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1.
Topics in Antiviral Medicine ; 30(1 SUPPL):315-316, 2022.
Article in English | EMBASE | ID: covidwho-1880880

ABSTRACT

Background: In the U.S/Mexico border region, drug tourism (DT) has been linked to increased HIV risk among people who inject drugs (sharing injection equipment) and paying for sex. Sex and DT from the U.S. to Mexico drive bidirectional cross-border mobility, and have consequently played an important role in HIV spread in the border region, but prior to the COVID19 pandemic, HIV incidence remained <2 per 100 person years (PY). We assessed HIV incidence and associated risk factors among PWID during the COVID-19 pandemic. Methods: Participants are from La Frontera, a longitudinal study of PWID aged ≥18 from 3 groups: PWID who injected drugs in Tijuana ≤24 months ago but live in San Diego (SD DTs), and non-drug tourist (NDT) PWID, who live in SD county or Tijuana (TJ) but have never used illicit drugs across the border. Beginning in Oct/2020, participants underwent surveys and provided samples for HIV and SARS-CoV-2 serology every 6 months, and an egocentric social network (SN) survey. HIV prevalence, bivariate incidence-density rates, incident rate-ratios (IRR), and exact 95% confidence intervals (CI) were calculated for independent variables between baseline and follow-up. Results: To date, among 611 participants at baseline, HIV prevalence was 7.6% (SD DT: 3.8%, SD NDT: 3.5%, TJ NDT: 15.8%). Of the HIV-PWID returning for their 6 months visit thus far (n=286;93% follow-up), eight HIV seroconversions occurred during 118 PY of follow-up (Incidence: 13.53/100PY;95% CI: 5.84-26.66). Although not significant, incidence was notably higher among TJ NDT (19.9/100PY vs 1.82/100 PY SD DT vs 0 SD NDT;IRR 10.94, 95% CI 0.35, 22.59 TJ NDT vs SD DT), those who shared syringes/works with a network member (30.34/100PY vs. 7.31/100PY;IRR 4.15, 95% CI 0.37,9.19) and non-heterosexual participants (29.31/100PY vs 5.38/100PY;IRR 4.67, 95% CI 0.39, 9.67). Conclusion: Preliminary HIV incidence rates among PWID in the U.S./Mexico border region during the pandemic are high, and suggest a new HIV outbreak among PWID residing in TJ. Mobile harm reduction services providing syringes and HIV testing, as well as coordination with the municipal HIV program to allow for ART initiation and PrEP are urgently needed to prevent a continuing outbreak.

2.
Clin Infect Dis ; 73(12): 2314-2317, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1592199

ABSTRACT

The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (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.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Phylogeny
3.
Topics in Antiviral Medicine ; 29(1):244, 2021.
Article in English | EMBASE | ID: covidwho-1250848

ABSTRACT

Background: As countries around the world review interventions for containing the COVID-19 pandemic, movement of populations has been identified as a key factor of viral dispersal and limiting the population flow intensity has been applied to contain the current COVID-19 epidemic. Evolutionary analyses of well-annotated sequencing data can provide insights into viral transmission dynamics. Herein, we characterized the dynamics of COVID-19 transmission within California and across the Mexico-California (MX/CA) border, the busiest land border-crossing area in the world, to inform the containment policy in this binational context. Methods: All publicly available SARS-CoV-2 full genome sequences (human host) available on the GISAID database were collected (as of Nov. 16th, 2020). After sequence curation, a multistep phylogenetic approach was applied to identify putative clusters of transmission within CA (across counties), MX (across states) and across the MX/CA border. These clades were analyzed with a discrete phylogeographic model to evaluate transmission dynamics of COVID-19 in the MX/CA region. Results: From a total of 174,324 SARS-CoV-2 sequences including 5,471 sequences from Mexico (7 States, n=223)/California (29 counties, n=5,248), we identified 622 unique introduction events into the study region, including 381 clusters of size ≥3 from ≥2 locations (i.e. CA county and/or MX state). Of these, 339 (89%) clusters were from CA only across 23 counties, 5 (1.3%) were from MX only across 6 states and 38 (10%) included sequences from both CA and MX Discrete phylogeographic analysis revealed a complex viral migration network within CA/MX and across the border (Figure 1A, left panel). Analyses of the 38 clusters including sequences from CA and MEX showed bidirectional migration events across the border (Figure 1B). In particular we showed migration events in the border region from the border state of Baja California, MX to the border county of San Diego, CA and from the border county of Imperial County, CA to the border state of Sonora, MX (Figure 1A, right panel). Conclusion: This comprehensive analysis of all publicly available COVID-19 sequences showed local transmission across regions within CA and MX as well as across neighboring locations across the border. Similar to the 2009 H1N1 pandemic, the MX/CA border does not appear to be a major barrier to the spread of COVID-19, necessitating coordinated transnational intervention approaches.

4.
Topics in Antiviral Medicine ; 29(1):269-270, 2021.
Article in English | EMBASE | ID: covidwho-1250626

ABSTRACT

Background: Closing labs to decrease spread of COVID-19 has impacted research progress. Serial testing could supplement other measures to help provide a safe lab environment. Methods: Lab employees who came to work at an academic laboratory at the University of California San Diego (UCSD) were invited and consented to perform their own anterior nasal swab or have a swab collected by an on-site physician. Nasal swabs were combined into one pool for each work shift. Each pool underwent nucleic acid testing (NAT) via qRT-PCR to detect SARS-CoV-2 RNA (FluxErgy). Results were available within one hour. Positive pools were deconvoluted and tested individually. Cost evaluation of the pooling approach was compared to individual NAT and to institutional guidelines for lab occupancy. Results: From Apr 9 to Oct 26, 2020 (28 weeks), 1,199 nasal swab samples collected from lab workers were batched in 194 pools of median size 7 [95%I: 3-11]. A median of 41 tests per week [95%I: 22-67] were performed in a total of 77 participants (Fig 1). 19 core staff were tested a median 54 times [95%I:13-95]. Of the 194 pools, 7 (3.6%, n=47 samples) were considered positive and required repeat testing of all participant samples in the pool as confirmation. One true positive was identified before work started. That participant was referred to their primary care provider. This early detection prevented a 2-week quarantine of 7 employees. Given ∼$65/hour salary per lab worker, this saved 420 hours of work and ∼$26,600 in wages. Current UCSD guidelines recommend decreasing staffing levels to 25% of pre-COVID-19 occupancy. Regular NAT allowed 100% staffing. Screening of lab technicians with the pooled NAT strategy over 6 months cost $25,740 but permitted 2,430 person-hours of additional work ($132,210 in wages), as compared to the recommended 75% reduction without testing. A similar approach with individual NAT would cost $124,020 (thus $98,280 saved by pooling). Conclusion: Regular pooled NAT for SARS-CoV-2 among lab personnel offers a cost-efficient way to maintain a safe lab environment without a reduction in staffing. This approach could be applied in other settings to help ensure safe work environments.

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