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.

Hyperendemic dengue transmission and identification of a locally evolved DENV-3 lineage, Papua New Guinea 2007-2010.

BACKGROUND: Dengue is endemic in the Western Pacific and Oceania and the region reports more than 200,000 cases annually. Outbreaks of dengue and severe dengue occur regularly and movement of virus throughout the region has been reported. Disease surveillance systems, however, in many areas are not fully established and dengue incidence is underreported. Dengue epidemiology is likely least understood in Papua New Guinea (PNG), where the prototype DENV-2 strain New Guinea C was first isolated by Sabin in 1944 but where routine surveillance is not undertaken and little incidence and prevalence data is available. METHODOLOGY/PRINCIPAL FINDINGS: Serum samples from individuals with recent acute febrile illness or with non-febrile conditions collected between 2007-2010 were tested for anti-DENV neutralizing antibody. Responses were predominantly multitypic and seroprevalence increased with age, a pattern indicative of endemic dengue. DENV-1, DENV-2 and DENV-3 genomes were detected by RT-PCR within a nine-month period and in several instances, two serotypes were identified in individuals sampled within a period of 10 days. Phylogenetic analysis of whole genome sequences identified a DENV-3 Genotype 1 lineage which had evolved on the northern coast of PNG which was likely exported to the western Pacific five years later, in addition to a DENV-2 Cosmopolitan Genotype lineage which had previously circulated in the region. CONCLUSIONS/SIGNIFICANCE: We show that dengue is hyperendemic in PNG and identify an endemic, locally evolved lineage of DENV-3 that was associated with an outbreak of severe dengue in Pacific countries in subsequent years, although severe disease was not identified in PNG. Additional studies need to be undertaken to understand dengue epidemiology and burden of disease in PNG.

Serological evidence for transmission of multiple dengue virus serotypes in Papua New Guinea and West Papua prior to 1963.

Little is known about the natural history of dengue in Papua New Guinea (PNG). We assessed dengue virus (DENV)-specific neutralizing antibody profiles in serum samples collected from northern and southern coastal areas and the highland region of New Guinea between 1959 and 1963. Neutralizing antibodies were demonstrated in sera from the northern coast of New Guinea: from Sabron in Dutch New Guinea (now known as West Papua) and from four villages in East Sepik in what is now PNG. Previous monotypic infection with DENV-1, DENV-2, and DENV-4 was identified, with a predominance of anti-DENV-2 neutralizing antibody. The majority of positive sera demonstrated evidence of multiple previous DENV infections and neutralizing activity against all four serotypes was detected, with anti-DENV-2 responses being most frequent and of greatest magnitude. No evidence of previous DENV infection was identified in the Asmat villages of the southern coast and a single anti-DENV-positive sample was identified in the Eastern Highlands of PNG. These findings indicate that multiple DENV serotypes circulated along the northern coast of New Guinea at different times in the decades prior to 1963 and support the notion that dengue has been a significant yet neglected tropical infection in PNG for many decades.

Emergence of a new lineage of dengue virus type 2 identified in travelers entering Western Australia from Indonesia, 2010-2012.

Dengue virus (DENV) transmission is ubiquitous throughout the tropics. More than 70% of the current global dengue disease burden is borne by people who live in the Asia-Pacific region. We sequenced the E gene of DENV isolated from travellers entering Western Australia between 2010-2012, most of whom visited Indonesia, and identified a diverse array of DENV1-4, including multiple co-circulating viral lineages. Most viruses were closely related to lineages known to have circulated in Indonesia for some time, indicating that this geographic region serves as a major hub for dengue genetic diversity. Most notably, we identified a new lineage of DENV-2 (Cosmopolitan genotype) that emerged in Bali in 2011-2012. The spread of this lineage should clearly be monitored. Surveillance of symptomatic returned travellers provides important and timely information on circulating DENV serotypes and genotypes, and can reveal the herald wave of dengue and other emerging infectious diseases.

Detection of enteric viral and bacterial pathogens associated with paediatric diarrhoea in Goroka, Papua New Guinea.

OBJECTIVES: The aim of this study was to investigate the viral and bacterial causes of acute watery diarrhoea in hospitalized children in Papua New Guinea. METHODS: A retrospective analysis was conducted on stool samples collected from 199 children (age <5 years) admitted to the paediatric ward of Goroka General Hospital from August 2009 through November 2010. A large range of viral and bacterial enteric pathogens were targeted using real-time PCR/RT-PCR assays. RESULTS: Young children were much more likely to be admitted with acute gastroenteritis, with 62.8% of patients aged <1 year and 88.4% aged <2 years. An enteric pathogen was detected in 69.8% (n=138) of patients. The most commonly detected pathogens were Shigella spp (26.6%), rotavirus (25.6%), adenovirus types 40/41 (11.6%), enterotoxigenic Escherichia coli (11.1%), enteropathogenic E. coli (8.5%), norovirus G2 (6.0%), and Campylobacter spp (4.0%). Norovirus G1, sapovirus, and Salmonella spp were also detected, but below our statistical limit of detection. Vibrio cholerae and astrovirus were not detected in any patients. Mixed infections were detected in 22.1% of patients, with Shigella and rotavirus most commonly detected in co-infections with other pathogens. CONCLUSIONS: This study demonstrates that Shigella and rotavirus are the major pathogens associated with acute paediatric gastroenteritis in this setting.

Evaluation of a rapid immunochromatographic assay for the detection of rotavirus, norovirus and adenovirus from children hospitalized with acute watery diarrhea.

We evaluated the IP-Triple I immunochromatographic rapid test for the detection of rotavirus, norovirus and adenovirus using stool samples from children with diarrhoea. The detection of norovirus and adenovirus was poor compared to polymerase chain reaction assays. However, high sensitivity (92%) and specificity (99%) were obtained for the detection of rotavirus.

Surveillance and molecular characterization of group A rotaviruses in Goroka, Papua New Guinea.

In this study, we investigated the molecular epidemiology of group A rotaviruses in cases of acute gastroenteritis in Goroka, Papua New Guinea. From April 2008 through November 2010, 813 diarrheal stool samples were collected from children < 5 years of age hospitalized with acute gastroenteritis. Rotavirus antigen was detected in 31.2% of samples using a commercial enzyme-linked immunosorbent assay. Genotyping revealed the presence of the globally circulating strains G1P[8] (50.0%), G3P[8] (23.0%), and G2P[4] (8.2%). The globally emerging strains G9 and G12 were detected in 1.2% and 6.1% of samples, respectively. Mixed infections were detected in a high proportion of samples (11.9%), with 9.0% and 3.7% of samples displaying multiple G and P genotypes, respectively.

Contribution of dengue fever to the burden of acute febrile illnesses in Papua New Guinea: an age-specific prospective study.

Malaria is a major contributor to the burden of febrile illnesses in Papua New Guinea (PNG). Dengue fever (DF) is likely to contribute; however, its epidemiology in PNG is poorly understood. We performed a prospective age-stratified study in outpatient clinics investigating the prevalence of DF; 578 patients were enrolled, and 317 patients with a negative rapid diagnostic test (RDT) for malaria were tested for dengue. Malaria was confirmed in 52% (301/578, 95% confidence interval [CI] = 48-56%), DF was diagnosed in 8% (46/578, 95% CI = 6-10%), and 40% (95% CI = 36-44%) had neither diagnosis. Among the 317 malaria RDT-negative patients, 14% (45/317, 95% CI = 10-18%) had DF. The seroprevalence of dengue immunoglobulin G (IgG) was 83% (204/247, 95% CI = 78-87%), and no dengue hemorrhagic fever was seen. This study provides good evidence for the first time that DF is common in PNG and is responsible for 8% of fever episodes. The common occurrence of DF in a population with presumed previous exposure to dengue is an important observation.

Cerebrospinal fluid levels of matrix metalloproteinase-9 and tissue inhibitor of metalloproteinase-1 in subacute sclerosing panencephalitis.

OBJECTIVES: To investigate the brain inflammation and damage in subacute sclerosing panencephalitis (SSPE), the cerebrospinal fluid (CSF) concentrations of matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of metalloproteinase-1 (TIMP-1) were determined in SSPE patients. METHODS: CSF MMP-9 and TIMP-1 levels were measured in 23 patients with SSPE in Papua New Guinea by ELISA. RESULTS: CSF MMP-9 levels and MMP-9/TIMP-1 ratios of SSPE patients were significantly higher than controls (p<0.001 and p=0.005, respectively). There were no significant differences in CSF TIMP-1 levels between SSPE patients and controls. CONCLUSIONS: Previous studies suggested that CSF MMP-9 levels reflect inflammatory damage to the brain. Our findings suggest that the MMP-9 level in CSF is an indicator of inflammatory damage to the brain in SSPE.

The impact of the Austronesian expansion: evidence from mtDNA and Y chromosome diversity in the Admiralty Islands of Melanesia.

The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of nonrecombining Y chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia, and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties, we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origins, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia and perhaps as a consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and human history in the Pacific region.

Serum levels of matrix metalloproteinase-9 and tissue inhibitors of metalloproteinases 1 in subacute sclerosing panencephalitis.

We determined the relationship between the serum concentrations of matrix metalloproteinase-9 (MMP-9) and tissue inhibitors of metalloproteinases 1 (TIMP-1) in 33 patients with subacute sclerosing panencephalitis (SSPE) to investigate the function of the blood-brain-barrier (BBB) in SSPE. Serum MMP-9 and TIMP-1 levels were measured by ELISA. Serum MMP-9 levels and MMP-9/TIMP-1 ratios of SSPE patients in Papua New Guinea (n = 24), and those in Japan (n = 9) were significantly higher than the each control (MMP-9, p = 0.0390, and p = 0.0023, respectively; MMP-9/TIMP-1, p = 0.0319, and p = 0.0009, respectively). Serum MMP-9 levels and MMP-9/TIMP-1 ratios of SSPE patients with Jabbour stage III (n = 13) were significantly higher than those with Jabbour stage II (n = 18) (p = 0.003, and p = 0.0412, respectively). There were no significant differences of serum TIMP-1 levels between the SSPE patients and controls. High serum MMP-9 and MMP-9/TIMP-1 levels will promote brain invasion through the BBB by immunocompetent cells in the blood. Our findings suggest that the balance of serum MMP-9 and TIMP-1 levels modulate the inflammatory cascade of SSPE.

Chlamydia trachomatis infection and distribution of serovars in the Eastern Highlands Province, Papua New Guinea.

We have used nested polymerase chain reaction (PCR) and the PCR-based endonuclease digestion method to genotype Chlamydia trachomatis serovars in 460 infected individuals from the Eastern Highlands Province of Papua New Guinea. Our study groups comprised women who presented in labour to the Goroka Base Hospital, their newborn infants, symptomatic children who presented to the hospital's Outpatients Department and men and women from 15 randomly selected villages in the Asaro Valley. In this analysis, the major outer membrane protein (MOMP) gene, omp1, of C. trachomatis was amplified using DNA obtained from the endocervix of women, urine from men, and both the eye and nasopharynx of children. Amplified DNAs were digested concurrently using Alul and a combination of EcoRI, Hinl and Hpall restriction enzymes. The mixtures were separated on electrophoretic gels and the respective serovars designated on the basis of resolved digested DNA patterns. Our results, which were confirmed also by omp1 sequence data, show serovars D, E, F, G, H and L3 to be present in the studied communities. The overall relative frequencies of these serovars were 30%, 21%, 25%, 1%, 20% and 2% respectively, with serovars D, E, F and H accounting for 97% of these infections. Double infections among these principal serovars were also detected in all our study groups but at a low overall frequency of 3%. Serovar D was the major agent involved in the aetiology of chlamydial infection in both children and adults though serovar F was the most frequent in newborn infants. Serovar H was relatively less frequent in symptomatic children. No trachoma-related serovars were detected, confirming the rarity of this disease in Papua New Guinea. In contrast, although clinical cases of lymphogranuloma venereum have not been described in the country, the detection of serovar L3 in this study suggests that it may occur. However, the association of L3 also with childhood infection indicates that it may be causing the same pathology as the serovars D-K that are associated with non-ulcerative sexually transmitted infections.

Analysis of serum and cerebrospinal fluid cytokine levels in subacute sclerosing panencephalitis in Papua New Guinea.

BACKGROUND: Subacute sclerosing panencephalitis (SSPE) is a rare progressive inflammatory disease characterized by the persistent infection of the brain by the measles virus. However, the immunological pathophysiology of SSPE is still unclear. METHODS: We measured the concentrations of interferon-gamma (IFN-gamma), tumor necrosis factor-alpha (TNF-alpha), interleukin-2 (IL-2), IL-4, IL-6, IL-10, and soluble TNF receptor 1 (sTNFR1) in the serum and cerebrospinal fluid (CSF) of 23 patients with SSPE in Papua New Guinea (PNG), a country with a high incidence of SSPE, and Japanese controls by cytometric bead array or ELISA. RESULTS: The serum IL-6 and IL-10 levels of SSPE patients were significantly higher than those of controls (p=0.0075, and p=0.0019, respectively). The serum IL-6 and IL-10 levels of SSPE patients with fever were significantly higher than those without fever (p=0.0107, and p=0.0006, respectively). The CSF IL-6 levels of SSPE patients were significantly higher than those of controls (p=0.0218). The CSF IL-6 levels of SSPE patients with myoclonic jerks were significantly higher than those without myoclonic jerks (p=0.0189). There were no differences in serum IFN-gamma, TNF-alpha, IL-2, IL-4, and sTNFR1, or CSF IFN-gamma, TNF-alpha, IL-2, IL-4, IL-10, and sTNFR1 levels between the affected patients and controls. CONCLUSION: Our present study suggests that serum IL-6 and IL-10 levels are related to fever, and the CSF IL-6 level, myoclonic jerks, in SSPE patients in PNG.

High prevalence of sexually transmitted infections among female sex workers in the eastern highlands province of Papua New Guinea: correlates and recommendations.

BACKGROUND: More than 200 female sex workers (FSWs) participating in commercial sex along the Highlands Highway of Papua New Guinea were identified in a previous survey. This has implications for the spread of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) to areas and population groups serviced by the road. GOAL: The goal of this study was to estimate the prevalence of gonorrhea, chlamydia, syphilis, trichomoniasis, and HIV among FSWs in Goroka and Kainantu in the Eastern Highlands Province (EHP) and to identify correlates that could be considered in intervention and control. STUDY: Self-identified FSWs recruited through the Goroka Sex Workers Peer-Mediated Programme were invited to participate. All consenting FSWs underwent pretest counseling and provided sociodemographic and behavioral data using a structured questionnaire. The women were also asked to self-collect vaginal specimens and to provide peripheral blood to detect the respective STIs and HIV. RESULTS: Results were available for 211 FSWs. None of the women were positive for HIV. The overall estimated rates for gonorrhea, chlamydia, syphilis, and trichomoniasis were 21%, 19%, 24%, and 51%, respectively. Seventy-four percent were positive for at least 1 STI and 43% had multiple STI infections. High-risk sexual behaviors were found to be common among the women, including low and inconsistent use of condoms, with most of them attributing this to unavailability, dislike by or familiarity with clients, and being drunk and/or high on marijuana. CONCLUSIONS: STIs are prevalent among FSWs in Goroka and Kainantu in the EHP and are maintained by widespread high-risk sexual behaviors, including low use of condoms. Implications for their spread through the highway warrants increased efforts in intervention. Apart from a need to promote condom acceptance, distribution, and use, other high-risk sexual behavior and correlates identified in this study provide important considerations for intervention and control in this population.