Comprehensive analyses reveal the impacts of vaccination status and physiological variables in early infection on viral persistence in COVID-19 patients: a retrospective single-center cohort study

BACKGROUNDViral persistence is a crucial factor that influences the communicability of SARS-CoV-2 infection. However, the impacts of vaccination status and physiological variables on viral RNA shedding have not been adequately clarified. METHODSIn this study, we retrospectively collected the clinical records of 377 hospitalized COVID-19 patients, which contained unvaccinated patients and patients received two doses of an inactivated vaccine or an mRNA vaccine. Firstly, we analyzed the impacts of vaccination on disease severity and viral RNA persistence. Next, to clarify the impacts of physiological variables on viral RNA shedding in COVID-19 patients, we retrieved 49 laboratory variables and analyzed their correlations with the duration of viral RNA shedding. Finally, we established a multivariate regression model to predict the duration of viral RNA shedding. RESULTSOur results showed that both inactivated and mRNA vaccines significantly reduced the rate of moderate cases, while the vaccine related shortening of viral RNA shedding were only observed in moderate patients. Correlation analysis showed that 10 significant laboratory variables were shared by the unvaccinated mild patients and mild patients inoculated with an inactivated vaccine, but not by the mild patients inoculated with an mRNA vaccine. Moreover, we demonstrated that a multivariate regression model established based on the variables correlating with viral persistence in unvaccinated mild patients could predict the duration of viral shedding for all groups of patients. CONCLUSIONSVaccination contributed limitedly to the clearance viral RNA in COVID-19 patients. While, laboratory variables in early infection could predict the persistence of viral RNA.

Omicron booster in ancestral strain vaccinated mouse augments protective immunities against both the Delta and Omicron variants

A booster vaccination is called for constraining the evolving epidemic of SARS-CoV-2. However, the necessity of a new COVID-19 vaccine is currently unclear. To compare the effect of an Omicron-matched S DNA vaccine and an ancestral S DNA vaccine in boosting cross-reactive immunities, we firstly immunized mice with two-dose of a DNA vaccine encoding the spike protein of the ancestral Wuhan strain. Then the mice were boosted with DNA vaccines encoding spike proteins of either the Wuhan strain or the Omicron variant. Specific antibody and T cell responses were measured at 4 weeks post boost. Our data showed that the Omicron-matched vaccine efficiently boosted RBD binding antibody and neutralizing antibody responses against both the Delta and the Omicron variants. Of note, antibody responses against the Omicron variant elicited by the Omicron-matched vaccine were much stronger than those induced by the ancestral S DNA vaccine. Meanwhile, CD8+ T cell responses against both the ancestral Wuhan strain and the Omicron strain also tended to be higher in mice boosted by the Omicron-matched vaccine than those in mice boosted with the ancestral S DNA vaccine, albeit no significant difference was observed. Our findings suggest that an Omicron-matched vaccine is preferred for boosting cross-reactive immunities.

Immunogenicity and safety of an inactivated SARS-CoV-2 vaccine in people living with HIV-1

BackgroundIt has been proven that inactivated COVID-19 vaccines are safe and effective in general population with intact immunity. However, their safety and immunogenicity have not been demonstrated in people living with HIV (PLWH). Methods42 HIV-1 infected individuals who were stable on cART and 28 healthy individuals were enrolled in this study. Two doses of an inactivated COVID-19 vaccine (BIBP-CorV) were given 4 weeks apart. The safety and reactogenicity of the vaccine were evaluated by observing clinical adverse events and solicited local and systemic reactions. Humoral responses were measured by anti-spike IgG ELISA and surrogate neutralization assays. Cell-mediated immune responses and vaccine induced T cell activation were measured by flow cytometry. FindingsAll the HIV-1 infected participants had a CD4+ T cell count of above 200 cells/L both at baseline and 4 weeks after vaccination. No solicited adverse reaction was observed among all participants. Similar binding antibody, neutralizing antibody and S protein specific T cell responses were elicited in PLWH and healthy individuals. Further analyses showed that PLWH with low baseline CD4+/CD8+ T cell ratios (<0{middle dot}6) generated lower antibody responses after vaccination than PLWH with medium (0{middle dot}6[~]1{middle dot}0) or high ([≥]1{middle dot}0) baseline CD4+/CD8+ T cell ratios (P<0{middle dot}01). The CD3+, CD4+ and CD8+ T cell counts of PLWH decreased significantly after vaccination, but it did not lead to any adverse clinical manifestation. Moreover, we found that the general burden of HIV-1 among the PLWH cohort decreased significantly (P=0{middle dot}0192) after vaccination. And the alteration of HIV-1 viral load was not significantly associated with the vaccine induced CD4+ T cell activation. InterpretationOur data demonstrate that the inactivated COVID-19 vaccine is safe and immunogenic in PLWH who are stable on cART with unsuppressed CD4 counts. FundingThis work was funded by the National Natural Science Foundation of China (Grant No. 81971559, 82041010). Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThe safety and efficacy of inactivated COVID-19 vaccines have been validated in general population with intact immunity. However, their safety and immunogenicity have not been demonstrated in people living with HIV (PLWH). Added value of this studyOur study provides the first evidence to show humoral and cellular immune responses to an inactivated vaccine in PLWH who have been stable on cART with good CD4 cell counts. We found that participants with HIV-1 generated antibody and T cell responses comparable with those of healthy individuals after two-dose vaccination. The baseline CD4/CD8 ratios while not the absolute CD4+ T cell counts were shown to be associated with the magnitudes of vaccine induced antibody responses. Moreover, we showed that the vaccine induced T cell activation did not increase the viral burden in PLWH on cART. On the contrary, the levels of plasma HIV-1 RNA decreased among a significant percentage of PLWH. Implications of all the available evidenceOur data demonstrate that the inactivated COVID-19 vaccine is safe and immunogenic in PLWH who are stable on cART with unsuppressed CD4 counts and indicate that this vaccine might be protective and efficacious against COVID-19 for people with HIV.

Pre-existing antibodies targeting a dominant linear antibody epitope on SARS-CoV-2 S2 cross-reacted with commensal gut bacteria and shaped immune responses elicited by a candidate vaccine

The origins of pre-existing SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the pre-existing S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by pre-existing antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we proved that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 specific monoclonal antibodies were isolated from naive SPF mice and proved to cross-react with commensal gut bacteria collected from both human and mouse. Mice with high levels of pre-existing S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of pre-existing S2 and P144 reactive antibodies correlated positively with RBD specific binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Finally, we provided data demonstrating that immunization of a SARS-CoV-2 S DNA vaccine could alter the gut microbiota compositions of mice.

Prevalence of toxoplasma, rubella virus, cytomegalovirus and herpes simplex virus infections among 3084 individuals with childbearing-age in Henan province / 中华临床感染病杂志

Objective To investigate the prevalence of toxoplasma gondii (Tox),rubella virus (RV),cytomegalovirus (CMV) and herpes simplex virus (HSV) infections (TORCH infections) among childbearing-age population in Henan province.Methods Enzyme-linked immunosorbent assay (ELISA) was applied to detect plasma TORCH IgM and IgG among 3084 childbearing-age men and women from theFirst Affiliated Hospital of Zhengzhou University during July and September,2011.The positive rates of anti-TORCH antibodies were compared among the various age and gender groups by x2 test.Results The total positive rate of anti-TORCH IgM was 5.5％ (170/3084),in which the positive rate of anti-RV IgM was the highest (2.9％),followed by anti-HSV IgM (1.0％).Within positive rate of anti-TORCH IgG,anti-HSV IgG was the highest (90.4％),followed by anti-CMV IgG (89.7％),RV IgG (48.1％) and Tox IgG (0.7％).The positive rate of anti-TORCH IgM was the lowest in individuals aged ＞ 30-40 year old.With the age increasing,the positive rates of anti-Tox IgG,anti-CMV IgG and anti-HSV IgG increased,but the positive rate of anti-RV IgG decreased.Women had higher positive rates of anti-CMV IgG and antiHSV IgG than men (x2 =83.470 and 7.026,P ＜ 0.O1).Conclusions Current infection of TORCH exists in childbearing-age population of Henan province,and the positive rate of anti-RV IgG is low.It is recommended to screen for TORCH infection in childbearing-age men and women.

The prevalence and dynamics of human immunodeficiency virus-1 subtypes among men who have sex with men in Beijing / 中华传染病杂志

Objective To investigate the subtype distribution and changing trend of human immunodeficiency virus (HIV)-1 strains among men who have sex with men (MSM) during 2005-2011 in Beijing.Methods Five serial cross-sectional surveys of MSM were conducted in the year of 2005-2006,2007,2008,2009,and 2010-2011 in Chaoyang district of Beijing.Whole blood samples were collected and then RNA was extracted.HIV-1 gag gene was characterized by reverse transcriptase and nested polymerase chain reaction (RT-PCR) amplification,DNA sequencing,and phylogenetic analysis of viral sequences to determine the HIV-1 subtypes.Results Phylogenetic analysis of the sequences revealed that the predominant subtypes of HIV-1 gag gene included subtype B,CRF01_AE and CRF07_BC.And CRF15_01B was detected from the year of 2008.In addition,significant changes of the distributions of subtypes and CRFs occurred from 2005 to 2011 in HIV+ MSM.Subtype B showed a significant decreased trend,while the proportions of CRF01 _AE and CRF07_BC significantly increased in the 7-year period,particularly that of CRF01_AE.Conclusions The substantial changes are observed in the diversity of HIV-1 strains circulating among MSM in Beijing during a 7-year period.

Cross-genome HIV-specific cytotoxic T-lymphocyte responses among HIV-1 infected individuals with varied infection time and routes / 中华检验医学杂志

Objective To investigate and compare the features of the HIV-1-specific CTL responses among three HIV-infected groups with varied infection history. Methods Three HIV-infeeted groups were enrolled in this study, including two groups infected by blood transmission (one group has been infected for more than 10 years and the other for 1-2 years) and one group of the man who have sex with man. The HIV-1-specific CTL responses were quantified by an IFN-γ based ELISPot assay with a peptide matrix system containing overlapping peptides spanning the entire HIV-1 Clade B genomic consensus sequences. Results The responding rate of CTL responses against all 17 peptide pools among the group that infected 1-2 years,the group infected more than 10 years and the group of MSM were 40% ,65% ,23%. One way ANOVO analysis showed that the responding rate of CTL responses against all 17 peptide pools were statistical significant among the three groups (F=19.96, P＜0.01);the magnitude of CTL responses of the three groups were 0-5 835 SFCs/106 PBMC, 0-7 225 SFCs/106PBMC, 0-9 740SFCs/106pBMC, Kruskal-Wallis test showed that the magnitude of CTL responses were statistical significant among the three groups( H = 101.90 , P ＜0.01);the breadth of CTL were 7 ( 2-11 ), 11(9-14) and 4 (2-6) respectively and Kruskal- Wallis test showed that the breadth of CTL had no statistical significant among the three groups( H = 34. 75 ,P ＜0. 01 ). The sequence of responding rate, magnitude and breadth of CTL from high to low was the group that had been infected for more than 10 years, the group infected 1-2 years and the sex transmission group. The common characteristics of the CTL response among the three groups were that the responding rate and the magnitude of the peptide Nef and Gag was higher than other peptide's. The magnitude of CTL responses among three different CD4count groups (CD4 ＜ 200/μl, CD4 200-500/μl, CD4 ≥500/μl,) was 0-18 475 SFCs/106pBMC, 350-34 095 SFCs/106pBMC, 490-21 550 SFCs/106 PBMC and had no statistic difference among the three different CD4 groups(H=2.93, P=0.23) while the breadth of CTL was 3(0-8), 10(2-17), 10 (1-17)respoctively and the breadth of CTL was lower in the group of CD4 count less than 200/μl than the other two groups( H = 14. 72, P ＜ 0. 01 ). The magnitude of CTL responses among three different viral load (VL)groups (VL＜ LDL, LDL ＜ VL ＜ 1 × 104 copys/ml, VL≥1 ×104 copys/ml) was 490-18 475 SFCs/106pBMC, 0-24 115 SFCs/106pBMC, 770-34 095 SFCs/106 pBMC and had no statistic difference among the three different viral load groups ( H = 0.79, P=0.67) and the breadth of the three different viral load groups CTL was 8( 1-17), 11 (0-17), 8 (1-16) and Kruskal-Wallis test showed that there was no statistic difference among the three different viral load groups (H =5.27, P =0. 07). Conclusions All groups predominantly develope T cell immune responses against Nef and Gag proteins. With the elapse of HIV infection, the CTL responses are increased in both magnitude and responding rate. This information is important for vaccine development.