2. Nine nucleotide mutations and 12 amino acid mutations were found in the spike protein. The index case shared 47 mutations with the Russian imported cases in Henan Province on October 14 and the local cases in Jiangxi Province in October. Moreover, their genomes were highly homologous and they all belonged to the Delta variant (AY.122 evolutionary branch).Conclusions:Continuous monitoring of imported COVID-19 cases and prolonging the period of quarantine were needed to reduce the risk of local outbreak and epidemic caused by imported COVID-19 cases. Analysis of the genomic characteristics of SARS-CoV-2 and the variations in nucleotides and amino acids was conducive to trace the origin of COVID-19 outbreak quickly and provide reference for precise control.