Longitudinal clinical and radiographic evaluation reveals interleukin-6 as an indicator of persistent pulmonary injury in COVID-19.

Rationale: Previous studies of coronavirus disease 2019 (COVID-19) were mainly focused on cross-sectional analysis. In this study, we sought to evaluate the dynamic changes of immunological and radiographic features, and the association with the outcome of pulmonary lesions in COVID-19 patients. Methods: Peripheral blood samples and radiographic data were collected longitudinally for up to 8 weeks from 158 laboratory-confirmed COVID-19 patients. The chest computed tomography (CT) scans were scored based on a semi-quantification assessment according to the extent of pulmonary abnormalities; the temporal change of the immunological and radiographic features was analyzed. Results: Compared with mild and moderate patients, severe patients had significantly decreased counts of lymphocytes, CD4+ T cells, CD8+ T cells, and CD19+ B cells but dramatically elevated counts of neutrophils and levels of interleukin (IL)-6. Sequential monitoring showed a sustained increase in lymphocytes counts and significantly decreased levels of IL-6 in severe patients during the disease course. Notably, patients with persistent pulmonary lesions (CT score ≥ 5 in week 8) showed high levels of IL-6 during the follow-up period, compared with those with recovery lesions (CT score < 5 in week 8). More importantly, the peak expression of IL-6 prior to the aggravated lung injury was mainly found in patients with persistent lesions, and multivariate analysis showed that IL-6 level upon admission was an independent factor associated with the persistent pulmonary injury. Conclusion: Prolonged elevation of IL-6 is associated with persistent pulmonary lesions in COVID-19 patients. Sequential monitoring and timely intervention of IL-6 may favor the clinical management of COVID-19.

Naturally occurring antiviral drug resistance in HIV patients who are mono-infected or co-infected with HBV or HCV in China.

Drug resistance mutations (DRMs) may reduce the efficacy of antiviral therapy. However, the studies focused on naturally occurring, pre-existing DRMs among co-infected patients in China are limited. To investigate DRMs prevalence in treatment-naïve human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) mono- and co-infected patients in China, a total of 570 patients were recruited for this study. DRMs sequences were amplified and successfully sequenced in 481 of these patients, who were grouped into three cohorts: (i) The HBV cohort included 100 HIV/HBV co-infected and 110 HBV mono-infected patients who were sequenced for HBV; (ii) The HCV cohort included 91 patients who were HIV/HCV co-infected and 72 who were HCV mono-infected for HCV sequencing; and (iii) The HIV cohort included 39 HIV mono-infected, 22 HIV/HCV, and 47 HIV/HBV co-infected patients for HIV sequencing. Next-generation sequencing and Sanger sequencing were used in this study. The results showed that in the HCV cohort, HCV genotypes 6a (P < 0.001) and 3b (P = 0.004) were more prevalent in HIV/HCV co-infected patients, however, the prevalence of HBV and HIV genotypes were similar within the HBV and HIV cohorts. HBV DRMs prevalence was significantly higher in HIV/HBV co-infected than HBV mono-infected patients (8.0% vs 0.9%, P = 0.015), whereas HCV and HIV DRMs did not differ within the HCV and HIV cohort (P > 0.05). This study revealed that HBV DRMs were more prevalent in HIV/HBV co-infected patients in China, while DRMs in HCV and HIV patients did not differ. Further dynamic surveillance of DRMs may be needed.

Scorpion Venom Antimicrobial Peptide Derivative BmKn2-T5 Inhibits Enterovirus 71 in the Early Stages of the Viral Life Cycle In Vitro.

Enterovirus 71 (EV71), a typical representative of unenveloped RNA viruses, is the main pathogenic factor responsible for hand, foot, and mouth disease (HFMD) in infants. This disease seriously threatens the health and lives of humans worldwide, especially in the Asia-Pacific region. Numerous animal antimicrobial peptides have been found with protective functions against viruses, bacteria, fungi, parasites, and other pathogens, but there are few studies on the use of scorpion-derived antimicrobial peptides against unenveloped viruses. Here, we investigated the antiviral activities of scorpion venom antimicrobial peptide BmKn2 and five derivatives, finding that BmKn2 and its derivative BmKn2-T5 exhibit a significant inhibitory effect on EV71. Although both peptides exhibit characteristics typical of amphiphilic α-helices in terms of their secondary structure, BmKn2-T5 displayed lower cellular cytotoxicity than BmKn2. BmKn2-T5 was further found to inhibit EV71 in a dose-dependent manner in vitro. Moreover, time-of-drug-addition experiments showed that BmKn2-T5 mainly restricts EV71, but not its virion or replication, at the early stages of the viral cycle. Interestingly, BmKn2-T5 was also found to suppress the replication of the enveloped viruses DENV, ZIKV, and HSV-1 in the early stages of the viral cycle, which suggests they may share a common early infection step with EV71. Together, the results of our study identified that the scorpion-derived antimicrobial peptide BmKn2-T5 showed valuable antiviral properties against EV71 in vitro, but also against other enveloped viruses, making it a potential new candidate therapeutic molecule.

HIV-1 tropism in low-level viral load HIV-1 infections during HAART in Guangdong, China.

Background: Since only a few studies have been conducted on the factors associated with different HIV-1 tropisms in low-level viral load HIV-1 infections in China, we investigated the sequences of HIV-1 V3 loop in prevalent HIV-1 subtypes and factors related to HIV-1 tropism and immune recovery in HIV-1 infections after 6 months of highly active antiretroviral therapy (HAART) in Guangdong, China. Methods: Plasma samples with HIV-1 RNA of 400-999 copies/mL were collected. We analyzed the amino acid sequence of the V3 loop by in silico prediction algorithms. Mann-Whitney and Chi-square tests were used for statistical comparison. Furthermore, logistic regression and multiple linear regression were used, respectively, for factors associated with 351 HIV-1 tropism and immune recovery of 67 cases with continued CD4+ T cell count during HAART. Results: There was a lower percentage of HIV-1 R5-tropic virus in CRF01_AE (66.3%) (p < 0.0001) and CRF55_01B (52.6%) (p < 0.0001) compared with both CRF07_BC (96.1%) and CRF08_BC (97.4%), respectively. Compared with the R5-tropic virus, higher proportions of IIe8/Val8, Arg11/Lys11, and Arg18/His18/Lys18 were observed in the X4-tropic virus of CRF01_AE and CRF07_BC (p < 0.0001). The baseline CD4+ T cell count (p < 0.0001) and baseline CD4+ T/CD8+ T ratio (p = 0.0006) of all R5-tropic infections were higher than those in the X4-tropic infection. The baseline CD4+ T cell count (odds ratio [OR] 0.9963, p = 0.0097), CRF07_BC (OR 0.1283, p = 0.0002), and CRF08_BC (OR 0.1124, p = 0.0381) were associated with less HIV-1 X4-tropism. The baseline CD4+ T cell count was a positive factor (p < 0.0001) in the recovery of CD4+ T cell count during HAART. Conclusion: R5-tropism represented the majority in low-level viral load HIV-1 infections receiving HAART for more than 6 months in Guangdong, China. The baseline immune level in the HIV-1 R5-tropic infections was higher than that in the X4-tropic infections. The amino acids of the 8th, 11th, and 18th of the HIV-1 V3 loop were more variable in the X4-tropic HIV-1. CRF01_AE, CRF55_01B, and lower baseline CD4+ T cell count were associated with more HIV-1 X4-tropism. The immune recovery during HAART was positively related to baseline CD4+ T cell count.

Clinical features and predictive factors related to liver injury in SARS-CoV-2 Delta and Omicron variant-infected patients.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants have become the dominant variants worldwide, and studies focused on liver injury in these patients are limited. MATERIALS AND METHODS: In this study, 157 SARS-CoV-2-infected patients were enrolled, including 77 Delta variant-infected patients and 80 Omicron variant-infected patients. Liver injury data and clinical data were summarized and compared between patients infected with the two variants, additionally, patients with or without liver injury were also compared and multivariate analysis was performed to explore the predictive factors related to liver injury in SARS-CoV-2-infected patients. RESULTS: Liver injury was found in 18 (23.4%)/15 (18.8%) in Delta/Omicron variant-infected patients on admission, and 4 (5.2%)/1 (1.3%) in Delta/Omicron variant-infected patients during hospitalization, respectively. The ratios of liver injury did not differ between the two groups ( χ2 = 1.571; P = 0.210). Among these patients, 17 (77.3%) and 12 (75.0%) Delta and Omicron variant-infected patients were considered to be related to SARS-CoV-2 infection, the biomarkers of liver function were mildly elevated, dominated by the parameter of cholangiocyte injury: 76.5% (13/17) and 83.3% (10/12) in Delta and Omicron variant-infected patients, and most of these patients recovered to normal during follow-up. Multivariate analysis showed that male sex [odds ratio (OR), 4.476; 95% confidence interval (CI), 1.235-16.222; P = 0.023] and high levels of peak viral load in the nasopharynx (OR, 3.022; 95% CI, 1.338-6.827; P = 0.008) were independent factors related to liver injury. CONCLUSION: Cholangiocyte injury biomarkers are dominated in Delta and Omicron variant-infected patients, male sex and high levels of peak viral load in the nasopharynx are predictive factors related to liver injury in SARS-CoV-2-infected patients.

Kinetics of Severity Biomarkers and Immunological Features of Methylprednisolone Therapy for Severe COVID-19 Patients.

In contrast to dexamethasone, the clinical efficacy of methylprednisolone (MP) remains controversial, and a systems biology study on its mechanism is lacking. In this study, a total of 38 severe COVID-19 patients were included. The demographics, clinical characteristics, and severity biomarkers including C-reactive protein (CRP), d-dimer, albumin, and Krebs von den Lungen 6 of patients receiving MP (n=26, 40 mg or 80 mg daily for 3-5 days) and supportive therapy (n=12) were compared. Longitudinal measurements of 92 cytokines in MP group from admission to over six months after discharge were performed by multiplex Proximity Extension Assay. The results showed that demographics, baseline clinical characteristics were similar in MP and non-MP groups. No death occurred and the hospital stays between the two groups were similar. Kinetics studies showed that MP was not better than supportive therapy at improving the four severity biomarkers. Cytokines in MP group were characterized by five clusters according to their baseline levels and responses to MP. The immunological feature of severe COVID-19 could be defined by the "core signature" cytokines in cluster 2: MCP-3, IL-6, IFN-γ, and CXCL10, which strongly correlated with each other and CRP, and are involved in cytokine release storm. The "core signature" cytokines were significantly upregulated at baseline and remained markedly elevated after MP treatment. Our work showed a short course of MP therapy could not rapidly improve the immune disorders among severe COVID-19 patients or clinical outcomes, also confirmed "core signature" cytokines, as severity biomarkers similar to CRP, could be applied to evaluate clinical treatment effect.

[Analysis of hepatitis C virus (HCV) subtypes in HIV/HCV co-infected and HCV mono-infected individuals in Guangdong province].

OBJECTIVE: To explore the transmission routes, genotypes/subtypes distribution and genetic character of HCV in HIV/HCV co-infected and HCV mono-infected individuals in Guangdong Province. METHODS: Reverse transcription (RT) nested PCR was performed to amplify the HCV NS5B gene region from 95 HIV/HCV co-infected and 99 HCV mono-infected individuals lived in Guangdong province. The PCR products were then sequenced for HCV subtyping. Genetic analysis was done by MEGA4 software. RESULTS: (1) HIV/HCV co-infected individuals infected HCV mostly through injection drug use (IDU, 78.9%), the HCV subtypes were identified as 6a (53.7%), 3a (17.9%), 1b (15.8%), 3b (11.6%) and 1a (1.0%) respectively, the genetic distance within subtype 1b was longer than those within other subtypes, the predominant HCV subtype in HIV/HCV co-infected individuals infected through IDU was 6a (60.0%). (2) HCV mono-infected individuals infected HCV mostly through blood or blood products transfusions (80.8%), the HCV subtypes were identified as 1b (67.7%), 6a (17.2%), 3a (6.1%), 2a (5.0%), 3b (2.0%), 4a (1.0%) and 5a (1.0%) respectively, the genetic distance within subtype 1b was also longer than those within other subtypes, the predominant HCV subtype in HCV mono-infected individuals infected through blood or blood products transfusions was 1b (76.2%). CONCLUSION: The diversity of HCV subtypes in HIV/HCV co-infected and HCV mono-infected individuals in Guangdong Province was high, both the major transmission route and HCV subtype between HIV/HCV co-infected individuals and HCV mono-infected individuals were different.

Absence of Integrase Inhibitor-Associated Resistance Among Antiretroviral Therapy-Naïve HIV-1-Infected Adults in Guangdong Province, China, in 2018.

BACKGROUND: Antiretroviral therapy (ART) containing an integrase strand transfer inhibitor (INSTI) plus two nucleoside reverse-transcriptase inhibitors has been recommended as a first-line regimen for ART-naïve HIV-1-infected patients in the latest Chinese Guidelines for Diagnosis and Treatment of HIV/AIDS. OBJECTIVE: To determine the prevalence of INSTI-related mutations among ART-naïve HIV-1-infected adults in Guangdong, China, in 2018. METHODS: The entire integrase gene was amplified from blood plasma. Demographic and epidemiological information was collected. INSTI mutations and antiretroviral susceptibility were interpreted using the Stanford University HIV Drug Resistance Database HIVdb program. RESULTS: Of 927 samples, 827 integrase sequences were successfully obtained. Among them, no major resistance mutations to INSTIs were identified, and four accessory mutations, including T97A (0.12%, 1/827), A128T (0.24%, 2/827), E157Q (0.85%, 7/827), and G163R (0.24%, 2/827), were found in twelve individuals. Two patient samples contained the G163R mutation conferring low-level resistance to elvitegravir and raltegravir. CONCLUSION: The overall prevalence of INSTI mutations remains low. Drug resistance mutation testing for the detection of INSTI drug resistance mutations in HIV treatment-naïve patients should be considered due to the circulation of polymorphisms contributing to INSTI resistance and the expected increasing use of this class of drugs.

Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity.

The novel coronavirus (2019-nCoV) infection caused pneumonia. we retrospectively analyzed the virus presence in the pharyngeal swab, blood, and the anal swab detected by real-time PCR in the clinical lab. Unexpectedly, the 2109-nCoV RNA was readily detected in the blood (6 of 57 patients) and the anal swabs (11 of 28 patients). Importantly, all of the 6 patients with detectable viral RNA in the blood cohort progressed to severe symptom stage, indicating a strong correlation of serum viral RNA with the disease severity (p-value = 0.0001). Meanwhile, 8 of the 11 patients with annal swab virus-positive was in severe clinical stage. However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Altogether, our results confirmed the presence of virus RNA in extra-pulmonary sites.

Author Correction: Temporal dynamics in viral shedding and transmissibility of COVID-19.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Temporal dynamics in viral shedding and transmissibility of COVID-19.

We report temporal patterns of viral shedding in 94 patients with laboratory-confirmed COVID-19 and modeled COVID-19 infectiousness profiles from a separate sample of 77 infector-infectee transmission pairs. We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset. We estimated that 44% (95% confidence interval, 25-69%) of secondary cases were infected during the index cases' presymptomatic stage, in settings with substantial household clustering, active case finding and quarantine outside the home. Disease control measures should be adjusted to account for probable substantial presymptomatic transmission.

Changing Epidemiology of Hepatitis C Virus Genotype among Patients with Human Immunodeficiency Virus/Hepatitis C Virus Co-Infection in China.

BACKGROUND: Co-infection with hepatitis C virus (HCV) has become the most common cause of death in human immunodeficiency virus (HIV) infected patients on antiretroviral therapy. The distribution of HCV genotypes varies with geographical regions and time, and limited studies have focused on the HCV genotype in HIV/HCV co-infection. METHODS: The distribution of HCV genotypes was evaluated in 414 patients with HIV/HCV co-infection in three regions (South, Central and Northwest) of China from 2008 to 2010. The NS5B region of HCV was characterized using nested reverse transcription polymerase chain reaction. Nucleotide sequences obtained were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. RESULTS: Genotype 3 was the most prevalent HCV strain (36.2%), followed by genotype 6 (30.0%), genotype 1 (28.5%), genotype 2 (5.1%), and genotype 5 (0.2%). The distribution varied geographically. Genotype 6 (37.6%) was the predominant strain while genotype 1 (20.2%) was less common in the South compared to the Central and Northwest regions (all P < 0.001). The distribution also varied temporally. There was no significant difference in genotype distribution in Guangdong (a province in the South region), between patient cohorts from 2005-2008 and 2009-2010. However, outside Guangdong, genotypes 3 and 6a became significantly more prevalent (22.4% vs.42.2%, P< 0.001; 8.0% vs. 19.8%, P = 0.004), and genotype 1 less prevalent (54.4% vs.26.6%, P< 0.001) over time. CONCLUSION: The most dramatic shift in genotypic distribution was the movement of HCV genotypes 3 and 6a outside of Guangdong in HIV/HCV co-infected patients. This movement appeared closely associated with transmission via injected drug use.

Complete Genome Sequence of a Hepatitis D Virus Genotype 1 Strain Isolated in Guangdong, China.

Here, we report the first complete genome sequence of a hepatitis D virus genotype 1 strain, GZ37, isolated in Guangzhou, Guangdong Province, China, in 2014. The sequence information provided here will help us understand the molecular epidemiology of hepatitis D virus and contribute to disease control in mainland China.

Measurement of subgroups of peripheral blood T lymphocytes in patients with severe acute respiratory syndrome and its clinical significance.

OBJECTIVE: To investigate the changes of subgroups of peripheral blood T lymphocytes in patients with severe acute respiratory syndrome (SARS) and its clinical significance. METHODS: Subgroups of blood T lymphocytes in 93 patients with SARS were detected by flow cytometer. The results detected in 64 normal subjects and 50 patients with AIDS served as controls. RESULTS: The numbers of CD(3)(+), CD(4)(+), and CD(8)(+) lymphocytes all significantly decreased in acute phase of patients with SARS [(722 +/- 533)/microliter, (438 +/- 353)/microliter, (307 +/- 217)/microliter] compared with those in normal controls [(1527 +/- 470)/microliter, (787 +/- 257)/microliter, (633 +/- 280)/microliter, all P <0.01], which was different from what we observed in patients with AIDS who had decreased CD(4)(+) [(296 +/- 298)/microliter] but increased CD(8)(+) [(818 +/- 566)/microliter] counts. The counts of CD(3)(+), CD(4)(+), and CD(8)(+) lymphocytes decreased more apparently in patients with severe SARS. All the five patients who died had CD(4)(+) counts less than 200/microliter. As the patients' condition improved, CD(3)(+), CD(4)(+), and CD(8)(+) counts gradually returned to normal ranges. CONCLUSION: The damage of cellular immunity is probably an important mechanism of pathogenesis of SARS.

[Measurement of subsets of blood T lymphocyte in 93 patients with severe acute respiratory syndrome and its clinical significance].

OBJECTIVE: To investigate the changes of subsets of blood T lymphocyte in patients with severe acute respiratory syndrome (SARS) and their clinical significance. METHODS: Subsets of blood T lymphocyte in 93 patients with SARS were detected by flow cytometer. The patients comprised 40 men and 53 women, aged 17 - 88 years (average 44 years). The results detected in 64 normal subjects and 50 patients with AIDS served as controls. RESULTS: The numbers of CD(3)(+), CD(4)(+), and CD(8)(+) lymphocytes all significantly decreased in acute phase of SARS patients compared with those in normal persons. Their findings was different from what we observed in patients with AIDS who had decreased CD(4)(+), but increased CD(8)(+) counts. The counts of CD(3)(+), CD(4)(+), and CD(8)(+) lymphocytes decreased more apparently in patients with critical SARS. All the five patients who died had CD(4)(+) counts less than 200/microl. As the patients' conditions improved, the counts of CD(3)(+), CD(4)(+), and CD(8)(+) gradually returned to normal. CONCLUSION: The patients with SARS were found having damage of cellular immunity markedly.

[Analysis of death causes of 345 cases with HIV/AIDS in Guangdong area].

OBJECTIVE: To analyze the death causes of 345 cases with HIV/AIDS in Guangdong area. METHODS: The situations of 345 hospitalized death cases with HIV/AIDS were conducted by retrospective analysis. RESULTS: (1)There were total 3406 hospitalized cases with HIV/AIDS in a hospital from January 2001 to December 2011 and 345 cases died, the fatality rate was 10. 13%. Since 2005 the introduction of free anti-viral treatment, the fatality rate of HIV/AIDS declined. The fatality rate of the patients whose CD4+ T lymphocyte counts <200 cells/microl was 14.61% (299/2046) and it was significantly higher than that of patients whose CD4 T lymphocyte counts >or=200 cells/microl (P <0.01). (2) 99.42% of the death cases had more than one kind of opportunistic infections (OI) and there were 924 cases of OI totally. 84. 64% of OI related to the death directly. Fungal infection was the most common in OI, followed by bacterial infection. Most OI occurred in the lungs, mouth, other systemic disseminated diseases, gastrointestine, central nerver system, septicemia, skin. The AIDS defining opportunistic infections such as several pneumonia, disseminated penicilliosis marneffei and CNS infections accounted for 29.65%. Other factors that caused HIV/AIDS death included opportunistic tumors, HIV related disease and non AIDS-related disease accounted for 15.36%. No accepted effective highly active antiretroviral therapy (HARRT) also constituted factors of death. Among cases which accepted HARRT treatment, only 6.96% had the period of treatment over three months. CONCLUSION: The fatality rate of end-stage AIDS patients was high and the opportunistic infections was the most important cause of death. Early diagnosis and treatment for opportunistic infections, timely effective HARRT were the key to improve the quality of life of AIDS patients.

[Relationship between psychological distress and T lymphocyte in HIV/AIDS patients].

OBJECTIVE: To explore the relationship between psychological distress and T lymphocyte counts in HIV/AIDS patients. METHODS: A total of 102 HIV/AIDS patients were measured by symptom check list (SCL-90), self-rating depressive scale (SDS) and self-rating anxiety scale (SAS). Patients were divided into 2 groups based on CD4+ T lymphocyte counts < 0.2 x 10(9)/L (group A) and > or = 0.2 x 10(9)/L(group B). RESULTS: 77 cases (75.49%) had psychological problems, including depression, relationship problems, psychosis, force etc. The prevalence of depression and anxiety were 67.65% (69/102) and 43.13% (44/102) respectively. The symptom of depression and anxiety of patients in group A were severer than those in group B (P < 0.05). The CD4+ T lymphocyte counts were significantly negatively correlated with the total score, depression score, paranoid score and psychosis score of SCL-90 (all P <0.05). CONCLUSION: Most of the HIV/AIDS patients were in an obviously abnormal psychological status. The psychological distress symptom of HIV/AIDS patients might had negative effects on the number of CD4+ T lymphocyte.