Indonesia first reported SARS-CoV-2 in March 2020. From March to April, clinical microbiology laboratory Universitas Indonesia in Jakarta received 4617 specimens with 12.6% positivity rate and 22% asymptomatic case. The result of this study could give an early picture of Indonesia’s COVID 19 outbreak situation.

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Background: SARS-CoV-2 rapid mutation generates many concerning new strains. Although lockdown had been applied to contain the disease, the household remains a critical place for its transmission. This study aimed to assess the variation of SARS-CoV-2 strains and their clinical manifestations within family clusters in Jakarta, Indonesia. Method: Naso-oropharyngeal swab specimens from family clusters positive for SARS-CoV-2 were collected for whole-genome sequencing. Their baseline data, symptoms, and source of infection were recorded. The whole-genome data was then analyzed with the bioinformatics program to evaluate the SARS-CoV-2 genome characteristic and submitted to GISAID for strain identification. The phylogenetic tree was built to observe the relationship between virus strain within the family cluster and its clinical manifestation. Result: This study obtained eight family clusters from twenty-two patients. Half of the cluster's source of infection was a family member who had to work at the office. The infection rate ranged from 37.5% to 100%. The phylogenetic tree showed that the same virus within a cluster could generate various clinical outcomes. Five clusters had one family member with pneumonia, while others had mild to no symptoms. Four breakthrough cases were detected in this study, which were infected by the virus from GH and GK clade.  Conclusion: Our study observed the SARS-CoV-2 transmission to the household setting through the workplace, which might become a common pathway if the pandemic status is removed. Although vaccination is expected to reduce the burden of COVID-19, adequate control measures remain essential, given that breakthrough infections are evident.

Latar belakang: Pulmonary Aspergillosis merupakan infeksi oportunistik pada populasi immunocompromised. Metode Polymerase Chain Reaction (PCR) diharapkan dapat menjadi pengganti kultur jamur sputum dengan hasil yang lebih cepat dan akurat. Metode: Dilakukan pencarian di PubMed, CENTRAL, EbscoHost, dan ProQuest sejak tanggal 1 -13 Oktober menggunakan kata kunci “Aspergillosis”, “Pulmonary Aspergillosis”, “sputum”, “PCR”, “sputum fungal culture”. Hasil pencarian di evaluasi menggunakan kriteria inklusi dan eksklusi. Studi yang terseleksi kemudian diperoleh full text nya dan dievaluasi kembali. Hasil akhir dari seleksi kemudian ditinjau secara kritis validity, importance, dan applicability-nya oleh ketiga penulis. Hasil: Didapatkan empat studi,dengan level of evidence 4, yang kemudian ditinjau secara kritis. Tiga studi menggunakan PCR pada sampel sputum sebagai index test, sementara satu studi menggunakannya sebagai refference test. Luaran dari tiga studi melaporkan sensitivitas dan spesifisitas dari PCR dengan sampel sputum, sedangkan satu studi melaporkan proporsi dari hasil PCR. Dua studi melaporkan sensitivitas PCR pada sampel sputum sebesar 100%, sementara satu studi melaporkan sensitivitas sebesar 38%. Dua studi juga melaporkan spesifisitas diatas 70%, sementara satu studi melaporkan spesifisitas sebesar 38.5%.Kesimpulan: Studi menunjukkan nilai sensitivitas dan spesifisitas yang menjanjikan terutama dengan hasil diperoleh dengan cepat. Akan tetapi rendahnya level of evidence dan biayanya yang cukup mahal, menyebabkan deteksi dengan metode PCR belum dapat digunakan sebagai modalitas diagnosis rutin.