SELECT 
  SQL_CALC_FOUND_ROWS products.product_id, 
  descr1.product as product, 
  companies.company as company_name, 
  products.product_type, 
  products.parent_product_id, 
  products.variation_sku, 
  companies.discreet_shipping as company_discreet_shipping 
FROM 
  cscart_products as products 
  LEFT JOIN cscart_product_descriptions as descr1 ON descr1.product_id = products.product_id 
  AND descr1.lang_code = 'en' 
  LEFT JOIN cscart_product_prices as prices ON prices.product_id = products.product_id 
  AND prices.lower_limit = 1 
  LEFT JOIN cscart_companies AS companies ON companies.company_id = products.company_id 
  INNER JOIN cscart_products_categories as products_categories ON products_categories.product_id = products.product_id 
  INNER JOIN cscart_categories ON cscart_categories.category_id = products_categories.category_id 
  AND (
    cscart_categories.usergroup_ids = '' 
    OR FIND_IN_SET(
      0, cscart_categories.usergroup_ids
    ) 
    OR FIND_IN_SET(
      1, cscart_categories.usergroup_ids
    )
  ) 
  AND cscart_categories.status IN ('A', 'H') 
  AND cscart_categories.storefront_id IN (0, 1) 
  LEFT JOIN cscart_product_popularity as popularity ON popularity.product_id = products.product_id 
WHERE 
  1 
  AND companies.status IN ('A') 
  AND products.company_id = 99 
  AND products.amount > 0 
  AND (
    products.usergroup_ids = '' 
    OR FIND_IN_SET(0, products.usergroup_ids) 
    OR FIND_IN_SET(1, products.usergroup_ids)
  ) 
  AND products.status IN ('A') 
  AND prices.usergroup_id IN (0, 0, 1) 
  AND products.company_id = 99 
  AND products.parent_product_id = 0 
GROUP BY 
  products.product_id 
ORDER BY 
  popularity.total desc, 
  products.product_id ASC

Query time 0.05675

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "3092.60"
    },
    "ordering_operation": {
      "using_filesort": true,
      "grouping_operation": {
        "using_temporary_table": true,
        "using_filesort": false,
        "nested_loop": [
          {
            "table": {
              "table_name": "companies",
              "access_type": "const",
              "possible_keys": [
                "PRIMARY"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "company_id"
              ],
              "key_length": "4",
              "ref": [
                "const"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 1,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "0.00",
                "eval_cost": "0.10",
                "prefix_cost": "0.00",
                "data_read_per_join": "15K"
              },
              "used_columns": [
                "company_id",
                "status",
                "company",
                "discreet_shipping"
              ]
            }
          },
          {
            "table": {
              "table_name": "products",
              "access_type": "ref",
              "possible_keys": [
                "PRIMARY",
                "status",
                "idx_parent_product_id"
              ],
              "key": "idx_parent_product_id",
              "used_key_parts": [
                "parent_product_id"
              ],
              "key_length": "4",
              "ref": [
                "const"
              ],
              "rows_examined_per_scan": 15524,
              "rows_produced_per_join": 305,
              "filtered": "1.97",
              "cost_info": {
                "read_cost": "884.27",
                "eval_cost": "30.53",
                "prefix_cost": "2436.68",
                "data_read_per_join": "1M"
              },
              "used_columns": [
                "product_id",
                "product_type",
                "status",
                "company_id",
                "amount",
                "usergroup_ids",
                "parent_product_id",
                "variation_sku"
              ],
              "attached_condition": "((`cscartdb`.`products`.`company_id` = 99) and (`cscartdb`.`products`.`amount` > 0) and ((`cscartdb`.`products`.`usergroup_ids` = '') or (0 <> find_in_set(0,`cscartdb`.`products`.`usergroup_ids`)) or (0 <> find_in_set(1,`cscartdb`.`products`.`usergroup_ids`))) and (`cscartdb`.`products`.`status` = 'A'))"
            }
          },
          {
            "table": {
              "table_name": "prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "product_id",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "ref": [
                "cscartdb.products.product_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 305,
              "filtered": "99.99",
              "cost_info": {
                "read_cost": "76.33",
                "eval_cost": "30.53",
                "prefix_cost": "2543.53",
                "data_read_per_join": "7K"
              },
              "used_columns": [
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "attached_condition": "((`cscartdb`.`prices`.`lower_limit` = 1) and (`cscartdb`.`prices`.`usergroup_id` in (0,0,1)))"
            }
          },
          {
            "table": {
              "table_name": "popularity",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY",
                "total"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "ref": [
                "cscartdb.products.product_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 305,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "76.32",
                "eval_cost": "30.53",
                "prefix_cost": "2650.38",
                "data_read_per_join": "9K"
              },
              "used_columns": [
                "product_id",
                "total"
              ]
            }
          },
          {
            "table": {
              "table_name": "products_categories",
              "access_type": "ref",
              "possible_keys": [
                "PRIMARY",
                "pt"
              ],
              "key": "pt",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "ref": [
                "cscartdb.products.product_id"
              ],
              "rows_examined_per_scan": 2,
              "rows_produced_per_join": 610,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "152.64",
                "eval_cost": "61.06",
                "prefix_cost": "2864.08",
                "data_read_per_join": "9K"
              },
              "used_columns": [
                "product_id",
                "category_id"
              ]
            }
          },
          {
            "table": {
              "table_name": "cscart_categories",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY",
                "c_status",
                "p_category_id"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "category_id"
              ],
              "key_length": "3",
              "ref": [
                "cscartdb.products_categories.category_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 30,
              "filtered": "5.00",
              "cost_info": {
                "read_cost": "152.64",
                "eval_cost": "3.05",
                "prefix_cost": "3077.77",
                "data_read_per_join": "102K"
              },
              "used_columns": [
                "category_id",
                "storefront_id",
                "usergroup_ids",
                "status"
              ],
              "attached_condition": "(((`cscartdb`.`cscart_categories`.`usergroup_ids` = '') or (0 <> find_in_set(0,`cscartdb`.`cscart_categories`.`usergroup_ids`)) or (0 <> find_in_set(1,`cscartdb`.`cscart_categories`.`usergroup_ids`))) and (`cscartdb`.`cscart_categories`.`status` in ('A','H')) and (`cscartdb`.`cscart_categories`.`storefront_id` in (0,1)))"
            }
          },
          {
            "table": {
              "table_name": "descr1",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY",
                "product_id"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "product_id",
                "lang_code"
              ],
              "key_length": "9",
              "ref": [
                "cscartdb.products.product_id",
                "const"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 30,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "11.78",
                "eval_cost": "3.05",
                "prefix_cost": "3092.60",
                "data_read_per_join": "116K"
              },
              "used_columns": [
                "product_id",
                "lang_code",
                "product"
              ]
            }
          }
        ]
      }
    }
  }
}