Genomic surveillance of SARS-CoV-2 strains circulating in Iran during six waves of the pandemic.

Background: SARS-CoV-2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS-CoV-2 genomes during the sixth wave of the COVID pandemic in Iran and compared them with five previous waves, for identifying SARS-CoV-2 variants, the genomic behavior of the virus, and understanding its characteristics. Methods: After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq and Nanopore platforms. The sequencing data were analyzed and compared with reference sequences. Results: In Iran during the first wave, V and L clades were detected. The second wave was recognized by G, GH, and GR clades. Circulating clades during the third wave were GH and GR. In the fourth wave, GRY (alpha variant), GK (delta variant), and one GH clade (beta variant) were detected. All viruses in the fifth wave were in GK clade (delta variant). In the sixth wave, Omicron variant (GRA clade) was circulating. Conclusions: Genome sequencing, a key strategy in genomic surveillance systems, helps to detect and monitor the prevalence of SARS-CoV-2 variants, monitor the viral evolution of SARS-CoV-2, identify new variants for disease prevention, control, and treatment, and also provide information for and conduct public health measures in this area. With this system, Iran could be ready for surveillance of other respiratory virus diseases besides influenza and SARS-CoV-2.

Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic.

PURPOSE: Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. METHODS: After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. RESULTS: During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd wave were GH and GR. In the fourth wave GRY (alpha variant), GK (delta variant) and one GH clade (beta variant) were detected. All viruses in the fifth wave were in clade GK (delta variant). There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. CONCLUSIONS: These findings display the significance of SARS-CoV2 monitoring to help on time detection of possible variants for pandemic control and vaccination plans.

The presence of SARS-CoV-2 in raw and treated wastewater in 3 cities of Iran: Tehran, Qom and Anzali during coronavirus disease 2019 (COVID-19) outbreak.

This study aimed to identifying the presence of SARS-CoV-2 RNA in raw and treated wastewater during the COVID-19 outbreak in Tehran, Qom and Anzali cities (Iran). From three wastewater treatment plants (WWTPs), 28 treated and untreated wastewater composite samples were collected from April 4 to May 2, 2020. In this study, polyethylene glycol 6000 (PEG 6000) was used through one-step real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) for identification of RNA viruses. SARS-CoV-2 RNA was elicited from wastewater composite samples in all inlet samples taken from the three above mentioned cities. The results of outlet samples were as follows: 1) Results from Qom and East Anzali outlets showed no trace of SARS-CoV-2 RNA despite the difference in treatment disinfection method used (chlorine vs. ultraviolet (UV) disinfection). 2. In Tehran, SARS-CoV-2 RNA was not detected in any of the outlet samples taken from the modules disinfected by UV. Out of the four samples taken from the modules disinfected by chlorine, two were positive for the SARS-CoV-2 RNA which could have been caused by deficiencies in operation and maintenance. It can be concluded that meeting the standards of operation and maintenance (O&M) in WWTPs can considerably ensure that wastewater does not act as one of the roots of transmission for the disease.

First Cases of SARS-CoV-2 in Iran, 2020: Case Series Report

In Jan 2020, the outbreak of the 2019 novel coronavirus (SARS-CoV-2) in Wuhan, Hubei Province of China spread increasingly to other countries worldwide which WHO declared it as a public health emergency of international concern. Iran was included in the affected countries. Throat swab specimens were collected and tested by using real-time reverse transcription PCR (RT-PCR) kit targeting the E region for screening and RNA dependent RNA polymerase for confirmation. Conventional RT-PCR was conducted for the N region and the PCR products were sequenced by Sanger sequencing. The first seven cases of SARS-CoV-2 infections were identified in Qom, Iran. This report describes the clinical and epidemiological features of the first cases of SARS-CoV-2 confirmed in Iran. Future research should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran.