Lessons Learned from Public Health and State Prison Collaborations during COVID-19 Pandemic and Multifacility Tuberculosis Outbreak, Washington, USA.

The large COVID-19 outbreaks in prisons in the Washington (USA) State Department of Corrections (WADOC) system during 2020 highlighted the need for a new public health approach to prevent and control COVID-19 transmission in the system's 12 facilities. WADOC and the Washington State Department of Health (WADOH) responded by strengthening partnerships through dedicated corrections-focused public health staff, improving cross-agency outbreak response coordination, implementing and developing corrections-specific public health guidance, and establishing collaborative data systems. The preexisting partnerships and trust between WADOC and WADOH, strengthened during the COVID-19 response, laid the foundation for a collaborative response during late 2021 to the largest tuberculosis outbreak in Washington State in the past 20 years. We describe challenges of a multiagency collaboration during 2 outbreak responses, as well as approaches to address those challenges, and share lessons learned for future communicable disease outbreak responses in correctional settings.

COVID-19 Outbreak Among Farmworkers - Okanogan County, Washington, May-August 2020.

Okanogan County, Washington, experienced increased community transmission of SARS-CoV-2, the virus that causes COVID-19, during summer 2020 (1). Multiple COVID-19 outbreaks occurred in agricultural settings, including a large outbreak among employees of a fruit grower during May-August. Because of this outbreak, Okanogan County Public Health and the Washington State Department of Health initiated one-time, on-site screening testing (2) of all orchard and warehouse employees in August 2020 and assessed risk factors for SARS-CoV-2 infection. Among 3,708 known orchard employees, a valid SARS-CoV-2 test result or information on COVID-19-like symptoms in the absence of a test was available for 3,013 (81%). Cumulative incidence of SARS-CoV-2 infection during approximately 3 months among tested orchard employees was 6%. Cumulative incidence was 12% in employees residing in the community, compared with 4% in employees residing in farmworker housing (p<0.001); point prevalence during the single screening testing event was 1% in both groups. Among 1,247 known warehouse employees, a valid result was available for 726 (58%). Cumulative incidence over approximately 3 months among tested warehouse employees was 23%, with substantial variation across job roles. Positive test results were received by 28% of employees who worked packing and sorting fruit, 24% of those in other roles in the packing and sorting area, 10% of forklift operators, 7% of employees in other warehouse roles, and 6% of office employees. Point prevalence among all warehouse workers was 1% at the screening testing event. Collaboration among employers, community groups, and public health authorities can reveal risk factors and help decrease farmworkers' risk for SARS-CoV-2 infection in the community and the workplace. Creation of a COVID-19 assessment and control plan by agricultural employers, with particular focus on indoor workers whose jobs limit physical distancing, could reduce workplace transmission.

Implementation Science to Respond to the COVID-19 Pandemic.

The COVID-19 pandemic continues to expand globally, requiring massive public health responses from national and local governments. These bodies have taken heterogeneous approaches to their responses, including when and how to introduce and enforce evidence-based interventions-such as social distancing, hand-washing, personal protective equipment (PPE), and testing. In this commentary, we reflect on opportunities for implementation science to contribute meaningfully to the COVID-19 pandemic response. We reflect backwards on missed opportunities in emergency preparedness planning, using the example of PPE stockpiling and supply management; this planning could have been strengthened through process mapping with consensus-building, microplanning with simulation, and stakeholder engagement. We propose current opportunities for action, focusing on enhancing the adoption, fidelity, and sustainment of hand washing and social distancing; we can combine qualitative data, policy analysis, and dissemination science to inform agile and rapid adjustment to social marketing strategies to enhance their penetration. We look to future opportunities to enhance the integration of new evidence in decision-making, focusing on serologic and virologic testing systems; we can leverage simulation and other systems engineering modeling to identify ideal system structures. Finally, we discuss the ways in which the COVID-19 pandemic challenges implementation science to become more rapid, rigorous, and nimble in its approach, and integrate with public health practice. In summary, we articulate the ways in which implementation science can inform, and be informed by, the COVID-19 pandemic, looking backwards, proposing actions for the moment, and approaches for the future.

Mortality Rate and Causes of Death Among Refugees Resettled in Washington State, 2006-2016.

Cause of death among refugees resettled in the United States is not well documented. This evaluation determined cause of death among refugees who resettled to and died in Washington State. Records of refugees who arrived in Washington State from 2006 to 2016 were linked to state death records for the same period. Rates and proportions of death were calculated and compared to those for all Washingtonians. From 2006 to 2016, 171 of 30,243 refugees (0.6%) resettled to and died in Washington. The age-adjusted all-cause mortality rate was 3.93 (95% CI 3.12-4.75) per 1000 refugees, compared to 6.98 (95% CI 6.96-7.00) per 1000 Washingtonians. Malignant neoplasms and heart disease were the leading causes of death for both refugees and Washingtonians. Determining cause of death among refugee populations can identify emerging trends in mortality. This information can be used to help inform disease and injury prevention interventions for refugee communities.

Global influenza seasonality to inform country-level vaccine programs: An analysis of WHO FluNet influenza surveillance data between 2011 and 2016.

By analyzing publicly available surveillance data from 2011-2016, we produced country-specific estimates of seasonal influenza activity for 118 countries in the six World Health Organization regions. Overall, the average country influenza activity period was 4.7 months. Our analysis characterized 100 countries (85%) with one influenza peak season, 13 (11%) with two influenza peak seasons, and five (4%) with year-round influenza activity. Surveillance data were limited for many countries. These data provide national estimates of influenza activity, which may guide planning for influenza vaccination implementation, program timing and duration, and policy development.

Sustained Responses to Measles Revaccination at 24 Months in HIV-infected Children on Antiretroviral Therapy in Kenya.

BACKGROUND: There are limited data on whether HIV-infected children in resource-limited countries who are receiving antiretroviral therapy (ART) are able to produce sustained, protective levels of measles antibody after multiple measles vaccinations. METHODS: We administered an additional measles vaccine to HIV-infected children 15 months to 12 years of age receiving ART in Nairobi, Kenya. Measles antibody concentrations were determined by enzyme-linked immunosorbent assay at enrollment, 1 month, 12 months and 24 months post revaccination. RESULTS: At enrollment, 125 (54%) of 232 study participants had protective concentrations of measles antibody. Measles seropositivity increased to 98% of all children at 1 month post revaccination but decreased to 71% at 12 months and 60% at 24 months post revaccination. Measles seroconversion and sustained measles seropositivity among those who were measles seronegative at enrollment was 25% at 24 months post revaccination. In this group, 39% of children with <50 copies/mL plasma HIV RNA measles seroconverted compared to 4% of children with plasma HIV RNA ≥1000 copies/mL (P = 0.018). CONCLUSIONS: Measles revaccination can result in a sustained antibody response in a subset of HIV-infected children receiving ART, especially among those with HIV suppression.

Influenza Seasonality in the Tropics and Subtropics - When to Vaccinate?

BACKGROUND: The timing of the biannual WHO influenza vaccine composition selection and production cycle has been historically directed to the influenza seasonality patterns in the temperate regions of the northern and southern hemispheres. Influenza activity, however, is poorly understood in the tropics with multiple peaks and identifiable year-round activity. The evidence-base needed to take informed decisions on vaccination timing and vaccine formulation is often lacking for the tropics and subtropics. This paper aims to assess influenza seasonality in the tropics and subtropics. It explores geographical grouping of countries into vaccination zones based on optimal timing of influenza vaccination. METHODS: Influenza seasonality was assessed by different analytic approaches (weekly proportion of positive cases, time series analysis, etc.) using FluNet and national surveillance data. In case of discordance in the seasonality assessment, consensus was built through discussions with in-country experts. Countries with similar onset periods of their primary influenza season were grouped into geographical zones. RESULTS: The number and period of peak activity was ascertained for 70 of the 138 countries in the tropics and subtropics. Thirty-seven countries had one and seventeen countries had two distinct peaks. Countries near the equator had secondary peaks or even identifiable year-round activity. The main influenza season in most of South America and Asia started between April and June. The start of the main season varied widely in Africa (October and December in northern Africa, April and June in Southern Africa and a mixed pattern in tropical Africa). Eight "influenza vaccination zones" (two each in America and Asia, and four in Africa and Middle East) were defined with recommendations for vaccination timing and vaccine formulation. The main limitation of our study is that FluNet and national surveillance data may lack the granularity to detect sub-national variability in seasonality patterns. CONCLUSION: Distinct influenza seasonality patterns, though complex, could be ascertained for most countries in the tropics and subtropics using national surveillance data. It may be possible to group countries into zones based on similar recommendations for vaccine timing and formulation.

Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease.

BACKGROUND: Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have invaded the germ line of both humans and non-human primates. Most ERVs are functionally crippled by deletions, mutations, and hypermethylation, leading to the view that they are inert genomic fossils. However, some ERVs can produce mRNA transcripts, functional viral proteins, and even non-infectious virus particles during certain developmental and pathological processes. While there have been reports of ERV-specific immunity associated with ERV activity in humans, adaptive immune responses to ERV-encoded gene products remain poorly defined and have not been investigated in the physiologically relevant non-human primate model of human disease. FINDINGS: Here, we identified the rhesus macaque equivalent of the biologically active human ERV-K (HML-2), simian ERV-K (SERV-K1), which retains intact open reading frames for both Gag and Env on chromosome 12 in the macaque genome. From macaque cells we isolated a spliced mRNA product encoding SERV-K1 Env, which possesses all the structural features of a canonical, functional retroviral Envelope protein. Furthermore, we identified rare, but robust T cell responses as well as frequent antibody responses targeting SERV-K1 Env in rhesus macaques. CONCLUSIONS: These data demonstrate that SERV-K1 retains biological activity sufficient to induce cellular and humoral immune responses in rhesus macaques. As ERV-K is the youngest and most active ERV family in the human genome, the identification and characterization of the simian orthologue in rhesus macaques provides a highly relevant animal model in which to study the role of ERV-K in developmental and disease states.

Measles seropositivity in HIV-infected Kenyan children on antiretroviral therapy.

This article describes results from a cross-sectional study among HIV-infected children 15 months to 12 years of age who were receiving antiretroviral therapy. We found a low prevalence of measles IgG seropositivity (45.7%) and identified CD4% ≥ 25 as a predictor. Most HIV-infected children on ART were not measles seropositive and might benefit from revaccination.

Vaccination against endogenous retrotransposable element consensus sequences does not protect rhesus macaques from SIVsmE660 infection and replication.

The enormous sequence diversity of HIV remains a major roadblock to the development of a prophylactic vaccine and new approaches to induce protective immunity are needed. Endogenous retrotransposable elements (ERE) such as endogenous retrovirus K (ERV)-K and long interspersed nuclear element-1 (LINE-1) are activated during HIV-1-infection and could represent stable, surrogate targets to eliminate HIV-1-infected cells. Here, we explored the hypothesis that vaccination against ERE would protect macaques from acquisition and replication of simian immunodeficiency virus (SIV). Following vaccination with antigens derived from LINE-1 and ERV-K consensus sequences, animals mounted immune responses that failed to delay acquisition of SIVsmE660. We observed no differences in acute or set point viral loads between ERE-vaccinated and control animals suggesting that ERE-specific responses were not protective. Indeed, ERE-specific T cells failed to expand anamnestically in vivo following infection with SIVsmE660 and did not recognize SIV-infected targets in vitro, in agreement with no significant induction of targeted ERE mRNA by SIV in macaque CD4+ T cells. Instead, lower infection rates and viral loads correlated significantly to protective TRIM5α alleles. Cumulatively, these data demonstrate that vaccination against the selected ERE consensus sequences in macaques did not lead to immune-mediated recognition and killing of SIV-infected cells, as has been shown for HIV-infected human cells using patient-derived HERV-K-specific T cells. Thus, further research is required to identify the specific nonhuman primate EREs and retroviruses that recapitulate the activity of HIV-1 in human cells. These results also highlight the complexity in translating observations of the interplay between HIV-1 and human EREs to animal models.

Seroprevalence of measles IgG among HIV-1-infected and uninfected Kenyan adults.

Despite global efforts to reduce measles incidence, outbreaks continue to occur in developing countries where HIV-1-infected adults represent a vulnerable population. Immunization campaigns have targeted children, although little is known about the levels of measles protection in adult populations in Kenya. The objective of this study was to determine seroprevalence and titers of measles IgG among HIV-1-infected and uninfected adults in Nairobi, Kenya. The presence of anti-measles IgG was measured in cryopreserved serum of 257 HIV-1-infected and 367 uninfected adults using a commercial ELISA (Enzygnost, Germany). The measles IgG concentration was calculated for those samples that were positive. Overall, 96% of adults were measles seropositive and the mean measles IgG concentration among those who were seropositive was 4134 mIU/ml, which is well above previously reported protective levels. There was no statistical difference in seroprevalence or antibody concentration between the HIV-infected and HIV-uninfected groups. While local vaccination efforts and circulating measles infection likely contribute to this high measles seroprevalence rate, these data are unique to an urban population and may not reflect a country-wide distribution. Our results suggest that reduced immunity among HIV-1-infected adults is not a major contributor to measles resurgence in Kenya.

Tertiary mutations stabilize CD8+ T lymphocyte escape-associated compensatory mutations following transmission of simian immunodeficiency virus.

Compensatory mutations offset fitness defects resulting from CD8(+) T lymphocyte (CD8(TL))-mediated escape, but their impact on viral evolution following transmission to naive hosts remains unclear. Here, we investigated the reversion kinetics of Gag(181-189)CM9 CD8(TL) escape-associated compensatory mutations in simian immunodeficiency virus (SIV)-infected macaques. Preexisting compensatory mutations did not result in acute-phase escape of the SIVmac239 CD8(TL) epitope Gag(181-189)CM9 and instead required a tertiary mutation for stabilization in the absence of Gag(181-189)CM9 escape mutations. Therefore, transmitted compensatory mutations do not necessarily predict rapid CD8(TL) escape.

T cells target APOBEC3 proteins in human immunodeficiency virus type 1-infected humans and simian immunodeficiency virus-infected Indian rhesus macaques.

APOBEC3 proteins mediate potent antiretroviral activity by hypermutating the retroviral genome during reverse transcription. To counteract APOBEC3 and gain a replicative advantage, lentiviruses such as human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) have evolved the Vif protein, which targets APOBEC3 proteins for proteasomal degradation. However, the proteasome plays a critical role in the generation of T cell peptide epitopes. Whether Vif-mediated destruction of APOBEC3 proteins leads to the generation and presentation of APOBEC3-derived T cell epitopes on the surfaces of lentivirus-infected cells remains unknown. Here, using peptides derived from multiple Vif-sensitive APOBEC3 proteins, we identified APOBEC3-specific T cell responses in both HIV-1-infected patients and SIV-infected rhesus macaques. These results raise the possibility that these T cell responses may be part of the larger antiretroviral immune response.

CD8+ and CD4+ cytotoxic T cell escape mutations precede breakthrough SIVmac239 viremia in an elite controller.

BACKGROUND: Virus-specific T cells are critical components in the containment of immunodeficiency virus infections. While the protective role of CD8+ T cells is well established by studies of CD8+ T cell-mediated viral escape, it remains unknown if CD4+ T cells can also impose sufficient selective pressure on replicating virus to drive the emergence of high-frequency escape variants. Identifying a high frequency CD4+ T cell driven escape mutation would provide compelling evidence of direct immunological pressure mediated by these cells. RESULTS: Here, we studied a SIVmac239-infected elite controller rhesus macaque with a 1,000-fold spontaneous increase in plasma viral load that preceded disease progression and death from AIDS-related complications. We sequenced the viral genome pre- and post-breakthrough and demonstrate that CD8+ T cells drove the majority of the amino acid substitutions outside of Env. However, within a region of Gag p27CA targeted only by CD4+ T cells, we identified a unique post-breakthrough mutation, Gag D205E, which abrogated CD4+ T cell recognition. Further, we demonstrate that the Gag p27CA-specific CD4+ T cells exhibited cytolytic activity and that SIV bearing the Gag D205E mutation escapes this CD4+ T cell effector function ex vivo. CONCLUSIONS: Cumulatively, these results confirm the importance of virus specific CD8+ T cells and demonstrate that CD4+ T cells can also exert significant selective pressure on immunodeficiency viruses in vivo during low-level viral replication. These results also suggest that further studies of CD4+ T cell escape should focus on cases of elite control with spontaneous viral breakthrough.

Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic.

The expression of endogenous retrotransposable elements, including long interspersed nuclear element 1 (LINE-1 or L1) and human endogenous retrovirus, accompanies neoplastic transformation and infection with viruses such as HIV. The ability to engender immunity safely against such self-antigens would facilitate the development of novel vaccines and immunotherapies. In this article, we address the safety and immunogenicity of vaccination with these elements. We used immunohistochemical analysis and literature precedent to identify potential off-target tissues in humans and establish their translatability in preclinical species to guide safety assessments. Immunization of mice with murine L1 open reading frame 2 induced strong CD8 T cell responses without detectable tissue damage. Similarly, immunization of rhesus macaques with human LINE-1 open reading frame 2 (96% identity with macaque), as well as simian endogenous retrovirus-K Gag and Env, induced polyfunctional T cell responses to all Ags, and Ab responses to simian endogenous retrovirus-K Env. There were no adverse safety or pathological findings related to vaccination. These studies provide the first evidence, to our knowledge, that immune responses can be induced safely against this class of self-antigens and pave the way for investigation of them as HIV- or tumor-associated targets.

Pyrosequencing reveals restricted patterns of CD8+ T cell escape-associated compensatory mutations in simian immunodeficiency virus.

CD8+ T cells play a major role in the containment of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication. CD8+ T cell-driven variations in conserved regions under functional constraints result in diminished viral replicative capacity. While compensatory mutations outside an epitope can restore replicative capacity, the kinetics with which they arise remains unknown. Additionally, certain patterns of linked mutations associated with CD8+ T cell epitope escape in these highly conserved regions may lead to variable levels of viral fitness. Here, we used pyrosequencing to investigate the kinetics and patterns of mutations surrounding the Mamu-A1*00101-bound Gag(181-189)CM9 CD8+ T cell epitope. We obtained more than 400 reads for each sequencing time point, allowing us to confidently detect the emergence of viral variants bearing escape mutations with frequencies as low as 1% of the circulating virus. With this level of detail, we demonstrate that compensatory mutations generally arise concomitantly with Gag(181-189)CM9 escape mutations. We observed distinct patterns of linked flanking mutations, most of which were found downstream of Gag(181-189)CM9. Our data indicate that, whereas Gag(181-189)CM9 escape is much more complex that previously appreciated, it occurs in a coordinated fashion, with very specific patterns of flanking mutations required for immune evasion. This is the first detailed report of the ontogeny of compensatory mutations that allow CD8+ T cell epitope escape in infected individuals.

Simian immunodeficiency virus-specific CD8+ T cells recognize Vpr- and Rev-derived epitopes early after infection.

The kinetics of CD8(+) T cell epitope presentation contribute to the antiviral efficacy of these cells yet remain poorly defined. Here, we demonstrate presentation of virion-derived Vpr peptide epitopes early after viral penetration and prior to presentation of Vif-derived epitopes, which required de novo Vif synthesis. Two Rev epitopes exhibited differential presentation kinetics, with one Rev epitope presented within 1 h of infection. We also demonstrate that cytolytic activity mirrors the recognition kinetics of infected cells. These studies show for the first time that Vpr- and Rev-specific CD8(+) T cells recognize and kill simian immunodeficiency virus (SIV)-infected CD4(+) T cells early after SIV infection.

Ack1 mediates Cdc42-dependent cell migration and signaling to p130Cas.

We previously showed that activation of the small GTPase Cdc42 promotes breast cell migration on a collagen matrix. Here we further define the signaling pathways that drive this response and show that Cdc42-mediated migration relies on the adaptor molecule p130(Cas). Activated Cdc42 enhanced p130(Cas) phosphorylation and its binding to Crk. Cdc42-driven migration and p130(Cas) phosphorylation were dependent on the Cdc42 effector Ack1 (activated Cdc42-associated kinase). Ack1 formed a signaling complex that also included Cdc42, p130(Cas), and Crk, formation of which was regulated by collagen stimulation. The interaction between Ack1 and p130(Cas) occurred through their respective SH3 domains, while the substrate domain of p130(Cas) was the major site of Ack1-dependent phosphorylation. Signaling through this complex is functionally relevant, because treatment with either p130(Cas) or Ack1 siRNA blocked Cdc42-induced migration. These results suggest that Cdc42 exerts its effects on cell migration in part through its effector Ack1, which regulates p130(Cas) signaling.