Genetic characterization of HIV-1 viruses among cases with antiretroviral therapy failure in Suzhou City, China.

BACKGROUND: This retrospective study aimed to characterize the distribution of HIV-1 genotypes and the prevalence of drug resistance mutations in people with antiretroviral treatment (ART) failure in Suzhou City, China. METHODS: Pol gene of HIV-1 viruses in blood samples of EDTA anticoagulants from 398 patients with failed antiviral treatment was successfully amplified by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system ( https://hivdb.stanford.edu/hivdb/by-mutations/ ). HIV-1 genotypes were determined by the REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv ). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method. RESULTS: Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in cases with ART failure was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identified, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C. CONCLUSIONS: The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and treatment of people with HIV infection. Treatment regimens for ART failure patients should be adjusted over time based on the outcome of drug resistance tests. NFLG sequencing facilitates the identification of new recombinants of HIV-1.

Real-world data in late presentation of HIV infection in Suzhou, China: Results from four consecutive cross-sectional surveys, 2017-2020.

Objectives: This study aimed to examine the real prevalence of late presentation of HIV infection and to identify factors associated with late HIV presentation among patients with newly diagnosed HIV/AIDS in Suzhou, China. Methods: Patients with newly diagnosed HIV/AIDS who registered in national AIDS surveillance system from 2017 to 2020 were included in this study. Late presentation (LP) of HIV infection was defined as HIV diagnosis with a CD4 count < 350 cells/µL or an AIDS-defining event. Multivariable logistic regression analyses were used to identify factors associated with LP. Results: A total of 2,300 patients were enrolled. 1,325 were classified as late presenters, showing a high percentage of 57.6% (95% CI: 54.5-60.7%) and a rise (P = 0.004) over the four-year period. Patients with newly diagnosed HIV/AIDS who were older than 24 years of age (aOR = 1.549, P = 0.001 for 25-39 years; aOR = 2.389, P < 0.001 for 40 years and older), were Suzhou registered residents (aOR = 1.259, P = 0.026), and were from inpatient and outpatient (aOR = 1.935, P < 0.001) were more likely to be late presentation. Conclusions: This study showed a high percentage and a rise of late presentation of HIV infection among patients with newly diagnosed HIV/AIDS in Suzhou, China, which is a challenge for future prevention and control of AIDS. Targeted measures should be urgently implemented to reduce late HIV diagnosis.

A fatal paediatric case infected with reassortant avian influenza A(H5N6) virus in Eastern China.

Avian influenza A(H5N6) keeps evolving, causing outbreaks in birds and sporadic infections in human. Here, we report a fatal paediatric infection caused by a novel reassortant H5N6 virus. The patient was an obese 9-year-old girl. She initiated with fever and cough, then developed pneumonia, acute respiratory distress syndrome (ARDS) and respiratory failure. Lower respiratory tract aspirates and anal swabs were serially taken till the patient's death. Viral isolation, genome sequencing and phylogenetic analysis were conducted. A novel reassortant H5N6 virus was isolated from the patient. Except the PA gene, all other 7 genes of the virus belonged to H5N6 genotype A (S4-like virus). The PA gene was probably obtained from Eurasian waterfowl influenza viruses. The H5N6 virus was consistently detected from the patient's respiratory samples till the 17th day after symptom onset, but not from anal swabs or urine sample by real-time reverse transcription polymerase chain reaction (RT-PCR). Significantly elevated (32-fold) serum antibodies to H5N6 virus were observed during the patient's course of disease. Aside from the identified novel reassortant H5N6 viral strain, obesity, delayed confirmation of aetiology and specific antiviral treatment, and prolonged virus shedding could have contributed to the poor clinical outcome.

Genetic Characterization of a Novel Reassortant H5N6 Avian Influenza Virus Identified from a 10-Year-Old Girl.

A 10-year-old girl was confirmed, by laboratory tests, to be infected with the H5N6 subtype of the highly pathogenic avian influenza virus in Suzhou city in November, 2018 (JSSZ01). The hemagglutinin (HA) gene of this H5N6 virus belonged to the 2.3.4.4 H5 clade, and the HA linkage peptide of the JSSZ01 strain was RERRRKR↓GLF with multiple basic amino acids. Q226L and G228S mutations were not observed, but S128P, S137A, and T160A substitutions were identified in the receptor binding sites. The resistance mutation D198N in the neuraminidase (NA) protein was also identified in this strain. Additionally, an 11 amino acid (AA positions 59-69) deletion was identified in the NA stalk region. Most genes of JSSZ01 exhibited highest identity with previously characterized H5N6 viruses, but its PA segment sequence was highly similar to previously identified avian H3 viruses (Accession Number: EPI596567 or EPI590058), indicating that JSSZ01 may be created by gene reassortment.

The fifth influenza A(H7N9) epidemic: A family cluster of infection in Suzhou city of China, 2016.

OBJECTIVE: Influenza A(H7N9) virus is known for its high pathogenicity in human. A family cluster of influenza A(H7N9) virus infection was identified in Suzhou, China. This study aimed to investigate the possibility of human-to-human transmission of the virus and examine the virologic features of this family cluster. METHODS: The clinical and epidemiologic data of two patients in the family cluster of influenza A(H7N9) virus infection were collected. Viral RNA in samples derived from the two patients, their close contacts, and the environments with likely influenza A(H7N9) virus transmission were tested by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay. Hemagglutination inhibition (HI) assay was used to detect virus-specific antibodies. Genetic sequencing and phylogenetic analysis were also performed. RESULTS: The index patient (Case 1), a 66-year old man, was virologically diagnosed with influenza A(H7N9) virus infection 12days after experiencing influenza-like symptoms, then died of multi-organ failure. His 39-year old daughter (Case 2), denying any other exposure to influenza A(H7N9) virus, became infected with influenza A(H7N9) virus following taking care of her father during his illness. Sequencing viral genomes isolated from the two patients showed nearly identical nucleotide sequence, and genetically resembled the viral genome isolated from a chicken in the wet market where the index patient once visited. All three influenza A(H7N9) viruses shared S138A, G186V, Q226L mutations in HA (H3) protein and a single basic amino acid (PEIPKGR↓G) at the cleavage site. CONCLUSIONS: Human-to-human transmission of influenza A(H7N9) virus most likely occurred in this household. The three-amino-acid mutations in HA protein were discovered in this study, which might have increased the binding affinity of influenza A(H7N9) virus to the receptor on trachea epithelial cells to facilitate viral transmission among humans.

Epidemiological and genetic characteristics of the fifth avian influenza A(H7N9) wave in Suzhou, China, from October 2016 to April 2017.

Human infections with H7N9 viruses can cause severe pneumonia and even death. To characterize the epidemiology and genetics of the H7N9 viruses circulating during from October 2016 to April 2017 in Suzhou, China, all pharyngeal swab samples were collected from severe acute respiratory infections (SARI) cases during this fifth wave of infection, and we amplified the H7N9 H7 and N9 genes using a real-time polymerase chain reaction (PCR). Positive samples were subjected to virus isolation and gene sequencing to analyze the evolution and variation of the H7N9 strains. The epidemiological features of H7N9 patients have not changed and there were no significant mutations in the key sites of the hemagglutinin (HA) gene sequence, but we identified the K526R and E627 K substitutions in the PB2 protein. In the neuraminidase (NA) protein, drug-resistant mutations (R294 K and H276Y) occurred in a few strains. Most of the H7N9 viruses isolated from Suzhou had no drug resistance mutations, but it is necessary to closely monitor and analyze the probable emergence of mutations and the spread of resistant strains. The reduction of the N-glycosylation site at position 42 of NA was observed in some strains.

Impact of food choice on sodium intake patterns from multiple NHANES surveys.

To examine how the food consumption from various food groups would impact American adults' sodium intake and whether this impact structurally changes over time, data were obtained from six-cycle National Health and Nutrition Examination Survey (NHANES) 1999-2010. Foods were categorized by the first two digits of the USDA food code. Regression models were employed to investigate the associations between the consumption of each food group and sodium intake, and whether there were changes in the associations in consecutive six cycles. Results show that the calorie consumption of oils, beverages and water, fruit juices, fruits, lamb, fruit products, and sugars and sweets had no significant impact on individuals' sodium intake, while calorie consumption of tomatoes, fish, dark-green vegetables, and crackers contributes the most to sodium intake. The contribution to sodium intake of most food groups does not change significantly over time, with the exception of salad dressing whose contribution to sodium intake increased in four consecutive years when compared to that of 1999-2000. The sodium amount contributed by one calorie consumption (sodium density) of most food was above the daily recommendation level, 1.2 mg per calorie per day. Lowering individuals' sodium intake involves either guiding individuals to consume more fruit related products or decreasing the amount of sodium in most food groups at the production or food preparation stages.

[Sequence analysis of G glycoprotein gene of human respiratory syncytial virus].

OBJECTIVE: To understand the variation of G glycoprotein gene of human respiratory syncytial virus (HRSV) obtained from Sichuan in 2010 and determine the dominant genotypes. METHODS: G glycoprotein gene of seven cases of subtype A and eleven cases of subtype B of HRSV were amplified by RT-PCR and sequenced. The phylogenetic trees were constructed to determine the subtype of samples. And then, the genetic variations of the second hypervariable region of G glycoprotein gene were studied. RESULTS: The nucleotide genetic distances of G glycoprotein gene in subtype A and subtype B HRSV were 0.022 +/- 0.005 and 0.073 +/- 0.010, respectively. Transitions were more prevalent than transversions, GA -AG were the most frequent transitions detected among group A viruses, while UC+CU transitions were the most among group B. Phylogenetic analyses demonstrated that 7 subtype A virus could be clustered into one genotype, genotype GA2, and 11 subtype B virus could be clustered into two genotypes, GB2 and BA. The length of G protein gene in group A was all 298aa, but in group B included 295aa, 312aa and 315aa. Selective pressure was purifying selection in both subtypes. 9 positively selected sites in group A and 1 in group B on the second hypervariable region of G protein were identified. CONCLUSION: GA2, GB2 and BA were the main genotype. The changes may favor virus escape from the host immune response including the variation of the G protein gene length, frequency of nucleotide changes and selective pressure.