Lymphocytic Choriomeningitis Virus Infection, Australia.

During a mouse plague in early 2021, a farmer from New South Wales, Australia, sought treatment for aseptic meningitis and was subsequently diagnosed with locally acquired lymphocytic choriomeningitis virus infection. Whole-genome sequencing identified a divergent and geographically distinct lymphocytic choriomeningitis virus strain compared with other published sequences.

Increasing proportion of herpes simplex virus type 1 among women and men diagnosed with first-episode anogenital herpes: a retrospective observational study over 14 years in Melbourne, Australia.

OBJECTIVES: Reports of rising herpes simplex virus type 1 (HSV-1) genital infections relative to HSV-2 have been published up to 2006 in Australia. These changes have been attributed to declining childhood immunity to HSV-1. We described the temporal trends of HSV-1 and HSV-2 up to 2017 in Melbourne, Australia, to determine if the earlier trend is continuing. METHODS: We conducted a retrospective review of the medical records of 4517 patients who were diagnosed with first episode of anogenital HSV infection at the Melbourne Sexual Health Centre, Australia, between January 2004 and December 2017. HSV-1 and HSV-2 were calculated as a proportion of all first episode of anogenital HSV infections. The change in the proportions of HSV-1 and HSV-2 over time was assessed by a χ2 trend test. Risk factors associated with HSV-1 were examined using a multivariable logistic regression model. RESULTS: The proportion of first episode of anogenital herpes due to HSV-1 increased significantly over time in women (from 45% to 61%; ptrend<0.001) and heterosexual men (from 38% to 41%; ptrend=0.01) but not in men who have sex with men (MSM) (ptrend=0.21). After adjusting for condom use, partner number and age, the annual increase remained significant only in women (OR 1.08, 95% CI 1.03 to 1.13, p<0.001). In MSM, HSV-1 caused up to two-thirds of anogenital herpes in most years and HSV-1 was more likely to be diagnosed at an anal site than genital site (OR 1.69, 95% CI 1.23 to 2.32, p<0.001). Younger age (<28 years) was an independent risk factor for HSV-1 in all groups. CONCLUSIONS: The proportion of first-episode anogenital herpes due to HSV-1 has been rising in women since 2004. HSV-1 has become the leading cause of anogenital herpes in younger populations, women and MSM.

Utility of a Stressed Single Nucleotide Polymorphism (SNP) Real-Time PCR Assay for Rapid Identification of Measles Vaccine Strains in Patient Samples.

Rapid differentiation of wild-type measles virus from measles vaccine strains is crucial during a measles outbreak and in a measles elimination setting. A real-time reverse transcription-PCR (rRT-PCR) for the rapid detection of measles vaccine strains was developed with high specificity and sensitivity equivalent to that of traditional measles genotyping methods. The "stressed" minor groove binder-TaqMan probe design approach achieves specificity to vaccine strains only, without compromising sensitivity. This assay, without requiring sequence genotyping, has proved to be extremely useful in outbreak settings for over 4 years at the Regional Measles Reference Laboratory for the Western Pacific Region.

Neutralization Assay for Zika and Dengue Viruses by Use of Real-Time-PCR-Based Endpoint Assessment.

The global spread and infective complications of Zika virus (ZKV) and dengue virus (DENV) have made them flaviviruses of public health concern. Serological diagnosis can be challenging due to antibody cross-reactivity, particularly in secondary flavivirus infections or when there is a history of flavivirus vaccination. The virus neutralization assay is considered to be the most specific assay for measurement of anti-flavivirus antibodies. This study describes an assay where the neutralization endpoint is measured by real-time PCR, providing results within 72 h. It demonstrated 100% sensitivity (24/24 ZKV and 15/15 DENV) and 100% specificity (11/11 specimens) when testing well-characterized sera. In addition, the assay was able to determine the correct DENV serotype in 91.7% of cases. The high sensitivity and specificity of the real-time PCR neutralization assay makes it suitable to use as a confirmatory test for sera that are reactive in commercial IgM/IgG enzyme immunoassays. Results are objective and the PCR-based measurement of the neutralization endpoint lends itself to automation so that throughput may be increased in times of high demand.

A norovirus intervariant GII.4 recombinant in Victoria, Australia, June 2016: the next epidemic variant?

A norovirus recombinant GII.P4_NewOrleans_2009/GII.4_Sydney_2012 was first detected in Victoria, Australia, in August 2015 at low frequency, and then re-emerged in June 2016, having undergone genetic changes. Analysis of 14 years' surveillance data from Victoria suggests a typical delay of two to seven months between first detection of a new variant and occurrence of a subsequent epidemic linked to that variant. We consider that the current recombinant strain has the potential to become a pandemic variant.

Norovirus genotype diversity associated with gastroenteritis outbreaks in Victoria in 2013.

The noroviruses are now considered a leading cause of outbreaks of non-bacterial gastroenteritis worldwide. Vaccine strategies against norovirus are currently under consideration but depend on a detailed knowledge of the capsid genotypes. This study examined the incidence of norovirus outbreaks in Victoria over 1 year (2013) and documented the genotypes occurring in the different outbreak settings (healthcare and non-healthcare) and age groups. It was found that 63.1% of gastroenteritis outbreaks were associated with norovirus, thereby showing norovirus to be the major viral cause of illness in gastroenteritis outbreaks. Sixteen capsid genotypes were identified and included GI.2, GI.3, GI.4, GI.6, GI.7, GI.8, GI.9, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13 and an as yet unclassified GII genotype. All genotypes found in the study, with the exception of GI.9, were detected in the elderly, indicating prior exposure to a norovirus genotype did not appear to confer long term immunity in many cases. The incidence of genotypes GII.1, GII.4 and GII.7 was linked with setting and age. As setting and age were correlated it was not possible to determine which variable was critical with the exception of GII.7, which appeared to be linked to age. The findings indicate that norovirus vaccine strategies should encompass a broad range of genotypes and, as setting or age may be important in determining genotype incidence, this should be taken into account as well.

Detection and genotyping of enteroviruses in cerebrospinal fluid in patients in Victoria, Australia, 2007-2013.

Genotyping by VP1 fragment polymerase chain reaction (PCR) and nucleic acid sequencing to detect enterovirus (EV) genotypes was performed directly on 729 EV PCR positive cerebrospinal fluid (CSF) samples collected between 2007 and 2012 from Victorian hospital inpatients. The overall genotype identification rate from CSF-positive material was 43%. The four most common genotypes identified were Echovirus 6 (24%), Echovirus 30 (17%), Echovirus 25 (10%), and Coxsackievirus A9 (10%), together comprising 61% of all EVs typed. The seasonal distribution of all EVs identified followed the recognized pattern of mainly summer epidemics. Three of the four predominant genotypes were present in each of the 6 years in which the study was conducted, with 20 other EV genotypes also detected, often in only a single year. Genotyping of EVs directly in CSF is faster, simpler and more sensitive than traditional virus neutralization assays performed on EV positive samples.

Reality check of laboratory service effectiveness during pandemic (H1N1) 2009, Victoria, Australia.

In Australia, the outbreak of pandemic (H1N1) 2009 began in Melbourne, Victoria; in the first 17 days, the Victorian Infectious Diseases Reference Laboratory detected 977 cases. Although the laboratory had a pandemic plan in place, a retrospective evaluation found 3 major variations from plan assumptions: 1) higher peak demand not limited by a case definition, 2) prolonged peak demand because containment attempts continued despite widespread influenza, and 3) unexpected influence of negative test results on public health actions. Although implementation of the plan was generally successful, the greatest challenges were limited availability of skilled staff and test reagents. Despite peak demand of 1,401 tests per day, results were provided within the usual 24 hours of specimen receipt; however, turnaround time seemed slower because of slow transport times (>3 days for 45% of specimens). Hence, effective laboratory capability might be enhanced by speeding transport of specimens and improving transmission of clinical data.

The etiology of community-acquired pneumonia in Australia: why penicillin plus doxycycline or a macrolide is the most appropriate therapy.

BACKGROUND: Available data on the etiology of community-acquired pneumonia (CAP) in Australia are very limited. Local treatment guidelines promote the use of combination therapy with agents such as penicillin or amoxycillin combined with either doxycycline or a macrolide. METHODS: The Australian CAP Study (ACAPS) was a prospective, multicenter study of 885 episodes of CAP in which all patients underwent detailed assessment for bacterial and viral pathogens (cultures, urinary antigen testing, serological methods, and polymerase chain reaction). Antibiotic agents and relevant clinical outcomes were recorded. RESULTS: The etiology was identified in 404 (45.6%) of 885 episodes, with the most frequent causes being Streptococcus pneumoniae (14%), Mycoplasma pneumoniae (9%), and respiratory viruses (15%; influenza, picornavirus, respiratory syncytial virus, parainfluenza virus, and adenovirus). Antibiotic-resistant pathogens were rare: only 5.4% of patients had an infection for which therapy with penicillin plus doxycycline would potentially fail. Concordance with local antibiotic recommendations was high (82.4%), with the most commonly prescribed regimens being a penicillin plus either doxycycline or a macrolide (55.8%) or ceftriaxone plus either doxycycline or a macrolide (36.8%). The 30-day mortality rate was 5.6% (50 of 885 episodes), and mechanical ventilation or vasopressor support were required in 94 episodes (10.6%). Outcomes were not compromised by receipt of narrower-spectrum beta-lactams, and they did not differ on the basis of whether a pathogen was identified. CONCLUSIONS: The vast majority of patients with CAP can be treated successfully with narrow-spectrum beta-lactam treatment, such as penicillin combined with doxycycline or a macrolide. Greater use of such therapy could potentially reduce the emergence of antibiotic resistance among common bacterial pathogens.

Proficiency of nucleic acid tests for avian influenza viruses, Australasia.

An avian influenza quality assurance program was used to provide information for laboratories on the sensitivity and specificity of their avian influenza nucleic acid testing. Most laboratories were able to correctly detect clinically relevant amounts of influenza virus (H5N1), and results improved as each subsequent panel was tested.

Personal protective equipment and antiviral drug use during hospitalization for suspected avian or pandemic influenza.

For pandemic influenza planning, realistic estimates of personal protective equipment (PPE) and antiviral medication required for hospital healthcare workers (HCWs) are vital. In this simulation study, a patient with suspected avian or pandemic influenza (API) sought treatment at 9 Australian hospital emergency departments where patient-staff interactions during the first 6 hours of hospitalization were observed. Based on World Health Organization definitions and guidelines, the mean number of "close contacts" of the API patient was 12.3 (range 6-17; 85% HCWs); mean "exposures" were 19.3 (range 15-26). Overall, 20-25 PPE sets were required per patient, with variable HCW compliance for wearing these items (93% N95 masks, 77% gowns, 83% gloves, and 73% eye protection). Up to 41% of HCW close contacts would have qualified for postexposure antiviral prophylaxis. These data indicate that many current national stockpiles of PPE and antiviral medication are likely inadequate for a pandemic.

Electron microscope detection of tubular aggregates in the mosquito cell line C6/36 treated with Culex australicus (mosquito) homogenate.

'Tubular aggregates' are morphologically distinct cytoplasmic structures that have been linked to a variety of pathological conditions. This report documents the presence of tubular aggregates in an insect cell line (C6/36 cells derived from Aedes albopictus) following inoculation of the cells with material derived from cell culture passaged homogenized Culex australicus mosquitoes. The tubular aggregates were detected in ∼2% of treated cells and had three morphological forms that were termed primary, secondary and tertiary, with progressively greater levels of structural complexity. The findings indicate that tubular aggregates can be induced in an insect cell culture system by an unidentified agent present in some mosquitoes.

Studies of measles viruses circulating in Australia between 1999 and 2001 reveals a new genotype.

Nineteen distinct measles virus (MV) strains associated with nine different genotypes were identified in five Australian states (Victoria, New South Wales, Queensland, Northern Territory and Western Australia) between 1999 and 2001. One of the strains identified is likely to represent a new genotype within the clade D viruses (proposed to be d9). No evidence for an indigenous MV strain was found. When epidemiologic information associated with the index case was available for the outbreaks, it usually supported introduction of the virus from overseas, with the main source being South East Asia. Changes in the circulation of MV in Australia since the early 1970s were also observed. Prior to the introduction of measles vaccine, the majority of the population acquired immunity through infection with wild-type virus in early childhood. Nowadays in Australia, young adults are at most risk of infection. The age range of cases in the study period was from 1 month to 48 years, with the majority (59%) of cases from individuals aged 18-30 years.

Rotavirus detection and characterisation in outbreaks of gastroenteritis in aged-care facilities.

BACKGROUND: Although rotavirus is a major cause of gastroenteritis in children, its role in adult gastroenteritis and the sensitivity of different methods for its detection in specimens collected from adults are less well understood. OBJECTIVES: (1) To examine the frequency and seasonality of rotavirus-associated gastroenteritis outbreaks in aged-care facilities in Victoria, Australia. (2) To determine rotavirus type in these outbreaks. (3) To determine whether other enteropathogenic agents are present in specimens from these outbreaks. (4) To examine the sensitivity of different methods (electron microscopy (EM), reverse transcription-polymerase chain reaction (RT-PCR), enzyme immunoassay (EIA) and latex agglutination (LA)) for the detection of rotavirus in specimens from adults. STUDY DESIGN: Specimens from gastroenteritis outbreaks in aged-care facilities forwarded to this laboratory for the years 1997-2000 were tested for enteropathogenic agents by various methods. Epidemiological, clinical and seasonal data from the rotavirus-positive outbreaks were analysed. RESULTS: Rotavirus was detected by EM in 18 out of 29 individuals associated with seven out of 53 (13%) gastroenteritis outbreaks in aged-care facilities; norovirus was detected in 22 outbreaks (42%) and astrovirus in one outbreak (2%). No mixed viral infection was found in any outbreak. All rotaviruses were typed as Group A by RT-PCR. The rotaviruses in the seven outbreaks were G-typed as follows: G2 (three outbreaks), G4 (two outbreaks), G1 (one outbreak) and G9 (one outbreak). The rotavirus-associated outbreaks were concentrated in mid-winter to mid-spring. The relative sensitivities of the Group A rotavirus detection methods (for the 29 specimens tested) were EM (18), first-round RT-PCR (11), second-round PCR (19), EIA-visual (19), EIA-photometric (19) and LA (13). CONCLUSIONS: In Victoria, Australia, outbreaks of gastroenteritis associated with rotavirus are quite common in aged-care facilities. They involve Group A rotavirus and have a winter/spring seasonality. G-types G1, G2, G4 and G9 were all detected. EIA, second-round PCR and EM proved sensitive methods for rotavirus detection whereas first-round RT-PCR and LA did not.

Rising HIV infection in Victoria: an analysis of surveillance data.

OBJECTIVES: To describe the epidemiology of HIV in Victoria between 1997 and 2002 using HIV surveillance data. METHODS: All HIV diagnoses notified to the Victorian HIV Registry from 1997 to 2002 were described. RESULTS: The average annual number of HIV notifications rose from 160 during 1997-99 to 216 during 2000-02, with the number of infections from men who have sex with men (MSM) increasing by 41%. Notifications from MSM acquired from casual or anonymous partners increased from 65 in 1997-99 to 92 in 2000-02. Infections attributable to heterosexual contact increased from an average number of 30 during 1997-99 to 46 during 2000-02, a 53% increase. CONCLUSIONS: This rise in HIV notifications in Victoria threatens this State's progress in controlling the HIV epidemic. IMPLICATIONS: The surveillance data demonstrate a need to implement effective, innovative and evidence-based programs for HIV prevention.

Evaluation of the Bioline Standard Diagnostics SD immunochromatographic norovirus detection kit using fecal specimens from Australian gastroenteritis incidents.

Human norovirus is a major cause of both sporadic cases and outbreaks of gastroenteritis and comprises two main genogroups (GI and GII) which, in turn, comprise a variety of genotypes. The current study examined the efficacy of the Bioline SD kit using fecal material from Australian gastroenteritis incidents. At best, the SD kit had a sensitivity of 62%. Freezing and thawing specimens before testing significantly improved sensitivity. The SD kit had a specificity of 98.6%. Genotype analysis (Open Reading Frame 2) indicated the SD kit could detect a range of genotypes and genotype variants including GI.1, GI.3, GI.4, GII.1, GII.3, GII.4 (unclassified), GII.4 (2006b), GII.4 (2009), GII.4 (2012) and GII.6 but the kit failed to detect GI.2 and GII.2 norovirus. The kit did not cross-react with a number of common fecal viruses including astrovirus, sapovirus, rotavirus or adenovirus. The kit was very easy to use and would be valuable in point-of-care testing.

Laboratory diagnosis, molecular characteristics, epidemiological and clinical features of an outbreak of measles in a low incidence population in Australia.

BACKGROUND: Prompt and accurate laboratory diagnosis of measles is essential for case detection, outbreak management and ongoing surveillance in low incidence countries. Several disease markers are employed for diagnosis and are important to determine epidemiological and molecular characteristics for future control measures. OBJECTIVES: To report different disease markers, genotypes and epidemiology of a measles outbreak in Australia, a low incidence country. STUDY DESIGN: A retrospective descriptive study of the clinical and epidemiological features and laboratory diagnosis in 16 confirmed measles cases using measles serum IgM/IgG, antigen detection (IFA), viral RNA detection by real-time PCR and genotyping results for respiratory and urine specimens processed in one reference laboratory. RESULTS: Of the 16 confirmed measles cases, 11 were young adults aged between 20-35 years and 15 were not age-appropriately vaccinated. The most common genotype detected was D9 (11/16), followed by D4 (1/16) and D8 (1/16). Two imported cases were from the Philippines (D4) and Italy (D9). Of six disease markers, respiratory swab PCR and serum IgM gave the highest percentage (100%) of positive samples for confirmed cases followed by urine PCR (90.9%), serum PCR (66.6%), urine IFA (54.5%) and respiratory IFA (46.2%). CONCLUSIONS: Measles should be considered in the differential diagnosis of a presentation with fever and rash, even in countries in the elimination phase of measles control. Genotyping is a powerful molecular-epidemiological tool to assist low incidence countries towards eradication goals. Improving vaccination coverage remains essential, particularly in young adults and travellers.

Evaluation of the RIDA(®)QUICK immunochromatographic norovirus detection assay using specimens from Australian gastroenteritis incidents.

A range of laboratory methods is now available for the detection of norovirus, a major cause of gastroenteritis. Recently, a commercial immunochromatographic assay for norovirus detection, the RIDA(®)QUICK assay, has become available, but there is still only limited information on its efficacy. This study examined the sensitivity and specificity of the RIDA(®)QUICK assay, using faecal material received for testing in a major diagnostic/reference laboratory in Australia. The sensitivity of the assay was found to be 83% and the specificity was 100%. No false positive norovirus results were found and the assay did not cross-react with common faecal viruses such as rotavirus, astrovirus, sapovirus and adenovirus. The assay was less reliable for genogroup I (GI) noroviruses than for genogroup II (GII) noroviruses. Genotypes detected by the assay included GII.1, GII.2, GII.3, GII.4, GII.6 and GII.7. The assay failed to detect any GI specimens in the test group. Genotypes not detected included GI.4 and GI.6. The assay was simple and quick to perform. It is valuable in a point-of-care situation or as a backup in a laboratory where a rapid initial norovirus result is required.