Follow-up after post-exposure prophylaxis before and during the COVID-19 pandemic in Brazil (preprint)

Although post-exposure prophylaxis (PEP) is a powerful tool to abort HIV infection within 72 hours of exposure, blocking the establishment of chronic infection, follow-up metrics of this intervention are scarce. As antiretroviral use delays diagnosis biomarkers, the moment to perform serological evaluations must be considered this to avoid missed diagnosis opportunities. We assessed the return adherence after PEP dispensation in service in the Sao Paulo metropolitan area and reviewed the literature, both showing limited adherence to current protocols and leading to difficulties in diagnosing early HIV infection. The current proposed date for the first return after PEP is associated with low adherence and may have limited capability to detect antibodies if the infection is present. Guidelines should allow a longer time after PEP discontinuation along with message reminders to encourage adherence and avoid false negative results that can be detrimental both to the patient and to the community.

P1 variant and amino acid mutations at Spike gene identified using Sanger protocol (preprint)

SARS-coV-2 variants, along with vaccination, mark the second year of the pandemic. The spike region is a focal point in COVID-19 pathogenesis, with different amino acid changes potentially modulating vaccine response and some being part of variant signatures. NGS is the standard tool to sequence the virus but limitations of different sources hinders expansion of genomic surveillance in many places. To improve surveillance capability we developed a Sanger based sequencing protocol to obtain coverage of most (>95%) spike gene. Eleven nasopharyngeal swabs collections had RNA extracted for real time PCR diagnosis and leftover RNA had up to 3785 bp sequenced at an ABI3500 using dye termination chemistry of nested PCR products of two reactions of one Step RT-PCR. P1 amino acid mutations signatures were present in 18% (2/11), with 82% (9/11) with three or more additional amino acid changes (GISAID CoVsurver list). Most sequences (86%, 7/8) from 2021 have the E484K, whereas the mutation was not present in samples collected in 2020 (0/4, p=0.015). The swiftness that favorable mutations to the virus may prevail and their potential impact in vaccines and other current interventions need broader surveillance and more public health attention.

PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL (preprint)

Background: Covid-19 Serology may document exposure and perhaps protection to the virus, and serological test may help understand epidemic dynamics. To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 among HPs in Adolfo Lutz Institute, State of Sao Paulo, Brazil. Methods: This study was performed among professionals of Adolfo Lutz Institute in Sao Paulo, Brazil and some administrative areas of the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay and SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants. Results: A total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA.. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity. Conclusions: We documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, with higher rates among outsourced workers and those with referring cohabitation with COVID-19 patients. COVID samples handling was not related to increased seropositivity. Some symptoms how strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings.

SARS-CoV-2 RNA detection using pooling of self-collected samples: Simple protocols may foster asymptomatic surveillance (preprint)

Background: Surveillance of COVID infection and isolation of infected individuals is one of the available tools to control the spread of SAR-CoV-2. Asymptomatic and pre symptomatic are responsible for substantial transmission. RNA or antigen tests are necessary to identify non-symptomatic individuals. We tested the feasibility of using samples pooling offering different collection alternatives (swab/throat wash/saliva) to volunteers of a public health institute. Methods: We evaluated pool samples from both reconstituted (frozen material from tested samples) and a prospective collection of asymptomatic volunteers. Some collections were paired for comparison. Pooled and some individual samples were extracted with QIAamp Viral RNA Mini Kit (Qiagen, USA) and/or Lucigen Quick Extract DNA extraction solution (BioSearch, USA) and submitted to rtCCR using (Allplex, Seegene, Korea). Results: A total of 240 samples from 130 new collections and 37 samples with known result were evaluated. Pool CT was generally higher than individual samples. Lucigen extraction showed higher CT, including false negative results for samples with high CT at Qiagen extraction. Paired Swab and TW samples showed comparable results. No volunteer from negative pools reported any symptom in the 2-3 days after collection. Conclusions: Clinical samples pooling to detect SARS-CoV-2 RNA is feasible and an economical way to test for COVID-19, especially in surveillance strategies targeting more infectiousness, higher viremia individuals. The use of Lucigen reagents show lower sensibility that may lead to false negative results with lower viremia samples. Combining throat wash with saliva may provide and interesting alternative for auto collection, but more comparative work is needed.

Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. (preprint)

Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute. Methods: Consecutive volunteer testing of LWH and external household and close contacts were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea). Results: Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease. Over a third (38%) of asymptomatic cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease.