Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea.

The coronavirus disease pandemic has highlighted the utility of pathogen genomics as a key part of comprehensive public health response to emerging infectious diseases threats, however, the ability to generate, analyse, and respond to pathogen genomic data varies around the world. Papua New Guinea (PNG), which has limited in-country capacity for genomics, has experienced significant outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with initial genomics data indicating a large proportion of cases were from lineages that are not well defined within the current nomenclature. Through a partnership between in-country public health agencies and academic organisations, industry, and a public health genomics reference laboratory in Australia a system for routine SARS-CoV-2 genomics from PNG was established. Here we aim to characterise and describe the genomics of PNG's second wave and examine the sudden expansion of a lineage that is not well defined but very prevalent in the Western Pacific region. We generated 1797 sequences from cases in PNG and performed phylogenetic and phylodynamic analyses to examine the outbreak and characterise the circulating lineages and clusters present. Our results reveal the rapid expansion of the B.1.466.2 and related lineages within PNG, from multiple introductions into the country. We also highlight the difficulties that unstable lineage assignment causes when using genomics to assist with rapid cluster definitions.

Barriers and enablers experienced by health care workers in swabbing for COVID-19 in Papua New Guinea: A multi-methods cross-sectional study.

OBJECTIVE: We aimed to identify the barriers and enablers that Health Care Workers (HCWs) in Papua New Guinea experienced in swabbing for COVID-19. METHODS: We conducted a cross-sectional multi-methods study: a qualitative scoping exercise and a telephone survey. The target population was COVID-19-trained HCWs from all provinces of Papua New Guinea. A descriptive analysis of survey responses was conducted alongside a rapid qualitative analysis of interviews and open-ended survey questions. RESULTS: Four thematic areas were identified: human resources, logistics, HCW attitudes and community attitudes. The survey response rate was 70.3% (407/579). Commonly reported barriers to COVID-19 swabbing were insufficient staff trained (74.0%, n = 301), inadequate staffing in general (64.9%, n = 264), insufficient supply of personal protective equipment (60.9%, n = 248) and no cold chain to store swabs (57.5%, n = 234). Commonly reported enablers to swabbing were community awareness and risk communication (80.8%, n = 329), consistent and sufficient supplies of personal protective equipment (67.8%, n = 276), increased surge workforce (63.9%, n = 260) and having a fridge to store swabs (59.7%, n = 243). CONCLUSIONS: A comprehensive community and HCW engagement strategy combined with innovations to improve the supply chain are needed to increase COVID-19 swabbing in Papua New Guinea to reach national testing targets. Investments in increasing numbers of frontline workforce, consistent supplies of PPE, swabs, transport medium, cold boxes and ability to make ice packs, in addtion to establishing regular tranport of specimens from the facility to the testing site will strengthen the supply chain. Innovations are needed to address these issues.

Substantial Decline in Use of HIV Preexposure Prophylaxis Following Introduction of COVID-19 Physical Distancing Restrictions in Australia: Results From a Prospective Observational Study of Gay and Bisexual Men.

BACKGROUND: In response to the novel coronavirus disease (COVID-19) pandemic, Australia introduced public health and physical distancing restrictions in late March 2020. We investigated the impact of these restrictions on HIV preexposure prophylaxis (PrEP) use among Australian gay and bisexual men (GBM). METHODS: Participants in an ongoing online cohort study previously reported PrEP use from 2014 to 2019. In April 2020, 847 HIV-negative and untested participants completed questionnaires assessing changes in PrEP use as a result of COVID-19 public health measures. Binary logistic multiple regression was used to estimate adjusted odds ratios (aOR) and 95% confidence intervals (95% CI) to compare changes in PrEP use behaviors. RESULTS: Among 847 men, mean age was 44.1 years (SD: 12.7). PrEP use rose from 4.9% in 2015 to 47.2% in 2020. Among those, 41.8% (n = 167) discontinued PrEP use during COVID-19 restrictions. Discontinuing PrEP during COVID-19 restrictions was independently associated with being less likely to have recently tested for HIV (aOR: 0.17; 95% CI: 0.09 to 0.34; P < 0.001) and less likely to report sex with casual partners (aOR: 0.28; 95% CI: 0.14 to 0.54; P < 0.001). CONCLUSIONS: By April 2020, following the introduction of COVID-19 restrictions, GBM dramatically reduced PrEP use, coinciding with a reduction in sexual activity. Longer-term impacts of COVID-19 restrictions on sexual behaviors among GBM need to be monitored because they may foreshadow fluctuations in prevention coverage and risk of HIV infection. Our findings indicate a potential need for clear, targeted information about resumption of PrEP and on-demand optimal dosing regimens in response to ongoing changes in restrictions.

Physical Distancing Due to COVID-19 Disrupts Sexual Behaviors Among Gay and Bisexual Men in Australia: Implications for Trends in HIV and Other Sexually Transmissible Infections.

INTRODUCTION: In March 2020, Australian state and federal governments introduced physical distancing measures alongside widespread testing to combat COVID-19. These measures may decrease people's sexual contacts and thus reduce the transmission of HIV and other sexually transmissible infections (STIs). We investigated the impact of physical distancing measures due to COVID-19 on the sexual behavior of gay and bisexual men in Australia. METHODS: Between April 4, 2020, and April 29, 2020, 940 participants in an ongoing cohort study responded to questions to measure changes in sexual behaviors during the COVID-19 pandemic. Men reported the date they become concerned about COVID-19 and whether they engaged in sexual behavior with regular or casual partners or "fuckbuddies" in the 6 months before becoming concerned about COVID-19 (hereafter referred to as "before COVID-19"), and following the date, they become concerned about COVID-19 (hereafter referred to as "since COVID-19"). Before and since COVID-19 was based on individual participants' own perceived date of becoming concerned about COVID-19. RESULTS: The mean age of was 39.9 years (SD: 13.4). Most participants (88.3%) reported sex with other men during the 6 months before COVID-19. Of the 587 men (62.4%) who reported sex with casual partners before COVID-19, 93 (15.8%) continued to do so in the period since COVID-19, representing a relative reduction of 84.2%. CONCLUSION: Gay and bisexual men in Australia have dramatically reduced their sexual contacts with other men since COVID-19. These behavioral changes will likely result in short-term reductions in new HIV and STI diagnoses. If sexual health screenings are undertaken before resuming sexual activity, this could present a novel opportunity to interrupt chains of HIV and STI transmission.