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

ABSTRACT: 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.

SUBMITTER: Palou T

PROVIDER: S-EPMC9278129 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSince 2004, the Global Fund-supported National Malaria Control Programme of Papua New Guinea (PNG) has been implementing country-wide free long-lasting insecticidal net (LLIN) distribution campaigns. In 2009, after the first distribution, only 32.5% of the population used a LLIN, mainly due to an insufficient number of nets available. This study investigated changes in mosquito net ownership and use following the continued free distribution of LLINs across PNG.MethodsFive villages from each province and 30 households from each village were randomly sampled in a country-wide household survey in 2010/11. A structured questionnaire administered to household heads recorded information on mosquito net ownership and use alongside household characteristics. Revised ownership and access indicators were applied in the analysis to reveal coverage gaps.ResultsThe survey covered 1,996 households in 77 villages. Ownership of at least one LLIN was reported by 81.8% of households, compared to 64.6% in 2009 (P?=?0.002). Sufficient LLINs to cover all household members (one net per two people) were found in 41.3% of the households (21.4% in 2009, P?<?0.001). Of all household members, 61.4% had access to a LLIN within their household (44.3% in 2009 P?=?0.002), and 48.3% slept under a LLIN (32.5% in 2009, P?=?0.001). LLIN use in children under five years amounted to 58.2%, compared to 39.5% in 2009 (P?<?0.001). Significant regional differences in coverage and changes over time were observed. A recent LLIN distribution was a key determinant of LLIN ownership (adj. OR?=?3.46) while families in high quality houses would frequently not own a LLIN (adj. OR?=?0.09). Residents were more likely to use LLINs than household guests (OR?=?2.04).ConclusionsRepeated LLIN distribution has led to significant increases in mosquito net ownership and use with few regional exceptions. Additional nets are required in areas where access is low, while major efforts are required to encourage the use of existing nets in region where access is high but use remains low. Complementary vector control approaches should also be considered in such settings.

Project description:BackgroundMale circumcision (MC) is a well-established component of HIV prevention in countries with high HIV prevalence and heterosexually driven epidemics. Delivery and monitoring of MC programs are reliant on good quality MC data. Such data are often generated through self-reported MC status surveys. This study examined self-reported MC status in comparison with genital photographs from men in Papua New Guinea (PNG).MethodsThis retrospective non-interventional study collated self-reported MC status data from the 'acceptability and feasibility of MC' study at 4 sites in PNG during 2010-2011. Participants reported their MC status based on an 8-category photographic classification covering the range of foreskin cutting practices in PNG. Genital photographs of 222 participants from this study were independently classified by 2 investigators. The 8-category photographic classification was simplified into a 3 category classification of 'no cut', 'straight cut' and 'round cut' before comparing for agreement between self-reporting and investigator assessment using Cohen's Kappa measure.ResultsUsing the 3-category classification, there was 90.6% (201/222) agreement between self-assessment and investigator classification (? value 0.805). Of the discordant 9.4% (21/222), 3.6% (8/222) self-classified as having a cut foreskin (5 straight cut; 3 round cut) while investigators classified as having no cut; 4.1% (9/222) self-classified as having no cut while investigators classified them as having had a cut (6 straight cut; 3 round cut) and 1.8% (4/222) self-classified as having a round cut while investigators classified as having a straight cut. Given the great variety of foreskin cutting practices and appearances, feasible explanations are suggested for two-thirds (13/21) of these discordant results.ConclusionsThis study demonstrates a high level of agreement between self-reporting and investigator assessment of MC status in PNG and suggests self-reporting of MC status to be highly reliable among men in PNG.

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

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