key: cord-1007270-dtsnl76a authors: Douglas, Nicholas M; Meumann, Ella M; Krause, Vicki L; Davies, Jane title: Successful containment to date of SARS‐CoV‐2 transmission in the Northern Territory date: 2020-10-28 journal: Med J Aust DOI: 10.5694/mja2.50840 sha: fcdb7b5400815fa73e18cd494c732f501730794f doc_id: 1007270 cord_uid: dtsnl76a nan The NT Centre for Disease Control (NTCDC) issued its first NT COVID-19 public health alert on 24 January 2020. Twenty-four subsequent alerts 1 have mostly followed the Australian Series of National Guidelines 2 with the exception that testing criteria have been broader and isolation procedures more conservative. All patients with coronavirus disease 2019 (COVID-19) were placed in mandated, supervised isolation until two negative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) swabs had been documented at least 24 hours apart. This isolation requirement was formulated prioritising viral containment at a time of limited data on duration of infectiousness. Surveillance testing of all hospitalised patients with respiratory illness and/or unexplained fever was commenced on March 3. Contact tracing and quarantine of close case contacts coordinated by the NTCDC has been rigorous and near complete. Pandemic clinics for assessing and swabbing suspect cases were mobilised rapidly in various locations. All patients diagnosed with COVID-19 in the Northern Territory were admitted to hospital for initial assessment by an infectious diseases team where possible. Blood and radiological investigations were at the discretion of the admitting doctors but were influenced by emerging evidence on relevant prognostic laboratory markers. 3,4,5 Once clinically stable, patients were transferred to an external supervised isolation facility. Daily clinical assessment continued to occur at these facilities. By departmental consensus, patients with COVID-19 could be treated with lopinavir-ritonavir 400/100mg once daily for up to 5 days provided patient consent was obtained. The ASCOT trial was not available for enrolment 6 whereas the REMAP-CAP trial 7 was available for patients admitted to the intensive care unit in Darwin. Diagnosis of SARS-CoV-2 infection was made by detection of SARS-CoV-2 RNA on dry flocked swabs (Copan, Italy) collected from the oropharynx and bilateral deep nasal passages, using one of two multiplex All initial positive assays were verified at the Victorian Infectious Diseases Reference Laboratory with 100% result concordance. Health Laboratory in Melbourne, Australia. RNA extraction was done using either the Qiagen QIAsymphony DSP Virus/Pathogen Kit or the QIAamp 96 Virus QIAcube HT Kit, and tiled amplicons were prepared using either ARTIC version 1 or version 3 primers (https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019) with published protocols (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w). Library preparation was done with NexteraXT kits and sequencing was done using Illumina NextSeq500/550 or iSeq100 platforms with 150bp paired-end reads. Data preparation, analysis and graphing were done using STATA 15.1 and R 3.6.0. Negative SARS-CoV-2 assays were arbitrarily assigned a Ct value of 35 for graphing purposes. The Kaplan-Meier method was used to present the cumulative probability of virologic clearance by time. All analyses were descriptive and therefore, tests of statistical significance were not done. Consensus sequences were generated by aligning reads to the Wuhan-Hu-1 (Genbank MN908947.3) reference genome with minimap2 v2.17, 8 and using the output of samtools4 mpileup v1.10 9 with ivar consensus v2.17. 10 The consensus sequences for the 27 NT SARS-CoV-2 genomes were uploaded to GISAID (https://www.gisaid.org, Supplementary Table 2 ). The 27 NT SARS-CoV-2 genomes were included in a phylogenetic analysis with 237 publicly available Australian and international genomes from GISAID for comparison (Supplementary Table 3) , with the exception of one genome which did not meet GISAID's quality requirements due to a 2-nucleotide gap. Only publicly available genomes with >29,000bp length, <1% Ns and <0.05% unique amino acid mutations were selected. Genomes were aligned to the Wuhan-Hu-1 reference genome using MAFFT v7.464. 11 The 5' and 3' untranslatable regions were trimmed from the alignment. Phylogenetic analysis was undertaken using IQ-TREE v1.6.12 12 with options "-mset HKY,TIM2,GTR -mfreq F -5 mrate G,R -alrt 1000 -bb 1000". Outlying genomes on unexpectedly long branches of the tree were excluded from the final analysis based on visual inspection. The tree was annotated using the ggtree package 13 in R v3.6.0. The lineage of the genomes was determined using Pangolin v1.1.11 (https://github.com/cov-lineages/pangolin). 14 Risk factors for severity and mortality in adult COVID-19 inpatients in Wuhan Risk factors of critical & mortal COVID-19 cases: a systematic literature review and meta-analysis Clinical features and treatment of COVID-19 patients in northeast Chongqing The Australasian COVID-19 Trial (ASCOT) to assess clinical outcomes in hospitalised patients with SARS-CoV-2 infection (COVID-19) treated with lopinavir/ritonavir and/or hydroxychloroquine compared to standard of care: a structured summary of a study protocol for a randomised controlled trial The randomized embedded multifactorial adaptive platform for community-acquired pneumonia (REMAP-CAP) study: rationale and design Minimap2: pairwise alignment for nucleotide sequences The sequence alignment/map format and SAMtools An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies Two methods for mapping and visualizing associated data on phylogeny using Ggtree A dynamic nomenclature proposal for SARS lineages to assist genomic epidemiology