Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil.

Background: Molecular epidemiology techniques allow us to track the HIV-1 transmission dynamics. Herein, we combined genetic, clinical and epidemiological data collected during routine clinical treatment to evaluate the dynamics and characteristics of transmission clusters of the most prevalent HIV-1 subtypes in the state of São Paulo, Brazil. Methods: This was a cross-sectional study conducted with 2,518 persons living with HIV (PLWH) from 53 cities in São Paulo state between Jan 2004 to Feb 2015. The phylogenetic tree of protease/reverse transcriptase (PR/RT) regions was reconstructed by PhyML and ClusterPicker used to infer the transmission clusters based on Shimodaira-Hasegawa (SH) greater than 90% (phylogenetic support) and genetic distance less than 6%. Results: Of a total of 2,518 sequences, 2,260 were pure subtypes at the PR/RT region, being B (88%), F1 (8.1%), and C (4%). About 21.2% were naïve with a transmitted drug resistance (TDR) rate of 11.8%. A total of 414 (18.3%) of the sequences clustered. These clusters were less evident in subtype B (17.7%) and F1 (15.1%) than in subtype C (40.2%). Clustered sequences were from PLWH at least 5 years younger than non-clustered among subtypes B (p < 0.001) and C (p = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; p < 0.05). The TDR rate in clustered patients was 15.4, 13.6, and 3.1% for subtypes B, F1, and C, respectively. Most of the infections in subtypes B (80%), C (64%), and F1 (59%) occurred within the state of São Paulo. The metropolitan area of São Paulo presented a high level of endogenous clustering for subtypes B and C. The São Paulo city had 46% endogenous clusters of subtype C. Conclusion: Our findings showed that MSM, antiretroviral therapy in Treatment-Naive (ART-naïve) patients, and HIV1-C, played an important role in the HIV epidemic in the São Paulo state. Further studies in transmission clusters are needed to guide the prevention intervention.

Humoral response to spike S1 and S2 and nucleocapsid proteins on microarray after SARS-CoV-2 infection.

Many aspects of the humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as its role in protection after natural infection, are still unclear. We evaluated IgA and IgG response to spike subunits 1 and 2 (S1 and S2) and Nucleocapsid proteins of SARS-COV-2 in serum samples of 109 volunteers with viral RNA detected or seroconversion with different clinical evolution (asymptomatic, mild, moderate, and severe coronavirus disease 2019), using the ViraChip® Test Kit. We observed that the quantification of antibodies to all antigens had a positive correlation to disease severity, which was strongly associated with the presence of comorbidities. Seroreversion was not uncommon even during the short (median of 77 days) observation, occurring in 15% of mild-asymptomatic cases at a median of 55 days for IgG and 46 days for IgA. The time to reach the maximal antibody response did not differ significantly among recovered and deceased volunteers. Our study illustrated the dynamic of anti-S1, anti-N, and anti-S2 IgA and IgG antibodies, and suggests that high production of IgG and IgA does not guarantee protection to disease severity and that functional responses that have been studied by other groups, such as antibody avidity, need further attention.

Inhibition of receptor-binding domain-ACE2 interaction after two doses of Sinovac's CoronaVac or AstraZeneca/Oxford's AZD1222 SARS-CoV-2 vaccines.

Practical laboratory proxies that correlate to vaccine efficacy may facilitate trials, identify nonresponders, and inform about boosting strategies. Among clinical and laboratory markers, assays that evaluate antibodies that inhibit receptor-binding domain (RBD) ligation to angiotensin-converting enzyme-2 receptor (receptor-binding inhibition [RBI]) may provide a surrogate for viral neutralization assays. We evaluated RBI before and after a median of 34 days (interquartile range [IQR]: 33-40) of the second dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Sinovac's CoronaVac (CN) or AstraZeneca/Oxford's AZD1222 (AZ) vaccines in 166 individuals. Both vaccines elicited high inhibitory titers in most subjects, 95% (158/166), with signal inhibition above 30% and 89% (127/143) with more than fourfold increase from prevaccination titers, but titers tend to decrease over time. Both postvaccination inhibitory titers (95%, IQR 85%-97% for AZ vs. 79%, IQR 60%-96% for CN, p = 0.004) and pre/post-titer increase (AZ 76%, IQR 51%-86% for AZ vs. 47%, IQR 24%-67% for CN, p < 0.0001) were higher among AZ vaccinees. Previous serological reactivity due to natural infection was associated with high prevaccination signal inhibition titers. The study documents a robust antibody response capable of interfering with RBD-angiotensin-converting enzyme binding. Evaluation of SARS-CoV-2 infection incidence in these populations is necessary to assess its association to protection and its duration.

Humoral response to spike S1 and S2 and nucleocapsidproteins on microarray after SARS­CoV­2 infection

Many aspects of the humoral immune response to severe acute respiratory syn-drome coronavirus 2 (SARS­CoV­2), such as its role in protection after natural in-fection, are still unclear. We evaluated IgA and IgG response to spike subunits 1 and2 (S1 and S2) and Nucleocapsid proteins of SARS­COV­2 in serum samples of 109volunteers with viral RNA detected or seroconversion with different clinical evolu-tion (asymptomatic, mild, moderate, and severe coronavirus disease 2019), using theViraChip®Test Kit. We observed that the quantification of antibodies to all antigenshad a positive correlation to disease severity, which was strongly associated with thepresence of comorbidities. Seroreversion was not uncommon even during the short(median of 77 days) observation, occurring in 15% of mild­asymptomatic cases at amedian of 55 days for IgG and 46 days for IgA. The time to reach the maximalantibody response did not differ significantly among recovered and deceased vo-lunteers. Our study illustrated the dynamic of anti­S1, anti­N, and anti­S2 IgA andIgG antibodies, and suggests that high production of IgG and IgA does not guaranteeprotection to disease severity and that functional responses that have been studiedby other groups, such as antibody avidity, need further attention. (AU)