Virologic and Immunologic Characterization of COVID-19 Recrudescence after Nirmatrelvir/Ritonavir Treatment (preprint)

We isolated a SARS-CoV-2 BA.2 variant from a person with COVID-19 recrudescence after nirmatrelvir/ritonavir treatment. Antiviral sensitivity and neutralizing antibody testing was performed and compared with parental SARS-CoV-2 and multiple variants of concern. We found that neither NM resistance nor absence of neutralizing immunity were likely causes of the recrudescence.

Prevalence and correlates of SARS-CoV-2 seropositivity among people who inject drugs in the San Diego-Tijuana border region (preprint)

BackgroundPeople who inject drugs may be at elevated SARS-CoV-2 risk due to their living conditions and/or exposures when seeking or using drugs. No study to date has reported upon risk factors for SARS-CoV-2 infection among people who inject drugs or sex workers. Methods and FindingsBetween October, 2020 and June, 2021, participants aged [≥]18 years from San Diego, California, USA and Tijuana, Baja California, Mexico who injected drugs within the last month underwent interviews and testing for SARS-CoV-2 RNA and antibodies. Binomial regressions identified correlates of SARS-CoV-2 seropositivity. Of 386 participants, SARS-CoV-2 seroprevalence was 36.3% (95% CI: 31.5%-41.1%); 92.1% had detectable IgM antibodies. Only 37.5% had previously been tested. Seroprevalence did not differ by country of residence. None tested RNA-positive. Most (89.5%) reported engaging in [≥]1 protective behavior [e.g., facemasks (73.5%), social distancing (46.5%), or increasing handwashing/sanitizers (22.8%)]. In a multivariate model controlling for sex, older age, and Hispanic/Latinx/Mexican ethnicity were independently associated with SARS-CoV-2 seropositivity, as was engaging in sex work (AdjRR: 1.63; 95% CI: 1.18-2.27) and having been incarcerated in the past six months (AdjRR: 1.49; 95% CI: 0.97-2.27). Presence of comorbidities and substance using behaviors were not associated with SARS-CoV-2 seropositivity. ConclusionsThis is the first study to show that sex work and incarceration were independently associated with SARS-CoV-2 infection. Despite engaging in protective measures, over one-third had evidence of infection, reinforcing the need for a coordinated binational response. Risk mitigation and vaccination is especially needed among older and Hispanic people who inject drugs and those with less agency to protect themselves, such as those who are sex workers or incarcerated.

Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution (preprint)

The emergence of new variants of SARS-CoV-2 herald a new phase of the pandemic. This study used state-of-the-art phylodynamic methods to ascertain that the rapid rise of B.1.1.7 "Variant of Concern" most likely occurred by global dispersal rather than convergent evolution from multiple sources.